Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 03:30:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/04_2023/7zh2_14718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/04_2023/7zh2_14718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/04_2023/7zh2_14718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/04_2023/7zh2_14718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/04_2023/7zh2_14718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh2_14718/04_2023/7zh2_14718_updated.pdb" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 132 5.16 5 C 15597 2.51 5 N 3986 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 162": "OE1" <-> "OE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C GLU 755": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24419 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7969 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7969 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7959 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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 chiralities: 2 Chain: "E" 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 chiralities: 2 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 chiralities: 2 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 11.63, per 1000 atoms: 0.48 Number of scatterers: 24419 At special positions: 0 Unit cell: (131.25, 143.85, 158.55, 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 132 16.00 O 4704 8.00 N 3986 7.00 C 15597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1302 " - " ASN A 109 " " NAG A1303 " - " ASN A 119 " " NAG A1304 " - " ASN A 158 " " NAG A1305 " - " ASN A 269 " " NAG A1306 " - " ASN A 318 " " NAG A1307 " - " ASN A 357 " " NAG A1308 " - " ASN A 602 " " NAG A1309 " - " ASN A 783 " " NAG A1310 " - " ASN A 699 " " NAG B1302 " - " ASN B 109 " " NAG B1303 " - " ASN B 119 " " NAG B1304 " - " ASN B 158 " " NAG B1305 " - " ASN B 269 " " NAG B1306 " - " ASN B 318 " " NAG B1307 " - " ASN B 357 " " NAG B1308 " - " ASN B 602 " " NAG B1309 " - " ASN B 783 " " NAG B1310 " - " ASN B 699 " " NAG C1302 " - " ASN C 109 " " NAG C1303 " - " ASN C 119 " " NAG C1304 " - " ASN C 158 " " NAG C1305 " - " ASN C 269 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 357 " " NAG C1308 " - " ASN C 602 " " NAG C1309 " - " ASN C 783 " " NAG C1310 " - " ASN C 699 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 8.62 Conformation dependent library (CDL) restraints added in 3.2 seconds 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 39 sheets defined 22.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.917A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.365A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 720 through 723 No H-bonds generated for 'chain 'A' and resid 720 through 723' Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 742 through 764 removed outlier: 3.637A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 removed outlier: 3.553A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 849 through 864 Processing helix chain 'A' and resid 883 through 891 Processing helix chain 'A' and resid 896 through 921 removed outlier: 5.794A pdb=" N LYS A 903 " --> pdb=" O TYR A 899 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 949 removed outlier: 3.555A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 965 removed outlier: 3.704A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1014 removed outlier: 3.544A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.864A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 removed outlier: 4.209A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 720 through 723 No H-bonds generated for 'chain 'B' and resid 720 through 723' Processing helix chain 'B' and resid 729 through 738 Processing helix chain 'B' and resid 742 through 764 removed outlier: 3.737A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 819 through 825 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 849 through 864 Processing helix chain 'B' and resid 882 through 891 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 902 through 921 Processing helix chain 'B' and resid 925 through 949 removed outlier: 4.578A pdb=" N LYS B 929 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 936 " --> pdb=" O VAL B 933 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 945 " --> pdb=" O ASN B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 965 removed outlier: 3.679A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1014 removed outlier: 3.587A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 391 through 396 removed outlier: 4.507A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 426 through 429 No H-bonds generated for 'chain 'C' and resid 426 through 429' Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 720 through 723 No H-bonds generated for 'chain 'C' and resid 720 through 723' Processing helix chain 'C' and resid 729 through 738 Processing helix chain 'C' and resid 742 through 764 removed outlier: 3.670A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 807 removed outlier: 3.528A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 849 through 863 Processing helix chain 'C' and resid 882 through 891 removed outlier: 3.506A pdb=" N GLY C 890 " --> pdb=" O TYR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 removed outlier: 3.582A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 921 removed outlier: 3.628A pdb=" N SER C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 949 removed outlier: 4.213A pdb=" N LYS C 929 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 945 " --> pdb=" O ASN C 942 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 948 " --> pdb=" O VAL C 945 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 949 " --> pdb=" O LYS C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 965 removed outlier: 3.584A pdb=" N ARG C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1014 removed outlier: 3.823A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing sheet with id= A, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.674A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 220 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 59 removed outlier: 4.069A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 161 through 164 removed outlier: 4.014A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 127 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 298 through 301 Processing sheet with id= E, first strand: chain 'A' and resid 312 through 315 removed outlier: 8.421A pdb=" N VAL A 313 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN A 526 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ARG A 315 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN A 528 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.649A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 348 through 350 Processing sheet with id= H, first strand: chain 'A' and resid 439 through 441 Processing sheet with id= I, first strand: chain 'A' and resid 674 through 678 removed outlier: 6.391A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.976A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 699 through 710 removed outlier: 3.578A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.693A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.665A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 51 through 59 removed outlier: 4.080A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.649A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.791A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 636 " --> pdb=" O PHE B 629 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 312 through 315 removed outlier: 8.388A pdb=" N VAL B 313 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN B 526 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ARG B 315 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN B 528 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.686A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= T, first strand: chain 'B' and resid 439 through 441 Processing sheet with id= U, first strand: chain 'B' and resid 674 through 678 removed outlier: 6.440A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 693 through 697 Processing sheet with id= W, first strand: chain 'B' and resid 699 through 710 removed outlier: 3.553A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.590A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id= Z, first strand: chain 'C' and resid 31 through 35 removed outlier: 3.925A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.129A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 161 through 164 removed outlier: 4.424A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 298 through 302 removed outlier: 4.591A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 312 through 315 removed outlier: 8.530A pdb=" N VAL C 313 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN C 526 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ARG C 315 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN C 528 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.664A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 348 through 350 Processing sheet with id= AG, first strand: chain 'C' and resid 439 through 441 Processing sheet with id= AH, first strand: chain 'C' and resid 674 through 678 removed outlier: 6.475A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 693 through 697 Processing sheet with id= AJ, first strand: chain 'C' and resid 699 through 710 removed outlier: 3.645A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.565A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 1069 through 1071 removed outlier: 4.147A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C1103 " --> pdb=" O PHE C1071 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 1076 through 1079 879 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.28 Time building geometry restraints manager: 9.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6006 1.33 - 1.46: 6550 1.46 - 1.58: 12235 1.58 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 24971 Sorted by residual: bond pdb=" N GLN C 786 " pdb=" CA GLN C 786 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.42e+01 bond pdb=" N ILE C 787 " pdb=" CA ILE C 787 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.04e-02 9.25e+03 1.36e+01 bond pdb=" N ILE C 81 " pdb=" CA ILE C 81 " ideal model delta sigma weight residual 1.460 1.494 -0.034 9.30e-03 1.16e+04 1.32e+01 bond pdb=" N ALA A 881 " pdb=" CA ALA A 881 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.08e+01 bond pdb=" N CYS A 159 " pdb=" CA CYS A 159 " ideal model delta sigma weight residual 1.454 1.497 -0.042 1.31e-02 5.83e+03 1.05e+01 ... (remaining 24966 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.85: 693 106.85 - 113.63: 13653 113.63 - 120.41: 9006 120.41 - 127.19: 10375 127.19 - 133.97: 206 Bond angle restraints: 33933 Sorted by residual: angle pdb=" C PHE A 880 " pdb=" N ALA A 881 " pdb=" CA ALA A 881 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" CA PHE A 880 " pdb=" C PHE A 880 " pdb=" O PHE A 880 " ideal model delta sigma weight residual 121.16 114.28 6.88 1.12e+00 7.97e-01 3.78e+01 angle pdb=" C SER C 785 " pdb=" N GLN C 786 " pdb=" CA GLN C 786 " ideal model delta sigma weight residual 121.54 133.21 -11.67 1.91e+00 2.74e-01 3.73e+01 angle pdb=" C ASN A 158 " pdb=" CA ASN A 158 " pdb=" CB ASN A 158 " ideal model delta sigma weight residual 111.86 119.38 -7.52 1.34e+00 5.57e-01 3.15e+01 angle pdb=" CA SER C 785 " pdb=" C SER C 785 " pdb=" O SER C 785 " ideal model delta sigma weight residual 121.16 114.88 6.28 1.12e+00 7.97e-01 3.14e+01 ... (remaining 33928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13414 17.96 - 35.91: 968 35.91 - 53.87: 150 53.87 - 71.83: 41 71.83 - 89.78: 23 Dihedral angle restraints: 14596 sinusoidal: 5665 harmonic: 8931 Sorted by residual: dihedral pdb=" CA THR C 468 " pdb=" C THR C 468 " pdb=" N PRO C 469 " pdb=" CA PRO C 469 " ideal model delta harmonic sigma weight residual 180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR B 468 " pdb=" C THR B 468 " pdb=" N PRO B 469 " pdb=" CA PRO B 469 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS C 725 " pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -53.86 -32.14 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 14593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3151 0.048 - 0.096: 485 0.096 - 0.145: 265 0.145 - 0.193: 9 0.193 - 0.241: 7 Chirality restraints: 3917 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.55e+00 chirality pdb=" CA ILE A 878 " pdb=" N ILE A 878 " pdb=" C ILE A 878 " pdb=" CB ILE A 878 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.43e+00 ... (remaining 3914 not shown) Planarity restraints: 4382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 158 " 0.049 2.00e-02 2.50e+03 4.71e-02 2.78e+01 pdb=" CG ASN A 158 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 158 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 158 " -0.066 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 158 " -0.043 2.00e-02 2.50e+03 4.57e-02 2.61e+01 pdb=" CG ASN C 158 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 158 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 158 " 0.073 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1093 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO A1094 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO A1094 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A1094 " 0.057 5.00e-02 4.00e+02 ... (remaining 4379 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 130 2.61 - 3.18: 20371 3.18 - 3.76: 33944 3.76 - 4.33: 51056 4.33 - 4.90: 84462 Nonbonded interactions: 189963 Sorted by model distance: nonbonded pdb=" O ASN C 119 " pdb=" OG SER C 120 " model vdw 2.038 2.440 nonbonded pdb=" O ASN A 119 " pdb=" OG SER A 120 " model vdw 2.042 2.440 nonbonded pdb=" OG1 THR B 106 " pdb=" OD1 ASN B 108 " model vdw 2.216 2.440 nonbonded pdb=" O PRO B 462 " pdb=" NZ LYS B 465 " model vdw 2.271 2.520 nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.278 2.440 ... (remaining 189958 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 30 through 864 or (resid 865 through 875 and (name N or na \ me CA or name C or name O or name CB )) or resid 876 through 899 or (resid 900 a \ nd (name N or name CA or name C or name O or name CB )) or resid 901 through 106 \ 7 or (resid 1068 through 1069 and (name N or name CA or name C or name O or name \ CB )) or resid 1070 through 1105 or resid 1301 through 1310)) selection = (chain 'B' and (resid 30 through 864 or (resid 865 through 875 and (name N or na \ me CA or name C or name O or name CB )) or resid 876 through 899 or (resid 900 a \ nd (name N or name CA or name C or name O or name CB )) or resid 901 through 106 \ 7 or (resid 1068 through 1069 and (name N or name CA or name C or name O or name \ CB )) or resid 1070 through 1105 or resid 1301 through 1310)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.440 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 61.670 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.003 0.065 24971 Z= 0.224 Angle : 0.622 12.049 33933 Z= 0.361 Chirality : 0.045 0.241 3917 Planarity : 0.004 0.106 4352 Dihedral : 13.208 89.781 8740 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3018 helix: 0.51 (0.20), residues: 684 sheet: 0.70 (0.20), residues: 627 loop : -1.53 (0.13), residues: 1707 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 343 time to evaluate : 2.794 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 346 average time/residue: 1.5761 time to fit residues: 618.0362 Evaluate side-chains 255 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 251 time to evaluate : 3.008 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.7501 time to fit residues: 6.7208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 0.4980 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 277 optimal weight: 8.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN A 692 ASN A 766 GLN A 877 GLN A 889 ASN A 908 GLN A 936 GLN A1088 GLN B 70 HIS B 321 ASN B 479 ASN B 827 ASN B 883 GLN B 889 ASN B 992 GLN C 32 GLN C 546 GLN C 769 GLN C 883 GLN ** C 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 24971 Z= 0.230 Angle : 0.602 7.870 33933 Z= 0.330 Chirality : 0.047 0.227 3917 Planarity : 0.005 0.067 4352 Dihedral : 6.045 77.978 3333 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3018 helix: 1.11 (0.19), residues: 705 sheet: 0.91 (0.21), residues: 561 loop : -1.42 (0.13), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 264 time to evaluate : 2.968 Fit side-chains outliers start: 57 outliers final: 24 residues processed: 294 average time/residue: 1.5432 time to fit residues: 515.8966 Evaluate side-chains 267 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 2.489 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 11 average time/residue: 0.8286 time to fit residues: 14.6555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 278 optimal weight: 0.0670 chunk 300 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 223 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A1088 GLN B 70 HIS B 744 GLN B 769 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 96 ASN C 479 ASN C 546 GLN C 737 GLN C 769 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.068 24971 Z= 0.133 Angle : 0.500 14.202 33933 Z= 0.269 Chirality : 0.043 0.222 3917 Planarity : 0.004 0.053 4352 Dihedral : 5.553 70.514 3333 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.72 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3018 helix: 1.49 (0.20), residues: 699 sheet: 0.82 (0.21), residues: 558 loop : -1.26 (0.13), residues: 1761 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 266 time to evaluate : 2.887 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 294 average time/residue: 1.5823 time to fit residues: 533.6247 Evaluate side-chains 261 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 2.937 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 5 average time/residue: 0.7580 time to fit residues: 8.4775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.3980 chunk 209 optimal weight: 0.0020 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A1088 GLN B 178 ASN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 546 GLN C 769 GLN ** C 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 24971 Z= 0.232 Angle : 0.600 11.604 33933 Z= 0.326 Chirality : 0.047 0.304 3917 Planarity : 0.005 0.048 4352 Dihedral : 5.939 64.203 3333 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.43 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.50 (0.14), residues: 3018 helix: 1.05 (0.19), residues: 729 sheet: 0.87 (0.21), residues: 570 loop : -1.44 (0.13), residues: 1719 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 248 time to evaluate : 3.076 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 30 residues processed: 286 average time/residue: 1.5634 time to fit residues: 509.0501 Evaluate side-chains 274 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 2.862 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 10 average time/residue: 0.7634 time to fit residues: 13.4046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 74 optimal weight: 0.0670 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A1088 GLN B 445 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 74 HIS C 96 ASN C 546 GLN ** C 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24971 Z= 0.221 Angle : 0.586 10.161 33933 Z= 0.319 Chirality : 0.046 0.263 3917 Planarity : 0.005 0.044 4352 Dihedral : 5.921 56.042 3333 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.59 (0.14), residues: 3018 helix: 0.97 (0.19), residues: 729 sheet: 0.84 (0.21), residues: 570 loop : -1.51 (0.13), residues: 1719 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 252 time to evaluate : 3.001 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 33 residues processed: 298 average time/residue: 1.5319 time to fit residues: 522.4669 Evaluate side-chains 272 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 2.721 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 27 residues processed: 8 average time/residue: 0.7817 time to fit residues: 11.6389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 4.9990 chunk 266 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 245 optimal weight: 0.0170 chunk 137 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 overall best weight: 3.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 917 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 201 GLN C 546 GLN C 769 GLN C1065 HIS C1095 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 24971 Z= 0.290 Angle : 0.656 9.988 33933 Z= 0.358 Chirality : 0.049 0.267 3917 Planarity : 0.005 0.043 4352 Dihedral : 6.162 53.593 3333 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.76 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.74 (0.14), residues: 3018 helix: 0.76 (0.19), residues: 738 sheet: 0.79 (0.21), residues: 570 loop : -1.60 (0.13), residues: 1710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 247 time to evaluate : 3.047 Fit side-chains outliers start: 69 outliers final: 38 residues processed: 297 average time/residue: 1.5219 time to fit residues: 515.8591 Evaluate side-chains 273 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 2.931 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 29 residues processed: 9 average time/residue: 0.6641 time to fit residues: 11.4912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 216 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 249 optimal weight: 0.0270 chunk 165 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A1065 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 96 ASN C 112 GLN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 24971 Z= 0.178 Angle : 0.553 9.322 33933 Z= 0.300 Chirality : 0.045 0.216 3917 Planarity : 0.004 0.043 4352 Dihedral : 5.833 55.018 3333 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.37 % Favored : 95.59 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.62 (0.14), residues: 3018 helix: 0.98 (0.19), residues: 729 sheet: 0.75 (0.21), residues: 552 loop : -1.50 (0.13), residues: 1737 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 250 time to evaluate : 2.609 Fit side-chains outliers start: 56 outliers final: 34 residues processed: 296 average time/residue: 1.5216 time to fit residues: 517.0610 Evaluate side-chains 269 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 2.832 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 2 average time/residue: 1.4831 time to fit residues: 7.2534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 187 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 546 GLN C 627 ASN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 24971 Z= 0.162 Angle : 0.530 10.318 33933 Z= 0.287 Chirality : 0.044 0.205 3917 Planarity : 0.004 0.042 4352 Dihedral : 5.604 57.094 3333 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.39 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3018 helix: 1.12 (0.20), residues: 729 sheet: 0.77 (0.21), residues: 552 loop : -1.44 (0.13), residues: 1737 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 246 time to evaluate : 2.985 Fit side-chains outliers start: 57 outliers final: 36 residues processed: 294 average time/residue: 1.4539 time to fit residues: 490.7190 Evaluate side-chains 273 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 2.887 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 5 average time/residue: 1.3254 time to fit residues: 11.6451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 259 optimal weight: 0.0670 chunk 273 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 overall best weight: 4.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 917 GLN A1040 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 96 ASN C 546 GLN C 769 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1065 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 24971 Z= 0.292 Angle : 0.649 8.775 33933 Z= 0.353 Chirality : 0.048 0.228 3917 Planarity : 0.005 0.043 4352 Dihedral : 6.084 54.739 3333 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.47 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.77 (0.14), residues: 3018 helix: 0.80 (0.19), residues: 729 sheet: 0.65 (0.21), residues: 552 loop : -1.56 (0.13), residues: 1737 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 244 time to evaluate : 2.766 Fit side-chains outliers start: 58 outliers final: 40 residues processed: 289 average time/residue: 1.5285 time to fit residues: 507.3962 Evaluate side-chains 281 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 2.758 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 35 residues processed: 5 average time/residue: 1.0881 time to fit residues: 10.4409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 304 optimal weight: 10.0000 chunk 280 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A 917 GLN A1040 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 32 GLN C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 24971 Z= 0.299 Angle : 0.665 9.380 33933 Z= 0.362 Chirality : 0.049 0.247 3917 Planarity : 0.005 0.048 4352 Dihedral : 6.241 52.731 3333 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.85 (0.14), residues: 3018 helix: 0.63 (0.19), residues: 738 sheet: 0.62 (0.20), residues: 615 loop : -1.67 (0.13), residues: 1665 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 242 time to evaluate : 2.808 Fit side-chains outliers start: 49 outliers final: 38 residues processed: 281 average time/residue: 1.5425 time to fit residues: 495.0416 Evaluate side-chains 276 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 33 residues processed: 5 average time/residue: 1.0031 time to fit residues: 9.5831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 101 optimal weight: 0.0980 chunk 249 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN A1040 HIS B 827 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 96 ASN C 445 HIS C 546 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.103714 restraints weight = 28297.003| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.66 r_work: 0.2906 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24971 Z= 0.193 Angle : 0.567 9.488 33933 Z= 0.308 Chirality : 0.046 0.265 3917 Planarity : 0.005 0.047 4352 Dihedral : 5.898 55.014 3333 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.72 (0.14), residues: 3018 helix: 0.87 (0.19), residues: 729 sheet: 0.76 (0.21), residues: 549 loop : -1.57 (0.13), residues: 1740 =============================================================================== Job complete usr+sys time: 8280.18 seconds wall clock time: 148 minutes 13.38 seconds (8893.38 seconds total)