Starting phenix.real_space_refine (version: dev) on Wed Apr 6 20:06:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0j_23612/04_2022/7m0j_23612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0j_23612/04_2022/7m0j_23612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0j_23612/04_2022/7m0j_23612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0j_23612/04_2022/7m0j_23612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0j_23612/04_2022/7m0j_23612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0j_23612/04_2022/7m0j_23612.pdb" } resolution = 3.52 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= 0.003 sd= 0.060 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 22827 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7609 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7609 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 7609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7609 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Time building chain proxies: 12.47, per 1000 atoms: 0.55 Number of scatterers: 22827 At special positions: 0 Unit cell: (137.54, 136.482, 172.454, 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 99 16.00 O 4341 8.00 N 3783 7.00 C 14604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.99 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=2.02 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=1.99 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 Time building additional restraints: 8.73 Conformation dependent library (CDL) restraints added in 3.8 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 48 sheets defined 27.5% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.542A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.179A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.551A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.652A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.750A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.114A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 868 through 885 removed outlier: 3.600A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.618A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.667A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.621A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.697A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.533A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.950A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.952A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.935A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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 783 removed outlier: 3.620A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.583A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.812A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.578A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.546A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.507A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.370A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.721A pdb=" N VAL B1129 " --> pdb=" O CYS B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.802A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.157A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.508A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.755A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.848A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.262A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 3.997A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.739A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.561A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.507A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.941A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.698A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.522A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.950A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.038A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.625A pdb=" N VAL C1129 " --> pdb=" O CYS C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.941A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.375A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.501A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.405A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.505A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.307A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.528A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.690A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.847A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.861A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.524A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.150A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.325A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.828A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.551A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.256A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.607A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.531A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.662A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.688A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.724A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.427A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.541A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.453A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.265A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.339A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.470A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.802A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.590A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.590A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 999 hydrogen bonds defined for protein. 2676 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: 9.88 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4479 1.32 - 1.45: 5721 1.45 - 1.57: 13008 1.57 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 23331 Sorted by residual: bond pdb=" CA ALA B 520 " pdb=" C ALA B 520 " ideal model delta sigma weight residual 1.524 1.565 -0.041 1.26e-02 6.30e+03 1.08e+01 bond pdb=" CZ ARG C1000 " pdb=" NH2 ARG C1000 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.07e+01 bond pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 1.517 1.547 -0.030 9.30e-03 1.16e+04 1.03e+01 bond pdb=" CA LEU C 229 " pdb=" C LEU C 229 " ideal model delta sigma weight residual 1.522 1.549 -0.027 8.40e-03 1.42e+04 1.02e+01 bond pdb=" CZ ARG A1039 " pdb=" NH2 ARG A1039 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 ... (remaining 23326 not shown) Histogram of bond angle deviations from ideal: 95.87 - 103.83: 223 103.83 - 111.79: 8781 111.79 - 119.75: 11017 119.75 - 127.71: 11595 127.71 - 135.67: 121 Bond angle restraints: 31737 Sorted by residual: angle pdb=" CA ASP A 427 " pdb=" CB ASP A 427 " pdb=" CG ASP A 427 " ideal model delta sigma weight residual 112.60 120.04 -7.44 1.00e+00 1.00e+00 5.53e+01 angle pdb=" CA ASP B 427 " pdb=" CB ASP B 427 " pdb=" CG ASP B 427 " ideal model delta sigma weight residual 112.60 119.73 -7.13 1.00e+00 1.00e+00 5.08e+01 angle pdb=" CA PHE A 643 " pdb=" CB PHE A 643 " pdb=" CG PHE A 643 " ideal model delta sigma weight residual 113.80 120.20 -6.40 1.00e+00 1.00e+00 4.10e+01 angle pdb=" CA ASP A1084 " pdb=" CB ASP A1084 " pdb=" CG ASP A1084 " ideal model delta sigma weight residual 112.60 118.92 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.17 -7.47 1.22e+00 6.72e-01 3.75e+01 ... (remaining 31732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12801 17.94 - 35.89: 858 35.89 - 53.83: 180 53.83 - 71.78: 51 71.78 - 89.72: 27 Dihedral angle restraints: 13917 sinusoidal: 5424 harmonic: 8493 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -175.72 89.72 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 171.05 -78.05 1 1.00e+01 1.00e-02 7.61e+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 93.00 151.17 -58.17 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 13914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2184 0.084 - 0.167: 1197 0.167 - 0.251: 223 0.251 - 0.335: 28 0.335 - 0.418: 7 Chirality restraints: 3639 Sorted by residual: chirality pdb=" CA GLU A 773 " pdb=" N GLU A 773 " pdb=" C GLU A 773 " pdb=" CB GLU A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA ASP C 745 " pdb=" N ASP C 745 " pdb=" C ASP C 745 " pdb=" CB ASP C 745 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 3636 not shown) Planarity restraints: 4098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.142 2.00e-02 2.50e+03 8.15e-02 1.66e+02 pdb=" CG TRP C 886 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " 0.111 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.049 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.062 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " 0.119 2.00e-02 2.50e+03 7.25e-02 1.31e+02 pdb=" CG TRP B 886 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " -0.100 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.047 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.101 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 200 " -0.154 2.00e-02 2.50e+03 7.89e-02 1.24e+02 pdb=" CG TYR B 200 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 200 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR B 200 " 0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR B 200 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 200 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR B 200 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR B 200 " -0.091 2.00e-02 2.50e+03 ... (remaining 4095 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 11340 3.00 - 3.48: 22163 3.48 - 3.95: 37449 3.95 - 4.43: 41630 4.43 - 4.90: 70630 Nonbonded interactions: 183212 Sorted by model distance: nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.528 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.534 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.549 2.440 nonbonded pdb=" OD1 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.570 2.440 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.572 2.440 ... (remaining 183207 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 14604 2.51 5 N 3783 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.160 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: 0.010 Extract box with map and model: 8.050 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.200 Process input model: 59.420 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.013 0.046 23331 Z= 0.818 Angle : 1.870 8.691 31737 Z= 1.263 Chirality : 0.096 0.418 3639 Planarity : 0.014 0.199 4098 Dihedral : 13.971 88.979 8325 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.38 % Favored : 92.16 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.04 % 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: -2.03 (0.14), residues: 2844 helix: -1.92 (0.16), residues: 651 sheet: -0.15 (0.22), residues: 540 loop : -1.54 (0.14), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 345 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 outliers start: 43 outliers final: 10 residues processed: 379 average time/residue: 0.3673 time to fit residues: 211.6910 Evaluate side-chains 161 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2565 time to fit residues: 7.9959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 264 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 603 ASN A 607 GLN A 804 GLN A 913 GLN A 935 GLN B 115 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 23331 Z= 0.215 Angle : 0.650 9.888 31737 Z= 0.353 Chirality : 0.046 0.187 3639 Planarity : 0.005 0.102 4098 Dihedral : 6.074 23.877 3102 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer Outliers : 1.37 % 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: -0.85 (0.15), residues: 2844 helix: 0.20 (0.19), residues: 651 sheet: -0.07 (0.19), residues: 699 loop : -1.14 (0.15), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 212 average time/residue: 0.3568 time to fit residues: 118.0410 Evaluate side-chains 137 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 2.731 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2055 time to fit residues: 9.8750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 264 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1106 GLN B 115 GLN B 207 HIS B 493 GLN B1002 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 317 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 23331 Z= 0.212 Angle : 0.579 12.364 31737 Z= 0.309 Chirality : 0.044 0.172 3639 Planarity : 0.004 0.051 4098 Dihedral : 5.334 24.757 3102 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 1.37 % 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: -0.47 (0.15), residues: 2844 helix: 0.82 (0.20), residues: 669 sheet: -0.09 (0.19), residues: 720 loop : -0.94 (0.15), residues: 1455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 3.153 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 outliers start: 35 outliers final: 15 residues processed: 187 average time/residue: 0.3210 time to fit residues: 97.9674 Evaluate side-chains 139 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 2.919 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2722 time to fit residues: 10.6326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 281 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 762 GLN A 764 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 394 ASN B 901 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 23331 Z= 0.272 Angle : 0.575 13.329 31737 Z= 0.304 Chirality : 0.044 0.185 3639 Planarity : 0.004 0.065 4098 Dihedral : 5.116 23.831 3102 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2844 helix: 1.03 (0.20), residues: 672 sheet: -0.06 (0.19), residues: 681 loop : -0.93 (0.15), residues: 1491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 169 average time/residue: 0.3268 time to fit residues: 90.5551 Evaluate side-chains 132 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2056 time to fit residues: 10.2316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 240 optimal weight: 0.0050 chunk 194 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 252 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 125 ASN B 901 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 23331 Z= 0.163 Angle : 0.522 10.150 31737 Z= 0.276 Chirality : 0.043 0.182 3639 Planarity : 0.004 0.047 4098 Dihedral : 4.764 21.572 3102 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.17 % 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: -0.21 (0.15), residues: 2844 helix: 1.28 (0.21), residues: 675 sheet: -0.03 (0.19), residues: 681 loop : -0.83 (0.15), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 157 average time/residue: 0.3434 time to fit residues: 88.8612 Evaluate side-chains 126 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 2.898 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2308 time to fit residues: 8.0865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.0270 chunk 253 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 23331 Z= 0.316 Angle : 0.587 11.182 31737 Z= 0.309 Chirality : 0.044 0.201 3639 Planarity : 0.005 0.148 4098 Dihedral : 4.877 20.364 3102 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.13 % 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: -0.36 (0.15), residues: 2844 helix: 1.08 (0.21), residues: 675 sheet: -0.18 (0.19), residues: 681 loop : -0.85 (0.15), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 149 average time/residue: 0.3251 time to fit residues: 80.1696 Evaluate side-chains 120 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 2.542 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2134 time to fit residues: 9.1152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 23331 Z= 0.270 Angle : 0.555 9.798 31737 Z= 0.295 Chirality : 0.044 0.224 3639 Planarity : 0.004 0.114 4098 Dihedral : 4.761 19.977 3102 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.02 % 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: -0.34 (0.15), residues: 2844 helix: 1.14 (0.20), residues: 675 sheet: -0.23 (0.19), residues: 693 loop : -0.84 (0.15), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 133 average time/residue: 0.3467 time to fit residues: 76.1622 Evaluate side-chains 118 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2153 time to fit residues: 8.8127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B1135 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 955 ASN C1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 23331 Z= 0.263 Angle : 0.552 8.650 31737 Z= 0.293 Chirality : 0.044 0.239 3639 Planarity : 0.004 0.103 4098 Dihedral : 4.711 19.263 3102 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2844 helix: 1.18 (0.20), residues: 675 sheet: -0.28 (0.18), residues: 717 loop : -0.82 (0.16), residues: 1452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 124 average time/residue: 0.3564 time to fit residues: 72.3397 Evaluate side-chains 115 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 2.702 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2334 time to fit residues: 8.3081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 205 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 165 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 23331 Z= 0.268 Angle : 0.556 8.310 31737 Z= 0.294 Chirality : 0.044 0.251 3639 Planarity : 0.004 0.101 4098 Dihedral : 4.672 19.174 3102 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2844 helix: 1.22 (0.21), residues: 672 sheet: -0.29 (0.18), residues: 708 loop : -0.83 (0.15), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 122 average time/residue: 0.3324 time to fit residues: 67.4832 Evaluate side-chains 111 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 2.578 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2230 time to fit residues: 5.1230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 289 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 230 optimal weight: 20.0000 chunk 23 optimal weight: 0.3980 chunk 178 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN B 493 GLN C 115 GLN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 23331 Z= 0.186 Angle : 0.524 7.856 31737 Z= 0.278 Chirality : 0.043 0.206 3639 Planarity : 0.004 0.093 4098 Dihedral : 4.481 19.651 3102 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.31 % 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: -0.17 (0.15), residues: 2844 helix: 1.41 (0.21), residues: 672 sheet: -0.26 (0.19), residues: 696 loop : -0.72 (0.16), residues: 1476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 128 average time/residue: 0.3371 time to fit residues: 71.7262 Evaluate side-chains 113 residues out of total 2559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2472 time to fit residues: 6.4250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 6.9990 chunk 245 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 96 optimal weight: 0.0040 chunk 237 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.113274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088780 restraints weight = 54827.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088744 restraints weight = 34908.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089357 restraints weight = 28763.092| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 23331 Z= 0.252 Angle : 0.547 7.845 31737 Z= 0.290 Chirality : 0.043 0.267 3639 Planarity : 0.004 0.096 4098 Dihedral : 4.539 19.294 3102 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.16 % 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: -0.18 (0.15), residues: 2844 helix: 1.43 (0.21), residues: 669 sheet: -0.31 (0.19), residues: 660 loop : -0.71 (0.16), residues: 1515 =============================================================================== Job complete usr+sys time: 3334.89 seconds wall clock time: 62 minutes 54.46 seconds (3774.46 seconds total)