Starting phenix.real_space_refine on Wed May 15 08:15:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtj_37835/05_2024/8wtj_37835.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtj_37835/05_2024/8wtj_37835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtj_37835/05_2024/8wtj_37835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtj_37835/05_2024/8wtj_37835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtj_37835/05_2024/8wtj_37835.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtj_37835/05_2024/8wtj_37835.pdb" } resolution = 4.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 146 5.16 5 C 19139 2.51 5 N 4992 2.21 5 O 5654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1027": "OE1" <-> "OE2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 29931 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8360 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 4 Chain: "B" Number of atoms: 8359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8359 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 4 Chain: "C" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8367 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 4 Chain: "E" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Time building chain proxies: 15.27, per 1000 atoms: 0.51 Number of scatterers: 29931 At special positions: 0 Unit cell: (157.04, 165.36, 230.88, 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 146 16.00 O 5654 8.00 N 4992 7.00 C 19139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.04 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.04 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.04 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.17 Conformation dependent library (CDL) restraints added in 5.8 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7126 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 44 sheets defined 28.9% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.609A pdb=" N GLU A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 733 through 739 removed outlier: 3.746A pdb=" N TYR A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 738 " --> pdb=" O CYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.849A pdb=" N SER A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 779 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.683A pdb=" N ASN A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.621A pdb=" N ALA A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 909 through 937 removed outlier: 3.861A pdb=" N ASN A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU A 918 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 961 removed outlier: 4.214A pdb=" N LEU A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.893A pdb=" N ILE A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 4.339A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1028 Processing helix chain 'A' and resid 1112 through 1114 No H-bonds generated for 'chain 'A' and resid 1112 through 1114' Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.948A pdb=" N GLU B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.713A pdb=" N PHE B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 4.079A pdb=" N TRP B 349 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.753A pdb=" N PHE B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 removed outlier: 3.595A pdb=" N VAL B 403 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 404 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 739 removed outlier: 3.949A pdb=" N ILE B 738 " --> pdb=" O CYS B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.608A pdb=" N SER B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 779 removed outlier: 3.860A pdb=" N THR B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN B 775 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 776 " --> pdb=" O LYS B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 801 removed outlier: 4.595A pdb=" N GLN B 800 " --> pdb=" O ASN B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 846 through 852 removed outlier: 3.517A pdb=" N PHE B 851 " --> pdb=" O ALA B 848 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN B 852 " --> pdb=" O GLN B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 881 Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 908 through 914 removed outlier: 3.770A pdb=" N VAL B 911 " --> pdb=" O THR B 908 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 912 " --> pdb=" O GLN B 909 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR B 913 " --> pdb=" O ASN B 910 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 914 " --> pdb=" O VAL B 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 908 through 914' Processing helix chain 'B' and resid 915 through 935 removed outlier: 3.838A pdb=" N ALA B 920 " --> pdb=" O GLN B 916 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 removed outlier: 4.752A pdb=" N VAL B 947 " --> pdb=" O LYS B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 984 removed outlier: 4.059A pdb=" N GLU B 984 " --> pdb=" O ASP B 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 981 through 984' Processing helix chain 'B' and resid 985 through 1028 removed outlier: 4.481A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1114 No H-bonds generated for 'chain 'B' and resid 1112 through 1114' Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.794A pdb=" N GLY C 195 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 360 through 366 removed outlier: 4.427A pdb=" N ILE C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.940A pdb=" N ILE C 406 " --> pdb=" O VAL C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 439 removed outlier: 3.987A pdb=" N SER C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 742 through 753 removed outlier: 3.670A pdb=" N SER C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.732A pdb=" N GLN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 759 " --> pdb=" O PHE C 755 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 778 " --> pdb=" O THR C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 801 removed outlier: 4.596A pdb=" N GLN C 800 " --> pdb=" O ASN C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 848 through 852 removed outlier: 3.927A pdb=" N PHE C 851 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN C 852 " --> pdb=" O GLN C 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 848 through 852' Processing helix chain 'C' and resid 862 through 881 Processing helix chain 'C' and resid 882 through 887 removed outlier: 3.562A pdb=" N ALA C 886 " --> pdb=" O TRP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 911 through 937 removed outlier: 7.163A pdb=" N LYS C 917 " --> pdb=" O TYR C 913 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 918 " --> pdb=" O GLU C 914 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 937 " --> pdb=" O SER C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 963 removed outlier: 4.473A pdb=" N VAL C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 980 Processing helix chain 'C' and resid 981 through 1028 removed outlier: 3.903A pdb=" N GLU C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1114 No H-bonds generated for 'chain 'C' and resid 1112 through 1114' Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.781A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.957A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.742A pdb=" N SER E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 157 through 192 removed outlier: 4.012A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.961A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.737A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.676A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.621A pdb=" N PHE E 327 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.538A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 412 removed outlier: 4.366A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 4.372A pdb=" N LEU E 418 " --> pdb=" O THR E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 446 Processing helix chain 'E' and resid 449 through 465 Processing helix chain 'E' and resid 472 through 481 removed outlier: 3.631A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.585A pdb=" N LEU E 503 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 529 removed outlier: 4.164A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.626A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.514A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.631A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 588 removed outlier: 3.804A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.609A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 52 removed outlier: 3.656A pdb=" N ASP A 50 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 269 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.860A pdb=" N GLY A 104 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 311 removed outlier: 4.043A pdb=" N VAL A 591 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 323 removed outlier: 3.747A pdb=" N LEU A 542 " --> pdb=" O PHE A 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 352 removed outlier: 4.159A pdb=" N ASN A 350 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A 395 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 394 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN A 433 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE A 370 " --> pdb=" O ASN A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 449 through 450 Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 550 removed outlier: 4.905A pdb=" N GLU A 579 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 574 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.496A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AB2, first strand: chain 'A' and resid 707 through 711 Processing sheet with id=AB3, first strand: chain 'A' and resid 714 through 717 Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 717 removed outlier: 6.746A pdb=" N GLY A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER A1051 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1057 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU A1059 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A1047 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A1061 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A1043 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 731 Processing sheet with id=AB6, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AB7, first strand: chain 'A' and resid 1090 through 1093 Processing sheet with id=AB8, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.651A pdb=" N SER B 57 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 45 through 48 Processing sheet with id=AC1, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.764A pdb=" N LEU B 81 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B 164 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 220 through 226 removed outlier: 6.692A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 223 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AC5, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.307A pdb=" N GLU B 320 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ASN B 538 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 322 " --> pdb=" O ASN B 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 350 through 354 removed outlier: 7.615A pdb=" N ASN B 433 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE B 370 " --> pdb=" O ASN B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 444 through 450 removed outlier: 3.664A pdb=" N GLY B 492 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASN B 446 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER B 490 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 448 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU B 488 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 547 through 550 Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 656 removed outlier: 4.006A pdb=" N GLU B 650 " --> pdb=" O ILE B 688 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR B 692 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN B 654 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 660 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.587A pdb=" N GLN B1067 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE B 714 " --> pdb=" O PRO B1065 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 716 " --> pdb=" O TYR B1063 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR B1063 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 718 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B1061 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR B 720 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B1059 " --> pdb=" O THR B 720 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 722 " --> pdb=" O VAL B1057 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B1057 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY B1055 " --> pdb=" O PRO B 724 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B1043 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 730 through 732 Processing sheet with id=AD3, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AD4, first strand: chain 'B' and resid 1090 through 1093 Processing sheet with id=AD5, first strand: chain 'C' and resid 25 through 27 removed outlier: 8.366A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE C 199 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AD7, first strand: chain 'C' and resid 49 through 52 Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.559A pdb=" N GLY C 100 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 123 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 168 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AE1, first strand: chain 'C' and resid 320 through 324 removed outlier: 4.219A pdb=" N LEU C 542 " --> pdb=" O PHE C 539 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 392 through 396 removed outlier: 4.069A pdb=" N TRP C 432 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AE4, first strand: chain 'C' and resid 650 through 656 removed outlier: 4.959A pdb=" N THR C 692 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN C 654 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.223A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.223A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1116 through 1117 Processing sheet with id=AE8, first strand: chain 'E' and resid 347 through 350 1094 hydrogen bonds defined for protein. 3045 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.72 Time building geometry restraints manager: 13.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9540 1.34 - 1.46: 7327 1.46 - 1.58: 13611 1.58 - 1.71: 1 1.71 - 1.83: 197 Bond restraints: 30676 Sorted by residual: bond pdb=" CG ARG E 393 " pdb=" CD ARG E 393 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.62e+00 bond pdb=" C ALA B 368 " pdb=" N PRO B 369 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.78e+00 bond pdb=" C ALA A 368 " pdb=" N PRO A 369 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.72e+00 bond pdb=" CA ARG B 154 " pdb=" CB ARG B 154 " ideal model delta sigma weight residual 1.539 1.626 -0.087 4.88e-02 4.20e+02 3.18e+00 bond pdb=" C ARG E 582 " pdb=" N PRO E 583 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.16e+00 ... (remaining 30671 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.82: 559 104.82 - 112.15: 14476 112.15 - 119.48: 10499 119.48 - 126.81: 15788 126.81 - 134.13: 416 Bond angle restraints: 41738 Sorted by residual: angle pdb=" CB MET E 455 " pdb=" CG MET E 455 " pdb=" SD MET E 455 " ideal model delta sigma weight residual 112.70 130.48 -17.78 3.00e+00 1.11e-01 3.51e+01 angle pdb=" CA MET C 149 " pdb=" CB MET C 149 " pdb=" CG MET C 149 " ideal model delta sigma weight residual 114.10 123.97 -9.87 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CB MET C 149 " pdb=" CG MET C 149 " pdb=" SD MET C 149 " ideal model delta sigma weight residual 112.70 127.11 -14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" N GLU E 571 " pdb=" CA GLU E 571 " pdb=" CB GLU E 571 " ideal model delta sigma weight residual 110.16 117.05 -6.89 1.48e+00 4.57e-01 2.17e+01 angle pdb=" C GLU E 571 " pdb=" N ASN E 572 " pdb=" CA ASN E 572 " ideal model delta sigma weight residual 121.94 113.04 8.90 2.00e+00 2.50e-01 1.98e+01 ... (remaining 41733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16274 17.93 - 35.86: 1667 35.86 - 53.79: 236 53.79 - 71.71: 69 71.71 - 89.64: 35 Dihedral angle restraints: 18281 sinusoidal: 7204 harmonic: 11077 Sorted by residual: dihedral pdb=" CB CYS A1078 " pdb=" SG CYS A1078 " pdb=" SG CYS A1122 " pdb=" CB CYS A1122 " ideal model delta sinusoidal sigma weight residual -86.00 -169.10 83.10 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 133 " pdb=" CB CYS B 133 " ideal model delta sinusoidal sigma weight residual -86.00 -162.97 76.97 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 133 " pdb=" CB CYS A 133 " ideal model delta sinusoidal sigma weight residual -86.00 -160.91 74.91 1 1.00e+01 1.00e-02 7.10e+01 ... (remaining 18278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3716 0.064 - 0.128: 816 0.128 - 0.192: 97 0.192 - 0.256: 9 0.256 - 0.319: 4 Chirality restraints: 4642 Sorted by residual: chirality pdb=" CB ILE B 98 " pdb=" CA ILE B 98 " pdb=" CG1 ILE B 98 " pdb=" CG2 ILE B 98 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU A 542 " pdb=" CB LEU A 542 " pdb=" CD1 LEU A 542 " pdb=" CD2 LEU A 542 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE C 199 " pdb=" CA ILE C 199 " pdb=" CG1 ILE C 199 " pdb=" CG2 ILE C 199 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 4639 not shown) Planarity restraints: 5407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 982 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO C 983 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 983 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 983 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 582 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO E 583 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 583 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 583 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 561 " 0.018 2.00e-02 2.50e+03 2.03e-02 7.20e+00 pdb=" CG PHE A 561 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 561 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 561 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 561 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 561 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 561 " -0.002 2.00e-02 2.50e+03 ... (remaining 5404 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5655 2.77 - 3.30: 29732 3.30 - 3.84: 54119 3.84 - 4.37: 60245 4.37 - 4.90: 99061 Nonbonded interactions: 248812 Sorted by model distance: nonbonded pdb=" O THR B 246 " pdb=" OG SER B 250 " model vdw 2.239 2.440 nonbonded pdb=" ND2 ASN E 134 " pdb=" OG SER E 167 " model vdw 2.244 2.520 nonbonded pdb=" OG1 THR B 496 " pdb=" OH TYR E 41 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR B 365 " pdb=" O PRO B 380 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASP E 382 " pdb=" OH TYR E 385 " model vdw 2.261 2.440 ... (remaining 248807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 822 or resid 846 through 1136)) selection = (chain 'B' and (resid 14 through 822 or resid 846 through 1136)) selection = (chain 'C' and (resid 14 through 822 or resid 846 through 1136)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 11.120 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 80.670 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 30676 Z= 0.229 Angle : 0.846 17.783 41738 Z= 0.437 Chirality : 0.052 0.319 4642 Planarity : 0.006 0.086 5407 Dihedral : 14.833 89.642 11032 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.64 % Favored : 91.33 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.13), residues: 3761 helix: -0.26 (0.16), residues: 934 sheet: -1.22 (0.21), residues: 586 loop : -2.48 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 432 HIS 0.009 0.001 HIS A 63 PHE 0.045 0.002 PHE A 561 TYR 0.028 0.002 TYR E 385 ARG 0.009 0.001 ARG B1010 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9692 (mmp) cc_final: 0.9331 (mmm) REVERT: B 173 MET cc_start: 0.8452 (ppp) cc_final: 0.8241 (ppp) REVERT: B 1099 PHE cc_start: 0.9600 (m-80) cc_final: 0.9119 (m-80) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.4319 time to fit residues: 71.5902 Evaluate side-chains 78 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 30.0000 chunk 285 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 192 optimal weight: 20.0000 chunk 152 optimal weight: 40.0000 chunk 295 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 chunk 179 optimal weight: 0.9990 chunk 219 optimal weight: 30.0000 chunk 342 optimal weight: 30.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 501 HIS A 637 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN B 637 ASN ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 922 GLN B 945 GLN ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1044 HIS C 58 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN C 747 ASN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 924 ASN C 945 GLN ** C1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30676 Z= 0.270 Angle : 0.645 11.249 41738 Z= 0.344 Chirality : 0.042 0.152 4642 Planarity : 0.005 0.066 5407 Dihedral : 5.527 31.162 4077 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.23 % Favored : 90.75 % Rotamer: Outliers : 0.09 % Allowed : 9.01 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3761 helix: 0.42 (0.17), residues: 974 sheet: -1.31 (0.22), residues: 581 loop : -2.36 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B1098 HIS 0.012 0.001 HIS A 63 PHE 0.019 0.002 PHE E 390 TYR 0.029 0.002 TYR E 385 ARG 0.008 0.001 ARG E 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9628 (mmp) cc_final: 0.9295 (mmm) REVERT: B 173 MET cc_start: 0.8639 (ppp) cc_final: 0.8225 (ppp) REVERT: B 1099 PHE cc_start: 0.9649 (m-80) cc_final: 0.9227 (m-80) REVERT: C 578 LEU cc_start: 0.9686 (tp) cc_final: 0.9428 (pt) REVERT: C 727 MET cc_start: 0.8888 (ppp) cc_final: 0.8527 (ppp) outliers start: 3 outliers final: 0 residues processed: 92 average time/residue: 0.4169 time to fit residues: 66.4483 Evaluate side-chains 74 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 284 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 342 optimal weight: 40.0000 chunk 370 optimal weight: 40.0000 chunk 305 optimal weight: 7.9990 chunk 340 optimal weight: 30.0000 chunk 116 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN A 931 GLN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30676 Z= 0.305 Angle : 0.680 13.084 41738 Z= 0.363 Chirality : 0.044 0.185 4642 Planarity : 0.005 0.067 5407 Dihedral : 5.704 31.400 4077 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 29.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.50 % Favored : 89.47 % Rotamer: Outliers : 0.03 % Allowed : 6.64 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3761 helix: 0.32 (0.16), residues: 998 sheet: -1.36 (0.23), residues: 551 loop : -2.45 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 203 HIS 0.012 0.002 HIS A 63 PHE 0.037 0.002 PHE C 894 TYR 0.020 0.002 TYR A 265 ARG 0.010 0.001 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 3.404 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: A 898 MET cc_start: 0.9648 (mmp) cc_final: 0.9353 (mmm) REVERT: B 173 MET cc_start: 0.8819 (ppp) cc_final: 0.8463 (ppp) REVERT: C 149 MET cc_start: 0.8121 (pmm) cc_final: 0.7913 (pmm) REVERT: C 727 MET cc_start: 0.8972 (ppp) cc_final: 0.8637 (ppp) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.4428 time to fit residues: 68.9280 Evaluate side-chains 70 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 40.0000 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 163 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 344 optimal weight: 7.9990 chunk 364 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 326 optimal weight: 30.0000 chunk 98 optimal weight: 1.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 HIS ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30676 Z= 0.180 Angle : 0.589 11.942 41738 Z= 0.307 Chirality : 0.043 0.163 4642 Planarity : 0.004 0.063 5407 Dihedral : 5.390 30.977 4077 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.47 % Favored : 90.51 % Rotamer: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3761 helix: 0.69 (0.17), residues: 993 sheet: -1.35 (0.22), residues: 576 loop : -2.42 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 302 HIS 0.008 0.001 HIS A 63 PHE 0.029 0.001 PHE C 894 TYR 0.016 0.001 TYR A 25 ARG 0.006 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 3.546 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: A 898 MET cc_start: 0.9691 (mmp) cc_final: 0.9411 (mmm) REVERT: B 173 MET cc_start: 0.8786 (ppp) cc_final: 0.8461 (ppp) REVERT: C 727 MET cc_start: 0.8919 (ppp) cc_final: 0.8507 (ppp) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.4135 time to fit residues: 61.8815 Evaluate side-chains 72 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 251 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30676 Z= 0.199 Angle : 0.590 12.419 41738 Z= 0.308 Chirality : 0.043 0.166 4642 Planarity : 0.004 0.061 5407 Dihedral : 5.300 30.689 4077 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.73 % Favored : 90.24 % Rotamer: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.14), residues: 3761 helix: 0.73 (0.17), residues: 998 sheet: -1.37 (0.22), residues: 573 loop : -2.40 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 275 HIS 0.008 0.001 HIS E 228 PHE 0.024 0.001 PHE C 894 TYR 0.015 0.001 TYR A 25 ARG 0.005 0.000 ARG E 245 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 3.522 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: A 898 MET cc_start: 0.9707 (mmp) cc_final: 0.9391 (mmm) REVERT: B 173 MET cc_start: 0.8861 (ppp) cc_final: 0.8558 (ppp) REVERT: C 727 MET cc_start: 0.8945 (ppp) cc_final: 0.8502 (ppp) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.4703 time to fit residues: 69.7877 Evaluate side-chains 70 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 20.0000 chunk 328 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 213 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 364 optimal weight: 0.6980 chunk 302 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30676 Z= 0.188 Angle : 0.588 10.990 41738 Z= 0.306 Chirality : 0.043 0.177 4642 Planarity : 0.004 0.061 5407 Dihedral : 5.231 30.401 4077 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.55 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.14), residues: 3761 helix: 0.85 (0.17), residues: 989 sheet: -1.27 (0.22), residues: 550 loop : -2.39 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 148 HIS 0.009 0.001 HIS E 228 PHE 0.021 0.001 PHE C 894 TYR 0.037 0.001 TYR E 385 ARG 0.004 0.000 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 4.407 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: A 898 MET cc_start: 0.9720 (mmp) cc_final: 0.9401 (mmm) REVERT: B 173 MET cc_start: 0.8867 (ppp) cc_final: 0.7726 (ptt) REVERT: C 727 MET cc_start: 0.8926 (ppp) cc_final: 0.8512 (ppp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.4331 time to fit residues: 61.6488 Evaluate side-chains 68 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 203 optimal weight: 20.0000 chunk 363 optimal weight: 30.0000 chunk 227 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 58 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 HIS ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 30676 Z= 0.362 Angle : 0.733 15.887 41738 Z= 0.392 Chirality : 0.045 0.224 4642 Planarity : 0.005 0.059 5407 Dihedral : 5.822 32.061 4077 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 35.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.96 % Favored : 88.01 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.13), residues: 3761 helix: 0.20 (0.16), residues: 1004 sheet: -1.39 (0.23), residues: 514 loop : -2.57 (0.12), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 349 HIS 0.015 0.002 HIS C 515 PHE 0.029 0.003 PHE A 460 TYR 0.022 0.002 TYR C 25 ARG 0.009 0.001 ARG E 245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9704 (mmp) cc_final: 0.9433 (mmm) REVERT: B 173 MET cc_start: 0.8871 (ppp) cc_final: 0.7896 (ptt) REVERT: C 727 MET cc_start: 0.9001 (ppp) cc_final: 0.8707 (ppp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.4064 time to fit residues: 57.8473 Evaluate side-chains 67 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 58 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 931 GLN ** C 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30676 Z= 0.247 Angle : 0.653 12.861 41738 Z= 0.342 Chirality : 0.044 0.194 4642 Planarity : 0.004 0.061 5407 Dihedral : 5.649 31.908 4077 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.26 % Favored : 89.71 % Rotamer: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.13), residues: 3761 helix: 0.46 (0.17), residues: 994 sheet: -1.32 (0.23), residues: 501 loop : -2.55 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 148 HIS 0.008 0.001 HIS E 228 PHE 0.020 0.002 PHE A 460 TYR 0.019 0.002 TYR B 913 ARG 0.008 0.001 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9717 (mmp) cc_final: 0.9431 (mmm) REVERT: B 173 MET cc_start: 0.8856 (ppp) cc_final: 0.8015 (ptt) REVERT: C 727 MET cc_start: 0.8940 (ppp) cc_final: 0.8595 (ppp) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.4196 time to fit residues: 61.9878 Evaluate side-chains 68 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 20.0000 chunk 348 optimal weight: 4.9990 chunk 317 optimal weight: 4.9990 chunk 338 optimal weight: 30.0000 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 305 optimal weight: 0.7980 chunk 320 optimal weight: 20.0000 chunk 337 optimal weight: 8.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN C 84 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 HIS E 63 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30676 Z= 0.173 Angle : 0.611 9.488 41738 Z= 0.315 Chirality : 0.044 0.212 4642 Planarity : 0.004 0.060 5407 Dihedral : 5.336 30.795 4077 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.10 % Favored : 89.87 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3761 helix: 0.81 (0.17), residues: 985 sheet: -1.31 (0.23), residues: 535 loop : -2.45 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 203 HIS 0.009 0.001 HIS E 228 PHE 0.017 0.001 PHE C 894 TYR 0.015 0.001 TYR A 25 ARG 0.003 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 3.615 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: A 898 MET cc_start: 0.9709 (mmp) cc_final: 0.9427 (mmm) REVERT: B 173 MET cc_start: 0.8856 (ppp) cc_final: 0.8037 (ptt) REVERT: C 727 MET cc_start: 0.8906 (ppp) cc_final: 0.8506 (ppp) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.4172 time to fit residues: 60.7182 Evaluate side-chains 69 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 0.9990 chunk 358 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 375 optimal weight: 7.9990 chunk 345 optimal weight: 6.9990 chunk 299 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 231 optimal weight: 0.0970 chunk 183 optimal weight: 10.0000 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30676 Z= 0.186 Angle : 0.616 14.332 41738 Z= 0.317 Chirality : 0.044 0.200 4642 Planarity : 0.004 0.066 5407 Dihedral : 5.274 30.399 4077 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.81 % Favored : 90.16 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.14), residues: 3761 helix: 0.86 (0.17), residues: 980 sheet: -1.21 (0.23), residues: 504 loop : -2.43 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 203 HIS 0.008 0.001 HIS E 228 PHE 0.015 0.001 PHE C 894 TYR 0.019 0.001 TYR B 869 ARG 0.004 0.000 ARG C1010 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 3.494 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: A 898 MET cc_start: 0.9711 (mmp) cc_final: 0.9428 (mmm) REVERT: B 173 MET cc_start: 0.8824 (ppp) cc_final: 0.7996 (ptt) REVERT: C 727 MET cc_start: 0.8897 (ppp) cc_final: 0.8515 (ppp) outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.4171 time to fit residues: 62.7130 Evaluate side-chains 70 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 9.9990 chunk 318 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 275 optimal weight: 0.8980 chunk 44 optimal weight: 40.0000 chunk 83 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 307 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.050496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.031434 restraints weight = 346985.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.031555 restraints weight = 259835.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.031752 restraints weight = 210599.504| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30676 Z= 0.254 Angle : 0.660 13.875 41738 Z= 0.345 Chirality : 0.044 0.176 4642 Planarity : 0.004 0.067 5407 Dihedral : 5.489 30.962 4077 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 28.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.06 % Favored : 88.91 % Rotamer: Outliers : 0.03 % Allowed : 0.63 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.13), residues: 3761 helix: 0.64 (0.17), residues: 993 sheet: -1.27 (0.23), residues: 503 loop : -2.48 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 148 HIS 0.009 0.002 HIS E 228 PHE 0.020 0.002 PHE B 76 TYR 0.022 0.002 TYR B 869 ARG 0.005 0.001 ARG A 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4378.00 seconds wall clock time: 83 minutes 42.99 seconds (5022.99 seconds total)