Starting phenix.real_space_refine on Tue Mar 19 22:18:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhl_31998/03_2024/7vhl_31998.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhl_31998/03_2024/7vhl_31998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhl_31998/03_2024/7vhl_31998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhl_31998/03_2024/7vhl_31998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhl_31998/03_2024/7vhl_31998.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhl_31998/03_2024/7vhl_31998.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 117 5.16 5 C 16252 2.51 5 N 4244 2.21 5 O 4849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 764": "OE1" <-> "OE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 978": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25462 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 8526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8526 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 54, 'TRANS': 1037} Chain breaks: 2 Chain: "B" Number of atoms: 8441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8441 Classifications: {'peptide': 1083} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 54, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 8495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8495 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 54, 'TRANS': 1033} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 13.95, per 1000 atoms: 0.55 Number of scatterers: 25462 At special positions: 0 Unit cell: (153.92, 149.76, 197.6, 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 117 16.00 O 4849 8.00 N 4244 7.00 C 16252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 529 " - pdb=" SG CYS C 581 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 640 " distance=2.03 Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 722 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C1016 " - pdb=" SG CYS C1027 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.05 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 722 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B1016 " - pdb=" SG CYS B1027 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 744 " distance=2.02 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A1016 " - pdb=" SG CYS A1027 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1110 " 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: 10.19 Conformation dependent library (CDL) restraints added in 5.0 seconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6106 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 50 sheets defined 24.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.539A pdb=" N ASN C 128 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.644A pdb=" N VAL C 398 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 610 through 615 Processing helix chain 'C' and resid 721 through 727 Processing helix chain 'C' and resid 730 through 740 Processing helix chain 'C' and resid 742 through 767 Processing helix chain 'C' and resid 800 through 810 removed outlier: 3.652A pdb=" N VAL C 810 " --> pdb=" O LEU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 850 through 867 Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 896 through 902 removed outlier: 4.245A pdb=" N LEU C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 923 removed outlier: 3.804A pdb=" N SER C 923 " --> pdb=" O GLN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 949 Processing helix chain 'C' and resid 950 through 952 No H-bonds generated for 'chain 'C' and resid 950 through 952' Processing helix chain 'C' and resid 960 through 968 removed outlier: 3.515A pdb=" N ILE C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 972 Processing helix chain 'C' and resid 973 through 1017 Processing helix chain 'C' and resid 1124 through 1129 removed outlier: 4.174A pdb=" N GLU C1128 " --> pdb=" O PRO C1124 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.585A pdb=" N TRP B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 375 through 379 removed outlier: 4.019A pdb=" N ASN B 379 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 4.379A pdb=" N ARG B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.513A pdb=" N TYR B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 610 through 614 removed outlier: 3.798A pdb=" N VAL B 613 " --> pdb=" O GLU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 730 through 739 removed outlier: 3.568A pdb=" N ASN B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 738 " --> pdb=" O SER B 734 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 739 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 767 removed outlier: 3.551A pdb=" N GLN B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 753 " --> pdb=" O ARG B 749 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 760 " --> pdb=" O VAL B 756 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 762 " --> pdb=" O GLN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 809 removed outlier: 3.562A pdb=" N LEU B 805 " --> pdb=" O PHE B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 838 Processing helix chain 'B' and resid 850 through 868 Processing helix chain 'B' and resid 870 through 875 removed outlier: 3.912A pdb=" N ALA B 874 " --> pdb=" O TRP B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 891 Processing helix chain 'B' and resid 892 through 894 No H-bonds generated for 'chain 'B' and resid 892 through 894' Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.202A pdb=" N LEU B 900 " --> pdb=" O THR B 896 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 901 " --> pdb=" O GLN B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 923 Processing helix chain 'B' and resid 924 through 928 removed outlier: 6.870A pdb=" N SER B 927 " --> pdb=" O SER B 924 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 928 " --> pdb=" O THR B 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 924 through 928' Processing helix chain 'B' and resid 929 through 950 removed outlier: 3.706A pdb=" N GLN B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 968 removed outlier: 3.651A pdb=" N ILE B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1016 removed outlier: 3.841A pdb=" N GLU B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLN B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ARG B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 980 " --> pdb=" O GLN B 976 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 985 " --> pdb=" O ILE B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1125 through 1131 removed outlier: 3.852A pdb=" N ASP B1130 " --> pdb=" O PRO B1127 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER B1131 " --> pdb=" O GLU B1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.774A pdb=" N LEU A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.227A pdb=" N ASN A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.607A pdb=" N VAL A 398 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 399' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 730 through 741 Processing helix chain 'A' and resid 742 through 767 removed outlier: 3.738A pdb=" N PHE A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 removed outlier: 3.510A pdb=" N ASP A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 839 Processing helix chain 'A' and resid 850 through 868 Processing helix chain 'A' and resid 870 through 875 removed outlier: 3.948A pdb=" N ALA A 874 " --> pdb=" O TRP A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 893 Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.344A pdb=" N LEU A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 923 Processing helix chain 'A' and resid 925 through 928 removed outlier: 3.903A pdb=" N ALA A 928 " --> pdb=" O THR A 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 950 through 952 No H-bonds generated for 'chain 'A' and resid 950 through 952' Processing helix chain 'A' and resid 960 through 968 removed outlier: 3.568A pdb=" N ILE A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1015 removed outlier: 6.010A pdb=" N VAL A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1129 removed outlier: 3.914A pdb=" N GLU A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.813A pdb=" N THR C 51 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 266 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 66 removed outlier: 4.025A pdb=" N ALA C 255 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR C 86 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 81 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 180 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 199 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 4.025A pdb=" N ALA C 255 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR C 86 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 81 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 195 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.207A pdb=" N VAL C 117 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 302 through 304 removed outlier: 3.558A pdb=" N THR C 590 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 316 through 319 removed outlier: 3.702A pdb=" N ARG C 319 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 544 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C 565 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY C 557 " --> pdb=" O ASP C 565 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.581A pdb=" N ILE C 349 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 386 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 424 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS C 369 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN C 428 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE C 365 " --> pdb=" O ASN C 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 352 through 353 removed outlier: 7.081A pdb=" N CYS C 352 " --> pdb=" O CYS C 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 443 through 445 Processing sheet with id=AB1, first strand: chain 'C' and resid 645 through 646 removed outlier: 5.436A pdb=" N GLU C 645 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR C 680 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 679 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 661 " --> pdb=" O ILE C 657 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 685 through 687 Processing sheet with id=AB3, first strand: chain 'C' and resid 695 through 697 removed outlier: 3.574A pdb=" N THR C1060 " --> pdb=" O SER C1081 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 706 removed outlier: 3.680A pdb=" N THR C1050 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET C1034 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR C1051 " --> pdb=" O HIS C1032 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N HIS C1032 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 709 through 712 Processing sheet with id=AB6, first strand: chain 'C' and resid 718 through 720 removed outlier: 3.696A pdb=" N THR C 843 " --> pdb=" O SER C 719 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 771 through 774 removed outlier: 5.294A pdb=" N ILE C 772 " --> pdb=" O ASN B 687 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1104 through 1109 removed outlier: 6.079A pdb=" N VAL C1106 " --> pdb=" O PHE C1073 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE C1073 " --> pdb=" O VAL C1106 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY C1108 " --> pdb=" O ALA C1071 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 removed outlier: 4.183A pdb=" N THR B 63 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 258 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 255 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 84 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 81 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 194 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 196 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 215 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.614A pdb=" N ASP B 53 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.636A pdb=" N VAL B 111 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 118 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B 117 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 163 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270 removed outlier: 4.122A pdb=" N ASP B 278 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 302 through 308 removed outlier: 5.446A pdb=" N ILE B 303 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR B 590 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 305 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 588 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 307 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 589 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 315 through 316 removed outlier: 6.872A pdb=" N GLU B 315 " --> pdb=" O ASN B 531 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.669A pdb=" N VAL B 386 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 505 " --> pdb=" O TYR B 387 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 352 through 353 removed outlier: 3.777A pdb=" N CYS B 516 " --> pdb=" O CYS B 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.624A pdb=" N THR B 367 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 500 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 501 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 391 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 443 through 445 Processing sheet with id=AD1, first strand: chain 'B' and resid 633 through 636 Processing sheet with id=AD2, first strand: chain 'B' and resid 645 through 646 removed outlier: 4.086A pdb=" N SER B 675 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 677 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 679 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 695 through 697 removed outlier: 4.114A pdb=" N THR B1060 " --> pdb=" O SER B1081 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 703 through 712 removed outlier: 3.576A pdb=" N GLY B1043 " --> pdb=" O ALA B1040 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR B1051 " --> pdb=" O HIS B1032 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS B1032 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 771 through 774 removed outlier: 6.034A pdb=" N ILE B 772 " --> pdb=" O ASN A 687 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1104 through 1109 removed outlier: 5.931A pdb=" N VAL B1106 " --> pdb=" O PHE B1073 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B1073 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B1108 " --> pdb=" O ALA B1071 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 50 through 55 removed outlier: 6.950A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.777A pdb=" N THR A 63 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 258 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.888A pdb=" N GLU A 87 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 199 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 97 through 98 removed outlier: 4.174A pdb=" N GLY A 98 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.813A pdb=" N VAL A 218 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 196 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AE4, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AE5, first strand: chain 'A' and resid 316 through 319 removed outlier: 3.646A pdb=" N VAL A 530 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.829A pdb=" N ILE A 349 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 386 " --> pdb=" O ILE A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.703A pdb=" N CYS A 352 " --> pdb=" O CYS A 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.848A pdb=" N THR A 367 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 426 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 369 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP A 427 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 645 through 646 removed outlier: 5.746A pdb=" N GLU A 645 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR A 680 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 695 through 697 removed outlier: 3.652A pdb=" N THR A1060 " --> pdb=" O SER A1081 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AF3, first strand: chain 'A' and resid 705 through 712 removed outlier: 7.103A pdb=" N GLY A1043 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER A1039 " --> pdb=" O GLY A1043 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A1045 " --> pdb=" O PRO A1037 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU A1047 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A1035 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A1049 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1065 through 1066 Processing sheet with id=AF5, first strand: chain 'A' and resid 1070 through 1074 removed outlier: 5.593A pdb=" N ALA A1071 " --> pdb=" O SER A1107 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2127 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: 10.76 Time building geometry restraints manager: 11.06 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: 8239 1.34 - 1.46: 6367 1.46 - 1.59: 11311 1.59 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 26064 Sorted by residual: bond pdb=" N CYS B 327 " pdb=" CA CYS B 327 " ideal model delta sigma weight residual 1.458 1.485 -0.028 7.40e-03 1.83e+04 1.40e+01 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.456 1.490 -0.033 9.50e-03 1.11e+04 1.23e+01 bond pdb=" N THR B 324 " pdb=" CA THR B 324 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.52e+00 bond pdb=" N LEU B 326 " pdb=" CA LEU B 326 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.35e+00 bond pdb=" C CYS B 327 " pdb=" N PRO B 328 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.30e-02 5.92e+03 3.23e+00 ... (remaining 26059 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.37: 714 106.37 - 113.28: 13941 113.28 - 120.19: 8783 120.19 - 127.10: 11813 127.10 - 134.01: 241 Bond angle restraints: 35492 Sorted by residual: angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 113.53 104.15 9.38 9.80e-01 1.04e+00 9.16e+01 angle pdb=" O ASN B 325 " pdb=" C ASN B 325 " pdb=" N LEU B 326 " ideal model delta sigma weight residual 122.09 126.44 -4.35 1.04e+00 9.25e-01 1.75e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA CYS B 327 " pdb=" C CYS B 327 " pdb=" O CYS B 327 " ideal model delta sigma weight residual 120.48 117.48 3.00 7.70e-01 1.69e+00 1.51e+01 angle pdb=" C ASP A 605 " pdb=" N VAL A 606 " pdb=" CA VAL A 606 " ideal model delta sigma weight residual 121.97 128.12 -6.15 1.80e+00 3.09e-01 1.17e+01 ... (remaining 35487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13973 17.98 - 35.95: 1309 35.95 - 53.93: 182 53.93 - 71.91: 30 71.91 - 89.88: 33 Dihedral angle restraints: 15527 sinusoidal: 6021 harmonic: 9506 Sorted by residual: dihedral pdb=" CB CYS A 653 " pdb=" SG CYS A 653 " pdb=" SG CYS A 662 " pdb=" CB CYS A 662 " ideal model delta sinusoidal sigma weight residual -86.00 1.53 -87.53 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS B 327 " pdb=" SG CYS B 327 " pdb=" SG CYS B 352 " pdb=" CB CYS B 352 " ideal model delta sinusoidal sigma weight residual -86.00 -7.79 -78.21 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS C1066 " pdb=" SG CYS C1066 " pdb=" SG CYS C1110 " pdb=" CB CYS C1110 " ideal model delta sinusoidal sigma weight residual 93.00 35.78 57.22 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 15524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3273 0.051 - 0.102: 613 0.102 - 0.153: 124 0.153 - 0.205: 4 0.205 - 0.256: 3 Chirality restraints: 4017 Sorted by residual: chirality pdb=" CA ILE B 323 " pdb=" N ILE B 323 " pdb=" C ILE B 323 " pdb=" CB ILE B 323 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL A 606 " pdb=" CA VAL A 606 " pdb=" CG1 VAL A 606 " pdb=" CG2 VAL A 606 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ASN B 325 " pdb=" N ASN B 325 " pdb=" C ASN B 325 " pdb=" CB ASN B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 4014 not shown) Planarity restraints: 4613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 469 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO C 470 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 322 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C ASN B 322 " -0.067 2.00e-02 2.50e+03 pdb=" O ASN B 322 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE B 323 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 775 " -0.036 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO C 776 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 776 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 776 " -0.031 5.00e-02 4.00e+02 ... (remaining 4610 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 915 2.71 - 3.26: 26667 3.26 - 3.80: 41092 3.80 - 4.35: 50903 4.35 - 4.90: 84741 Nonbonded interactions: 204318 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 265 " model vdw 2.161 2.440 nonbonded pdb=" O ASP C 411 " pdb=" NH2 ARG C 448 " model vdw 2.187 2.520 nonbonded pdb=" OG SER A 340 " pdb=" O LEU A 443 " model vdw 2.193 2.440 nonbonded pdb=" OG1 THR C 86 " pdb=" O LYS C 178 " model vdw 2.193 2.440 nonbonded pdb=" O LEU B 950 " pdb=" OG SER B 959 " model vdw 2.207 2.440 ... (remaining 204313 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 345 or (resid 346 and (name N or name CA or nam \ e C or name O or name CB )) or resid 347 through 612 or resid 626 or resid 631 t \ hrough 1131)) selection = (chain 'B' and (resid 14 through 518 or (resid 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 through 613 or resid 631 through 1131)) \ selection = (chain 'C' and (resid 14 through 185 or (resid 186 and (name N or name CA or nam \ e C or name O or name CB )) or resid 187 through 345 or (resid 346 and (name N o \ r name CA or name C or name O or name CB )) or resid 347 through 518 or (resid 5 \ 19 and (name N or name CA or name C or name O or name CB )) or resid 520 through \ 613 or resid 631 through 812 or resid 833 through 1131)) } 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: 1.490 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: 8.440 Check model and map are aligned: 0.370 Set scattering table: 0.260 Process input model: 70.720 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.140 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.002 0.038 26064 Z= 0.155 Angle : 0.543 9.381 35492 Z= 0.291 Chirality : 0.042 0.256 4017 Planarity : 0.004 0.108 4613 Dihedral : 13.845 89.882 9304 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 3245 helix: 1.43 (0.21), residues: 686 sheet: -0.96 (0.22), residues: 584 loop : -1.71 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 143 HIS 0.003 0.001 HIS A 236 PHE 0.017 0.001 PHE B 126 TYR 0.015 0.001 TYR A 161 ARG 0.004 0.000 ARG B 889 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 2.953 Fit side-chains revert: symmetry clash REVERT: C 758 GLN cc_start: 0.7875 (tp-100) cc_final: 0.7225 (mm-40) REVERT: B 108 LEU cc_start: 0.8253 (tp) cc_final: 0.7959 (tp) REVERT: B 144 MET cc_start: 0.5897 (ppp) cc_final: 0.5683 (ppp) REVERT: A 758 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7343 (mm-40) outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 0.3402 time to fit residues: 64.3285 Evaluate side-chains 74 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 131 optimal weight: 30.0000 chunk 254 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 154 optimal weight: 30.0000 chunk 189 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26064 Z= 0.184 Angle : 0.535 7.986 35492 Z= 0.280 Chirality : 0.042 0.187 4017 Planarity : 0.004 0.069 4613 Dihedral : 4.336 51.084 3510 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.20 % Favored : 91.74 % Rotamer: Outliers : 0.21 % Allowed : 6.20 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3245 helix: 1.68 (0.21), residues: 678 sheet: -0.96 (0.21), residues: 631 loop : -1.64 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 249 HIS 0.003 0.001 HIS C 66 PHE 0.016 0.001 PHE B 148 TYR 0.019 0.001 TYR C 260 ARG 0.002 0.000 ARG B 889 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 3.081 Fit side-chains REVERT: C 758 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7397 (mm-40) REVERT: B 108 LEU cc_start: 0.8552 (tp) cc_final: 0.8311 (tp) REVERT: B 378 LEU cc_start: 0.8999 (mt) cc_final: 0.8788 (mt) REVERT: A 758 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7627 (mm-40) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.3623 time to fit residues: 53.2183 Evaluate side-chains 73 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 319 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 237 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 GLN ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26064 Z= 0.267 Angle : 0.556 8.117 35492 Z= 0.291 Chirality : 0.042 0.192 4017 Planarity : 0.004 0.055 4613 Dihedral : 4.512 54.775 3510 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.24 % Favored : 90.69 % Rotamer: Outliers : 0.56 % Allowed : 10.57 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3245 helix: 1.50 (0.21), residues: 682 sheet: -1.02 (0.21), residues: 617 loop : -1.71 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 143 HIS 0.004 0.001 HIS C 646 PHE 0.023 0.001 PHE B 368 TYR 0.023 0.001 TYR B1094 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 2.624 Fit side-chains REVERT: B 108 LEU cc_start: 0.8656 (tp) cc_final: 0.8429 (tp) REVERT: B 168 MET cc_start: 0.2435 (mmp) cc_final: 0.2211 (mmp) REVERT: B 378 LEU cc_start: 0.8930 (mt) cc_final: 0.8641 (mt) REVERT: B 857 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: B 1094 TYR cc_start: 0.8309 (t80) cc_final: 0.8105 (t80) REVERT: A 136 TYR cc_start: 0.5164 (m-80) cc_final: 0.4894 (m-80) outliers start: 16 outliers final: 10 residues processed: 89 average time/residue: 0.3311 time to fit residues: 51.4664 Evaluate side-chains 79 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 757 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 292 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 153 optimal weight: 0.0570 chunk 32 optimal weight: 9.9990 chunk 141 optimal weight: 30.0000 chunk 198 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 314 optimal weight: 0.9990 chunk 155 optimal weight: 0.0870 chunk 281 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26064 Z= 0.141 Angle : 0.496 8.216 35492 Z= 0.259 Chirality : 0.041 0.151 4017 Planarity : 0.004 0.054 4613 Dihedral : 4.320 57.074 3510 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.70 % Favored : 92.23 % Rotamer: Outliers : 0.85 % Allowed : 11.84 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3245 helix: 1.67 (0.21), residues: 691 sheet: -0.90 (0.21), residues: 613 loop : -1.63 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 249 HIS 0.003 0.001 HIS B1048 PHE 0.011 0.001 PHE A 126 TYR 0.016 0.001 TYR C 256 ARG 0.005 0.000 ARG C 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 3.040 Fit side-chains REVERT: C 758 GLN cc_start: 0.7875 (tp-100) cc_final: 0.7527 (mm-40) REVERT: B 108 LEU cc_start: 0.8589 (tp) cc_final: 0.8289 (tp) REVERT: B 168 MET cc_start: 0.2309 (mmp) cc_final: 0.2074 (mmp) REVERT: B 378 LEU cc_start: 0.8996 (mt) cc_final: 0.8715 (mt) REVERT: A 136 TYR cc_start: 0.5152 (m-80) cc_final: 0.4881 (m-80) REVERT: A 624 TRP cc_start: 0.6196 (p90) cc_final: 0.5884 (p-90) outliers start: 24 outliers final: 10 residues processed: 97 average time/residue: 0.3289 time to fit residues: 56.7955 Evaluate side-chains 79 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 757 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 261 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 233 optimal weight: 0.3980 chunk 129 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 160 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26064 Z= 0.175 Angle : 0.502 8.138 35492 Z= 0.260 Chirality : 0.041 0.211 4017 Planarity : 0.004 0.054 4613 Dihedral : 4.279 58.525 3510 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.04 % Favored : 91.90 % Rotamer: Outliers : 0.85 % Allowed : 13.60 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3245 helix: 1.75 (0.21), residues: 685 sheet: -0.89 (0.21), residues: 623 loop : -1.61 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 249 HIS 0.002 0.000 HIS C1067 PHE 0.025 0.001 PHE C 420 TYR 0.021 0.001 TYR B1094 ARG 0.002 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 3.071 Fit side-chains REVERT: C 758 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7713 (mm-40) REVERT: C 981 ILE cc_start: 0.9279 (pt) cc_final: 0.8836 (mt) REVERT: B 168 MET cc_start: 0.2347 (mmp) cc_final: 0.2102 (mmp) REVERT: B 378 LEU cc_start: 0.8982 (mt) cc_final: 0.8716 (mt) REVERT: A 136 TYR cc_start: 0.5173 (m-80) cc_final: 0.4892 (m-80) REVERT: A 884 MET cc_start: 0.7513 (mtp) cc_final: 0.7307 (mtt) outliers start: 24 outliers final: 19 residues processed: 95 average time/residue: 0.3196 time to fit residues: 54.7621 Evaluate side-chains 89 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 757 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 314 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26064 Z= 0.185 Angle : 0.504 9.949 35492 Z= 0.261 Chirality : 0.041 0.239 4017 Planarity : 0.004 0.053 4613 Dihedral : 4.270 58.793 3510 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.14 % Favored : 91.80 % Rotamer: Outliers : 1.06 % Allowed : 14.52 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3245 helix: 1.71 (0.21), residues: 691 sheet: -0.85 (0.21), residues: 609 loop : -1.59 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 249 HIS 0.002 0.000 HIS C1067 PHE 0.016 0.001 PHE C 583 TYR 0.016 0.001 TYR C1051 ARG 0.002 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 70 time to evaluate : 3.013 Fit side-chains REVERT: C 758 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7762 (mm-40) REVERT: C 1013 MET cc_start: 0.8486 (tpp) cc_final: 0.7938 (ttm) REVERT: B 168 MET cc_start: 0.2320 (mmp) cc_final: 0.2073 (mmp) REVERT: B 378 LEU cc_start: 0.8977 (mt) cc_final: 0.8715 (mt) REVERT: A 136 TYR cc_start: 0.5197 (m-80) cc_final: 0.4896 (m-80) REVERT: A 624 TRP cc_start: 0.6247 (p90) cc_final: 0.5956 (p-90) outliers start: 30 outliers final: 22 residues processed: 98 average time/residue: 0.3137 time to fit residues: 54.9593 Evaluate side-chains 91 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 757 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 229 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 chunk 313 optimal weight: 7.9990 chunk 196 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN C 944 ASN ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A1090 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26064 Z= 0.316 Angle : 0.577 8.355 35492 Z= 0.300 Chirality : 0.042 0.247 4017 Planarity : 0.004 0.054 4613 Dihedral : 4.571 56.422 3510 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.74 % Favored : 90.20 % Rotamer: Outliers : 1.52 % Allowed : 15.15 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 3245 helix: 1.42 (0.20), residues: 689 sheet: -1.01 (0.21), residues: 643 loop : -1.74 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.005 0.001 HIS C 236 PHE 0.033 0.002 PHE C 420 TYR 0.020 0.001 TYR C1051 ARG 0.003 0.000 ARG B 889 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 69 time to evaluate : 3.066 Fit side-chains revert: symmetry clash REVERT: C 144 MET cc_start: 0.5022 (pmm) cc_final: 0.4314 (pmm) REVERT: C 1013 MET cc_start: 0.8561 (tpp) cc_final: 0.7935 (ttm) REVERT: B 378 LEU cc_start: 0.8938 (mt) cc_final: 0.8660 (mt) REVERT: A 507 GLU cc_start: 0.7034 (pm20) cc_final: 0.5757 (tp30) outliers start: 43 outliers final: 31 residues processed: 109 average time/residue: 0.3097 time to fit residues: 60.4336 Evaluate side-chains 97 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 66 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain A residue 1015 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 2.9990 chunk 125 optimal weight: 40.0000 chunk 187 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A1020 GLN A1090 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26064 Z= 0.176 Angle : 0.514 8.365 35492 Z= 0.266 Chirality : 0.041 0.176 4017 Planarity : 0.004 0.054 4613 Dihedral : 4.421 58.955 3510 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 1.13 % Allowed : 15.82 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3245 helix: 1.58 (0.21), residues: 694 sheet: -0.95 (0.21), residues: 617 loop : -1.69 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 624 HIS 0.003 0.001 HIS B1048 PHE 0.013 0.001 PHE C 583 TYR 0.016 0.001 TYR C1051 ARG 0.003 0.000 ARG B 889 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.5034 (pmm) cc_final: 0.4330 (pmm) REVERT: C 1013 MET cc_start: 0.8494 (tpp) cc_final: 0.7957 (ttm) REVERT: B 168 MET cc_start: 0.1253 (mmp) cc_final: 0.0950 (mmp) REVERT: B 378 LEU cc_start: 0.8933 (mt) cc_final: 0.8670 (mt) REVERT: B 888 TYR cc_start: 0.7457 (m-10) cc_final: 0.7225 (m-10) REVERT: A 136 TYR cc_start: 0.5142 (m-80) cc_final: 0.4891 (m-80) outliers start: 32 outliers final: 27 residues processed: 103 average time/residue: 0.3332 time to fit residues: 59.6818 Evaluate side-chains 98 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 71 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 1015 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 284 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 229 optimal weight: 30.0000 chunk 89 optimal weight: 0.3980 chunk 263 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26064 Z= 0.210 Angle : 0.523 8.269 35492 Z= 0.271 Chirality : 0.041 0.176 4017 Planarity : 0.004 0.054 4613 Dihedral : 4.421 58.632 3510 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.57 % Favored : 91.37 % Rotamer: Outliers : 1.27 % Allowed : 15.93 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 3245 helix: 1.55 (0.21), residues: 695 sheet: -0.97 (0.21), residues: 648 loop : -1.69 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP A 624 HIS 0.003 0.001 HIS C 646 PHE 0.034 0.001 PHE C 420 TYR 0.017 0.001 TYR C1051 ARG 0.003 0.000 ARG B 889 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 70 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.4995 (pmm) cc_final: 0.4274 (pmm) REVERT: C 1013 MET cc_start: 0.8511 (tpp) cc_final: 0.7991 (ttm) REVERT: B 168 MET cc_start: 0.1243 (mmp) cc_final: 0.0956 (mmp) REVERT: B 378 LEU cc_start: 0.8934 (mt) cc_final: 0.8671 (mt) REVERT: B 888 TYR cc_start: 0.7534 (m-10) cc_final: 0.7242 (m-10) REVERT: A 136 TYR cc_start: 0.5148 (m-80) cc_final: 0.4916 (m-80) REVERT: A 624 TRP cc_start: 0.5036 (p-90) cc_final: 0.4774 (p90) outliers start: 36 outliers final: 32 residues processed: 105 average time/residue: 0.3531 time to fit residues: 64.4981 Evaluate side-chains 101 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 1015 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 7.9990 chunk 308 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 214 optimal weight: 0.9990 chunk 323 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C1072 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN B 939 ASN A 128 ASN A 739 GLN A1090 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 26064 Z= 0.415 Angle : 0.653 8.650 35492 Z= 0.341 Chirality : 0.044 0.189 4017 Planarity : 0.004 0.055 4613 Dihedral : 4.929 51.702 3510 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.28 % Favored : 88.66 % Rotamer: Outliers : 1.34 % Allowed : 16.03 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3245 helix: 0.96 (0.20), residues: 703 sheet: -1.03 (0.20), residues: 654 loop : -1.98 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 624 HIS 0.006 0.001 HIS C 646 PHE 0.020 0.002 PHE B 126 TYR 0.022 0.002 TYR A 195 ARG 0.004 0.001 ARG A 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 69 time to evaluate : 2.794 Fit side-chains revert: symmetry clash REVERT: C 1013 MET cc_start: 0.8569 (tpp) cc_final: 0.7905 (ttm) REVERT: B 168 MET cc_start: 0.1481 (mmp) cc_final: 0.1147 (mmp) REVERT: B 378 LEU cc_start: 0.8909 (mt) cc_final: 0.8599 (mt) REVERT: B 888 TYR cc_start: 0.7485 (m-10) cc_final: 0.7161 (m-80) outliers start: 38 outliers final: 34 residues processed: 106 average time/residue: 0.3117 time to fit residues: 57.9578 Evaluate side-chains 99 residues out of total 2842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 65 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 1015 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 265 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 47 optimal weight: 10.0000 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN C1072 HIS ** B 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN B 939 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.072944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053271 restraints weight = 120778.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054164 restraints weight = 72684.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054871 restraints weight = 44287.329| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 26064 Z= 0.183 Angle : 0.539 10.159 35492 Z= 0.279 Chirality : 0.042 0.207 4017 Planarity : 0.004 0.055 4613 Dihedral : 4.620 56.078 3510 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.98 % Favored : 91.96 % Rotamer: Outliers : 1.23 % Allowed : 16.28 % Favored : 82.49 % 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: -1.35 (0.15), residues: 3245 helix: 1.36 (0.20), residues: 703 sheet: -1.05 (0.20), residues: 650 loop : -1.80 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 624 HIS 0.004 0.001 HIS B1048 PHE 0.021 0.001 PHE A 333 TYR 0.016 0.001 TYR C1051 ARG 0.004 0.000 ARG A 625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.03 seconds wall clock time: 63 minutes 28.98 seconds (3808.98 seconds total)