Starting phenix.real_space_refine (version: dev) on Fri Feb 24 13:48:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlc_25987/02_2023/7tlc_25987.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlc_25987/02_2023/7tlc_25987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlc_25987/02_2023/7tlc_25987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlc_25987/02_2023/7tlc_25987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlc_25987/02_2023/7tlc_25987.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlc_25987/02_2023/7tlc_25987.pdb" } resolution = 2.83 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= 0.000 sd= 1.000 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 Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C ASP 830": "OD1" <-> "OD2" Residue "C TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23058 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "B" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7759 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 54, 'TRANS': 937} Chain breaks: 10 Chain: "C" Number of atoms: 7695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7695 Classifications: {'peptide': 984} Link IDs: {'CIS': 2, 'PTRANS': 52, 'TRANS': 929} Chain breaks: 11 Time building chain proxies: 12.49, per 1000 atoms: 0.54 Number of scatterers: 23058 At special positions: 0 Unit cell: (129.076, 128.018, 171.396, 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 105 16.00 O 4382 8.00 N 3827 7.00 C 14744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.01 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=1.99 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 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=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.05 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: 8.54 Conformation dependent library (CDL) restraints added in 3.6 seconds 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5542 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 50 sheets defined 27.1% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.363A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.221A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.694A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.853A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.570A 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: 3.739A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.586A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.677A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.631A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.574A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.531A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.316A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.668A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.111A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.997A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.922A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.656A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.522A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.015A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.883A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.555A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.420A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.875A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.138A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.621A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.770A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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: 3.747A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.626A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.568A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.535A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.542A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.177A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.748A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.559A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.559A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.804A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.819A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.531A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.350A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.596A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.596A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.063A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.063A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.899A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.475A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.611A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.195A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.517A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.850A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.707A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.579A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.649A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.314A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.684A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG B 102 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.597A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.042A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.042A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.760A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.525A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.512A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.325A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.391A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.622A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.496A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.316A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.460A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.329A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.131A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.131A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.741A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.356A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.392A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.392A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.526A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.84 Time building geometry restraints manager: 9.26 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: 5895 1.33 - 1.46: 4628 1.46 - 1.58: 12928 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23580 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.58e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.18e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.70e-03 2.23e+04 1.04e+01 bond pdb=" CZ ARG C1039 " pdb=" NH2 ARG C1039 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG A1039 " pdb=" NH2 ARG A1039 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.98e+00 ... (remaining 23575 not shown) Histogram of bond angle deviations from ideal: 96.46 - 104.22: 333 104.22 - 111.99: 9403 111.99 - 119.75: 10512 119.75 - 127.51: 11671 127.51 - 135.28: 173 Bond angle restraints: 32092 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.97 -8.27 1.22e+00 6.72e-01 4.59e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.35 -7.65 1.22e+00 6.72e-01 3.93e+01 angle pdb=" CA ASP B 796 " pdb=" CB ASP B 796 " pdb=" CG ASP B 796 " ideal model delta sigma weight residual 112.60 118.57 -5.97 1.00e+00 1.00e+00 3.56e+01 angle pdb=" CA ASP A1084 " pdb=" CB ASP A1084 " pdb=" CG ASP A1084 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.39 -6.69 1.22e+00 6.72e-01 3.00e+01 ... (remaining 32087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13019 17.78 - 35.55: 845 35.55 - 53.33: 129 53.33 - 71.11: 64 71.11 - 88.89: 29 Dihedral angle restraints: 14086 sinusoidal: 5503 harmonic: 8583 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.61 78.61 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.90 76.90 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 155.57 -62.57 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 14083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2296 0.084 - 0.168: 1134 0.168 - 0.253: 197 0.253 - 0.337: 35 0.337 - 0.421: 9 Chirality restraints: 3671 Sorted by residual: 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 2.30 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA LYS B 417 " pdb=" N LYS B 417 " pdb=" C LYS B 417 " pdb=" CB LYS B 417 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE C 833 " pdb=" N PHE C 833 " pdb=" C PHE C 833 " pdb=" CB PHE C 833 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 3668 not shown) Planarity restraints: 4153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 269 " 0.204 2.00e-02 2.50e+03 1.07e-01 2.30e+02 pdb=" CG TYR A 269 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR A 269 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TYR A 269 " -0.093 2.00e-02 2.50e+03 pdb=" CE1 TYR A 269 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 269 " -0.050 2.00e-02 2.50e+03 pdb=" CZ TYR A 269 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 269 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 269 " -0.160 2.00e-02 2.50e+03 8.35e-02 1.40e+02 pdb=" CG TYR B 269 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 269 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR B 269 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR B 269 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 269 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR B 269 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 269 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 279 " 0.140 2.00e-02 2.50e+03 7.83e-02 1.23e+02 pdb=" CG TYR A 279 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 279 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR A 279 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR A 279 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 279 " -0.051 2.00e-02 2.50e+03 pdb=" CZ TYR A 279 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 279 " 0.126 2.00e-02 2.50e+03 ... (remaining 4150 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 11083 2.99 - 3.47: 22307 3.47 - 3.95: 39211 3.95 - 4.42: 44167 4.42 - 4.90: 75046 Nonbonded interactions: 191814 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.518 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.530 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.530 2.440 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.551 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.559 2.440 ... (remaining 191809 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' and (resid 27 through 620 or resid 641 through 1147)) selection = (chain 'C' and (resid 27 through 827 or resid 854 through 1147)) } 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 105 5.16 5 C 14744 2.51 5 N 3827 2.21 5 O 4382 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 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.950 Check model and map are aligned: 0.350 Process input model: 61.030 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4706 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 0.044 23580 Z= 0.807 Angle : 1.824 10.171 32092 Z= 1.239 Chirality : 0.095 0.421 3671 Planarity : 0.015 0.232 4153 Dihedral : 13.372 88.887 8427 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.28 % Favored : 94.48 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 2878 helix: -0.90 (0.17), residues: 669 sheet: 0.05 (0.20), residues: 613 loop : -1.04 (0.15), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 398 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 15 residues processed: 430 average time/residue: 1.1145 time to fit residues: 565.7542 Evaluate side-chains 268 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 2.618 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 3.3765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 0.5980 chunk 266 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 779 GLN A 784 GLN A1005 GLN B 196 ASN B 207 HIS B 703 ASN B 779 GLN B1002 GLN C 613 GLN C 751 ASN C 784 GLN C1002 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 23580 Z= 0.204 Angle : 0.625 11.847 32092 Z= 0.331 Chirality : 0.047 0.220 3671 Planarity : 0.004 0.055 4153 Dihedral : 5.630 27.510 3135 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.14 (0.15), residues: 2878 helix: 1.31 (0.20), residues: 673 sheet: -0.02 (0.18), residues: 698 loop : -0.75 (0.15), residues: 1507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 313 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 32 residues processed: 362 average time/residue: 1.0304 time to fit residues: 444.6157 Evaluate side-chains 269 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 2.536 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 9 average time/residue: 0.3750 time to fit residues: 8.6258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 222 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 314 GLN A 613 GLN A 914 ASN A1005 GLN A1108 ASN B 188 ASN B 422 ASN B 564 GLN B 607 GLN B 675 GLN B 914 ASN B1010 GLN C 613 GLN C 907 ASN C 965 GLN C1002 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4719 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 23580 Z= 0.379 Angle : 0.661 11.058 32092 Z= 0.343 Chirality : 0.049 0.172 3671 Planarity : 0.004 0.046 4153 Dihedral : 5.357 26.837 3135 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.28 (0.15), residues: 2878 helix: 1.25 (0.20), residues: 678 sheet: -0.12 (0.18), residues: 688 loop : -0.87 (0.15), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 241 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 54 residues processed: 317 average time/residue: 1.0700 time to fit residues: 404.7780 Evaluate side-chains 275 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 221 time to evaluate : 2.700 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 36 residues processed: 18 average time/residue: 0.5237 time to fit residues: 16.8540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.0870 chunk 201 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 254 optimal weight: 0.8980 chunk 76 optimal weight: 0.0070 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 914 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1108 ASN B 188 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 955 ASN B1010 GLN C 613 GLN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4697 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23580 Z= 0.179 Angle : 0.537 12.124 32092 Z= 0.279 Chirality : 0.044 0.156 3671 Planarity : 0.004 0.038 4153 Dihedral : 4.834 23.364 3135 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.04 (0.15), residues: 2878 helix: 1.68 (0.20), residues: 690 sheet: -0.18 (0.18), residues: 684 loop : -0.74 (0.15), residues: 1504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 244 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 44 residues processed: 306 average time/residue: 1.0778 time to fit residues: 392.1522 Evaluate side-chains 261 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 2.496 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 38 residues processed: 6 average time/residue: 0.6854 time to fit residues: 8.7909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 709 ASN A 914 ASN A1106 GLN B 188 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 703 ASN C 613 GLN C 675 GLN C 914 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4732 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.083 23580 Z= 0.496 Angle : 0.686 11.583 32092 Z= 0.353 Chirality : 0.050 0.177 3671 Planarity : 0.005 0.042 4153 Dihedral : 5.237 27.417 3135 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 2878 helix: 1.12 (0.20), residues: 686 sheet: -0.27 (0.18), residues: 682 loop : -1.00 (0.15), residues: 1510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 230 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 61 residues processed: 304 average time/residue: 1.0530 time to fit residues: 386.1779 Evaluate side-chains 282 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 221 time to evaluate : 2.871 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 43 residues processed: 18 average time/residue: 0.6164 time to fit residues: 18.8116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 0.5980 chunk 255 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 166 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 284 optimal weight: 0.6980 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 641 ASN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 388 ASN B 804 GLN B 935 GLN B1106 GLN C 613 GLN C 675 GLN C 913 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4701 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 23580 Z= 0.169 Angle : 0.528 13.420 32092 Z= 0.273 Chirality : 0.044 0.157 3671 Planarity : 0.004 0.040 4153 Dihedral : 4.675 23.213 3135 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.03 (0.15), residues: 2878 helix: 1.88 (0.20), residues: 668 sheet: -0.23 (0.18), residues: 681 loop : -0.76 (0.15), residues: 1529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 225 time to evaluate : 2.735 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 47 residues processed: 285 average time/residue: 1.0347 time to fit residues: 357.2648 Evaluate side-chains 263 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 216 time to evaluate : 2.507 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 40 residues processed: 7 average time/residue: 0.4344 time to fit residues: 7.9126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 160 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 158 optimal weight: 0.0970 chunk 283 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 613 GLN A 914 ASN B 188 ASN B 703 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4724 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 23580 Z= 0.377 Angle : 0.613 12.323 32092 Z= 0.314 Chirality : 0.047 0.168 3671 Planarity : 0.004 0.042 4153 Dihedral : 4.885 26.123 3135 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.29 (0.15), residues: 2878 helix: 1.48 (0.20), residues: 679 sheet: -0.32 (0.18), residues: 683 loop : -0.89 (0.15), residues: 1516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 224 time to evaluate : 2.951 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 51 residues processed: 286 average time/residue: 1.0329 time to fit residues: 358.3736 Evaluate side-chains 262 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 43 residues processed: 8 average time/residue: 0.4195 time to fit residues: 8.9844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 140 optimal weight: 0.2980 chunk 26 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1113 GLN B 188 ASN B1010 GLN C 331 ASN C 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4700 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 23580 Z= 0.164 Angle : 0.521 14.124 32092 Z= 0.267 Chirality : 0.044 0.151 3671 Planarity : 0.004 0.040 4153 Dihedral : 4.502 22.553 3135 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.04 (0.15), residues: 2878 helix: 2.01 (0.20), residues: 667 sheet: -0.21 (0.19), residues: 673 loop : -0.75 (0.15), residues: 1538 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 225 time to evaluate : 2.689 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 44 residues processed: 274 average time/residue: 1.0755 time to fit residues: 353.6562 Evaluate side-chains 257 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 213 time to evaluate : 2.869 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 37 residues processed: 7 average time/residue: 0.4877 time to fit residues: 8.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 247 optimal weight: 6.9990 chunk 264 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 81 optimal weight: 0.6980 chunk 238 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 914 ASN B 188 ASN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4705 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23580 Z= 0.191 Angle : 0.529 13.523 32092 Z= 0.270 Chirality : 0.044 0.156 3671 Planarity : 0.004 0.042 4153 Dihedral : 4.428 22.408 3135 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.07 (0.15), residues: 2878 helix: 1.98 (0.20), residues: 679 sheet: -0.14 (0.19), residues: 679 loop : -0.76 (0.15), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 225 time to evaluate : 2.689 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 44 residues processed: 273 average time/residue: 1.0300 time to fit residues: 341.9929 Evaluate side-chains 261 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 2.856 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 4 average time/residue: 0.7056 time to fit residues: 7.7687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 233 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 180 optimal weight: 0.0010 chunk 143 optimal weight: 7.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 188 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1088 HIS C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4707 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 23580 Z= 0.208 Angle : 0.534 14.067 32092 Z= 0.272 Chirality : 0.044 0.161 3671 Planarity : 0.004 0.040 4153 Dihedral : 4.433 22.759 3135 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.08 (0.15), residues: 2878 helix: 1.97 (0.20), residues: 679 sheet: -0.14 (0.19), residues: 671 loop : -0.72 (0.15), residues: 1528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 218 time to evaluate : 2.705 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 44 residues processed: 264 average time/residue: 1.0318 time to fit residues: 329.9912 Evaluate side-chains 261 residues out of total 2590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 2.900 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 4 average time/residue: 0.6401 time to fit residues: 7.1843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 233 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 239 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 43 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 188 ASN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.192776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127354 restraints weight = 22786.351| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.25 r_work: 0.3559 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 23580 Z= 0.178 Angle : 0.521 13.869 32092 Z= 0.265 Chirality : 0.044 0.149 3671 Planarity : 0.004 0.040 4153 Dihedral : 4.331 21.784 3135 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.16 (0.15), residues: 2878 helix: 2.05 (0.20), residues: 679 sheet: -0.11 (0.19), residues: 668 loop : -0.68 (0.15), residues: 1531 =============================================================================== Job complete usr+sys time: 7269.88 seconds wall clock time: 130 minutes 29.29 seconds (7829.29 seconds total)