Starting phenix.real_space_refine on Mon Mar 25 14:16:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxe_32177/03_2024/7vxe_32177.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxe_32177/03_2024/7vxe_32177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxe_32177/03_2024/7vxe_32177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxe_32177/03_2024/7vxe_32177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxe_32177/03_2024/7vxe_32177.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxe_32177/03_2024/7vxe_32177.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 114 5.16 5 C 15900 2.51 5 N 4182 2.21 5 O 4734 1.98 5 H 24366 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49296 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 16432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 16432 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 16432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 16432 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 16432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 16432 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 21.91, per 1000 atoms: 0.44 Number of scatterers: 49296 At special positions: 0 Unit cell: (161.764, 148.648, 196.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 O 4734 8.00 N 4182 7.00 C 15900 6.00 H 24366 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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: 38.30 Conformation dependent library (CDL) restraints added in 5.2 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 46 sheets defined 23.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.491A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.507A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.533A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.697A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.609A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.513A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.727A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.980A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.705A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.575A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.007A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.600A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.950A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.840A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.179A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.869A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.624A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.917A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.776A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.714A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.191A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.686A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.517A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.848A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.649A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.100A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.968A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.570A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.656A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.512A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.236A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.679A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.597A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.542A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.555A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.990A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.003A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.558A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.538A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.968A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.222A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.347A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.442A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.150A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.110A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.510A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.947A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.798A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.080A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.638A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.523A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.187A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.501A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.292A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.606A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.096A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.324A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.118A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.531A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.136A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.531A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.658A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.522A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.719A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.113A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.860A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 807 through 808 removed outlier: 4.577A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 963 hydrogen bonds defined for protein. 2682 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: 21.69 Time building geometry restraints manager: 39.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 24360 1.04 - 1.23: 818 1.23 - 1.43: 10086 1.43 - 1.63: 14464 1.63 - 1.83: 144 Bond restraints: 49872 Sorted by residual: bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.23e+01 bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.482 -0.148 2.34e-02 1.83e+03 3.99e+01 bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.475 -0.142 2.34e-02 1.83e+03 3.66e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.34e-02 1.83e+03 2.96e+01 bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.34e-02 1.83e+03 2.86e+01 ... (remaining 49867 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.04: 828 107.04 - 113.78: 58415 113.78 - 120.51: 16680 120.51 - 127.25: 13662 127.25 - 133.99: 235 Bond angle restraints: 89820 Sorted by residual: angle pdb=" C ASP A 215 " pdb=" CA ASP A 215 " pdb=" CB ASP A 215 " ideal model delta sigma weight residual 116.63 111.47 5.16 1.16e+00 7.43e-01 1.98e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 116.63 111.56 5.07 1.16e+00 7.43e-01 1.91e+01 angle pdb=" C ASP B 215 " pdb=" CA ASP B 215 " pdb=" CB ASP B 215 " ideal model delta sigma weight residual 116.34 111.51 4.83 1.40e+00 5.10e-01 1.19e+01 angle pdb=" N ASP C 142 " pdb=" CA ASP C 142 " pdb=" C ASP C 142 " ideal model delta sigma weight residual 110.46 115.40 -4.94 1.48e+00 4.57e-01 1.11e+01 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 111.48 108.36 3.12 9.40e-01 1.13e+00 1.10e+01 ... (remaining 89815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 22505 17.98 - 35.97: 490 35.97 - 53.95: 376 53.95 - 71.94: 466 71.94 - 89.92: 112 Dihedral angle restraints: 23949 sinusoidal: 12807 harmonic: 11142 Sorted by residual: dihedral pdb=" SG CYS A 738 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " pdb=" CA CYS A 760 " ideal model delta sinusoidal sigma weight residual 79.00 4.72 74.28 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" CA LYS C 795 " pdb=" C LYS C 795 " pdb=" N ASP C 796 " pdb=" CA ASP C 796 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ALA C 352 " pdb=" C ALA C 352 " pdb=" N TRP C 353 " pdb=" CA TRP C 353 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 23946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2535 0.030 - 0.061: 916 0.061 - 0.091: 165 0.091 - 0.121: 255 0.121 - 0.151: 50 Chirality restraints: 3921 Sorted by residual: chirality pdb=" CA ILE B 68 " pdb=" N ILE B 68 " pdb=" C ILE B 68 " pdb=" CB ILE B 68 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3918 not shown) Planarity restraints: 7518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 913 " -0.108 2.00e-02 2.50e+03 1.20e-01 2.17e+02 pdb=" CD GLN A 913 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN A 913 " 0.108 2.00e-02 2.50e+03 pdb=" NE2 GLN A 913 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 913 " 0.179 2.00e-02 2.50e+03 pdb="HE22 GLN A 913 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 239 " -0.100 2.00e-02 2.50e+03 1.11e-01 1.84e+02 pdb=" CD GLN A 239 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN A 239 " 0.099 2.00e-02 2.50e+03 pdb=" NE2 GLN A 239 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 239 " 0.164 2.00e-02 2.50e+03 pdb="HE22 GLN A 239 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 913 " 0.094 2.00e-02 2.50e+03 1.04e-01 1.61e+02 pdb=" CD GLN C 913 " -0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN C 913 " -0.093 2.00e-02 2.50e+03 pdb=" NE2 GLN C 913 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 913 " -0.154 2.00e-02 2.50e+03 pdb="HE22 GLN C 913 " 0.152 2.00e-02 2.50e+03 ... (remaining 7515 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2321 2.20 - 2.80: 101297 2.80 - 3.40: 127694 3.40 - 4.00: 173648 4.00 - 4.60: 264860 Nonbonded interactions: 669820 Sorted by model distance: nonbonded pdb=" O GLN A 563 " pdb="HH11 ARG A 577 " model vdw 1.598 1.850 nonbonded pdb=" O SER C 438 " pdb=" H LEU C 441 " model vdw 1.631 1.850 nonbonded pdb=" O ASP B 389 " pdb=" HZ1 LYS B 528 " model vdw 1.634 1.850 nonbonded pdb="HH22 ARG C 34 " pdb=" O PRO C 217 " model vdw 1.634 1.850 nonbonded pdb=" H MET C 731 " pdb=" OE1 GLN C 774 " model vdw 1.639 1.850 ... (remaining 669815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.840 Extract box with map and model: 10.500 Check model and map are aligned: 0.850 Set scattering table: 0.500 Process input model: 152.930 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 173.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5215 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.169 25506 Z= 0.192 Angle : 0.452 5.259 34695 Z= 0.268 Chirality : 0.042 0.151 3921 Planarity : 0.002 0.035 4506 Dihedral : 7.362 80.781 9135 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.79 (0.12), residues: 3150 helix: -1.55 (0.17), residues: 655 sheet: -0.77 (0.15), residues: 770 loop : -1.18 (0.12), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.002 0.000 HIS C 66 PHE 0.014 0.001 PHE C 490 TYR 0.012 0.001 TYR A 453 ARG 0.003 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 613 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.6664 (t80) cc_final: 0.6415 (t80) REVERT: A 933 LYS cc_start: 0.7576 (mttt) cc_final: 0.7374 (ttmm) REVERT: B 91 TYR cc_start: 0.6677 (t80) cc_final: 0.5491 (t80) REVERT: B 228 ASP cc_start: 0.6449 (t0) cc_final: 0.5205 (t0) REVERT: B 936 ASP cc_start: 0.7311 (m-30) cc_final: 0.6956 (m-30) REVERT: B 1052 PHE cc_start: 0.6842 (m-10) cc_final: 0.6592 (m-80) REVERT: C 735 SER cc_start: 0.7851 (t) cc_final: 0.7633 (t) REVERT: C 1054 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6885 (mm-40) REVERT: C 1122 VAL cc_start: 0.7528 (t) cc_final: 0.7224 (t) outliers start: 0 outliers final: 0 residues processed: 613 average time/residue: 0.9548 time to fit residues: 869.8054 Evaluate side-chains 473 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 0.0570 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 519 HIS A 901 GLN A 949 GLN A 969 ASN A1119 ASN A1135 ASN B 14 GLN B 188 ASN B 606 ASN B 907 ASN B 965 GLN B1113 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 954 GLN C1071 GLN C1074 ASN C1119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 25506 Z= 0.313 Angle : 0.571 6.107 34695 Z= 0.312 Chirality : 0.046 0.204 3921 Planarity : 0.004 0.050 4506 Dihedral : 4.068 18.986 3417 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % Rotamer: Outliers : 1.04 % Allowed : 4.67 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 3150 helix: 0.67 (0.19), residues: 668 sheet: -0.40 (0.16), residues: 739 loop : -0.86 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 104 HIS 0.010 0.002 HIS A1064 PHE 0.024 0.002 PHE B 906 TYR 0.025 0.002 TYR B 265 ARG 0.012 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 481 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.6063 (t0) cc_final: 0.5798 (t70) REVERT: A 304 LYS cc_start: 0.7268 (tptm) cc_final: 0.6998 (mtpp) REVERT: B 228 ASP cc_start: 0.6757 (t0) cc_final: 0.6408 (t0) REVERT: B 1028 LYS cc_start: 0.7905 (mttt) cc_final: 0.6568 (ttmt) REVERT: C 1107 ARG cc_start: 0.7149 (ttm110) cc_final: 0.6498 (tpt-90) outliers start: 29 outliers final: 12 residues processed: 496 average time/residue: 0.9757 time to fit residues: 719.3237 Evaluate side-chains 442 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 430 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 918 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 289 optimal weight: 0.1980 chunk 312 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 ASN A1119 ASN B 762 GLN B 901 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 314 GLN C 564 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25506 Z= 0.266 Angle : 0.495 7.023 34695 Z= 0.266 Chirality : 0.044 0.185 3921 Planarity : 0.004 0.070 4506 Dihedral : 3.915 17.161 3417 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 1.04 % Allowed : 6.00 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3150 helix: 1.23 (0.20), residues: 667 sheet: -0.27 (0.16), residues: 763 loop : -0.73 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.007 0.001 HIS A1064 PHE 0.025 0.002 PHE B 797 TYR 0.017 0.002 TYR B 265 ARG 0.006 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 453 time to evaluate : 4.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.7304 (tptm) cc_final: 0.7033 (mtpp) REVERT: A 936 ASP cc_start: 0.6449 (m-30) cc_final: 0.6219 (m-30) REVERT: A 1028 LYS cc_start: 0.8105 (mttt) cc_final: 0.7586 (ttmt) REVERT: B 228 ASP cc_start: 0.6803 (t0) cc_final: 0.6202 (t0) REVERT: B 781 VAL cc_start: 0.7882 (t) cc_final: 0.6712 (m) outliers start: 29 outliers final: 24 residues processed: 459 average time/residue: 1.0300 time to fit residues: 703.0912 Evaluate side-chains 447 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 423 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 0.0570 chunk 275 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A1119 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 616 ASN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25506 Z= 0.292 Angle : 0.510 6.778 34695 Z= 0.273 Chirality : 0.044 0.208 3921 Planarity : 0.004 0.051 4506 Dihedral : 4.056 17.928 3417 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.14 % Rotamer: Outliers : 1.08 % Allowed : 6.50 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3150 helix: 1.34 (0.19), residues: 680 sheet: -0.14 (0.17), residues: 746 loop : -0.75 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.011 0.002 HIS C 207 PHE 0.025 0.002 PHE A 906 TYR 0.024 0.002 TYR A1138 ARG 0.006 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 446 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.7335 (tptm) cc_final: 0.7124 (mtpp) REVERT: A 737 ASP cc_start: 0.7013 (t0) cc_final: 0.6707 (m-30) REVERT: A 778 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8433 (t) REVERT: A 1028 LYS cc_start: 0.8253 (mttt) cc_final: 0.7030 (mtpp) REVERT: B 1041 ASP cc_start: 0.6928 (t0) cc_final: 0.6724 (t0) REVERT: C 615 VAL cc_start: 0.7365 (p) cc_final: 0.7099 (m) REVERT: C 883 THR cc_start: 0.8459 (m) cc_final: 0.8066 (t) REVERT: C 1125 ASN cc_start: 0.6972 (p0) cc_final: 0.6645 (p0) outliers start: 30 outliers final: 23 residues processed: 454 average time/residue: 1.0165 time to fit residues: 684.9451 Evaluate side-chains 444 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 420 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 30.0000 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 212 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 156 optimal weight: 0.1980 chunk 275 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25506 Z= 0.267 Angle : 0.483 6.724 34695 Z= 0.258 Chirality : 0.043 0.178 3921 Planarity : 0.004 0.063 4506 Dihedral : 4.006 17.734 3417 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.79 % Rotamer: Outliers : 1.19 % Allowed : 7.22 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3150 helix: 1.53 (0.20), residues: 680 sheet: -0.15 (0.17), residues: 754 loop : -0.72 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.006 0.001 HIS C1058 PHE 0.022 0.002 PHE B 194 TYR 0.026 0.001 TYR C1138 ARG 0.012 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 430 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 VAL cc_start: 0.8121 (t) cc_final: 0.7849 (p) REVERT: A 737 ASP cc_start: 0.6955 (t0) cc_final: 0.6677 (m-30) REVERT: A 1028 LYS cc_start: 0.8397 (mttt) cc_final: 0.7605 (mtpp) REVERT: A 1125 ASN cc_start: 0.7697 (p0) cc_final: 0.7421 (p0) REVERT: B 1041 ASP cc_start: 0.6759 (t0) cc_final: 0.6554 (t0) REVERT: C 615 VAL cc_start: 0.7429 (p) cc_final: 0.7179 (m) REVERT: C 883 THR cc_start: 0.8505 (m) cc_final: 0.8122 (t) outliers start: 33 outliers final: 30 residues processed: 439 average time/residue: 1.0223 time to fit residues: 657.8977 Evaluate side-chains 441 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 411 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 307 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 616 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25506 Z= 0.207 Angle : 0.464 6.568 34695 Z= 0.245 Chirality : 0.042 0.178 3921 Planarity : 0.003 0.056 4506 Dihedral : 3.933 17.393 3417 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 1.11 % Allowed : 7.76 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3150 helix: 1.74 (0.20), residues: 680 sheet: -0.10 (0.17), residues: 768 loop : -0.67 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.004 0.001 HIS C1064 PHE 0.017 0.001 PHE B 194 TYR 0.021 0.001 TYR A1138 ARG 0.011 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 424 time to evaluate : 4.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 VAL cc_start: 0.8178 (t) cc_final: 0.7912 (p) REVERT: A 737 ASP cc_start: 0.6883 (t0) cc_final: 0.6649 (m-30) REVERT: A 1028 LYS cc_start: 0.8302 (mttt) cc_final: 0.7544 (mttm) REVERT: B 302 THR cc_start: 0.7842 (m) cc_final: 0.7489 (t) REVERT: B 1107 ARG cc_start: 0.6276 (mtt180) cc_final: 0.6024 (tpt170) REVERT: C 615 VAL cc_start: 0.7425 (p) cc_final: 0.7186 (m) REVERT: C 883 THR cc_start: 0.8520 (m) cc_final: 0.8110 (t) outliers start: 31 outliers final: 23 residues processed: 432 average time/residue: 1.0099 time to fit residues: 641.2398 Evaluate side-chains 434 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 411 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 710 ASN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 25506 Z= 0.432 Angle : 0.556 6.132 34695 Z= 0.301 Chirality : 0.045 0.176 3921 Planarity : 0.005 0.121 4506 Dihedral : 4.334 19.186 3417 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.75 % Rotamer: Outliers : 1.44 % Allowed : 8.15 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3150 helix: 1.32 (0.19), residues: 688 sheet: -0.22 (0.17), residues: 757 loop : -0.87 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.009 0.002 HIS A1058 PHE 0.031 0.002 PHE A 906 TYR 0.024 0.002 TYR B 756 ARG 0.008 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 419 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.6119 (t0) cc_final: 0.5903 (t70) REVERT: A 642 VAL cc_start: 0.8179 (t) cc_final: 0.7975 (p) REVERT: A 1028 LYS cc_start: 0.8352 (mttt) cc_final: 0.7630 (mttm) REVERT: A 1084 ASP cc_start: 0.5835 (p0) cc_final: 0.5565 (p0) REVERT: B 192 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5736 (m-80) REVERT: B 302 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7625 (t) REVERT: C 92 PHE cc_start: 0.6655 (t80) cc_final: 0.6213 (t80) REVERT: C 326 ILE cc_start: 0.7299 (mm) cc_final: 0.6964 (tt) REVERT: C 615 VAL cc_start: 0.7628 (p) cc_final: 0.7426 (m) REVERT: C 710 ASN cc_start: 0.6737 (m-40) cc_final: 0.6514 (m110) REVERT: C 883 THR cc_start: 0.8565 (m) cc_final: 0.8141 (t) outliers start: 40 outliers final: 29 residues processed: 431 average time/residue: 0.9907 time to fit residues: 627.9741 Evaluate side-chains 442 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 411 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A1119 ASN B 762 GLN B1010 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25506 Z= 0.214 Angle : 0.477 5.311 34695 Z= 0.254 Chirality : 0.043 0.176 3921 Planarity : 0.004 0.103 4506 Dihedral : 4.090 19.366 3417 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.35 % Rotamer: Outliers : 1.11 % Allowed : 8.91 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3150 helix: 1.68 (0.20), residues: 688 sheet: -0.12 (0.17), residues: 760 loop : -0.78 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.004 0.001 HIS C1064 PHE 0.016 0.001 PHE B 800 TYR 0.020 0.001 TYR A1138 ARG 0.010 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 414 time to evaluate : 4.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ASP cc_start: 0.6013 (t0) cc_final: 0.5772 (t70) REVERT: A 642 VAL cc_start: 0.8172 (t) cc_final: 0.7963 (p) REVERT: A 690 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6956 (mm110) REVERT: A 1084 ASP cc_start: 0.5764 (p0) cc_final: 0.5561 (p0) REVERT: A 1086 LYS cc_start: 0.7956 (ptpp) cc_final: 0.7745 (ptpp) REVERT: B 302 THR cc_start: 0.7904 (m) cc_final: 0.7538 (t) REVERT: C 92 PHE cc_start: 0.6646 (t80) cc_final: 0.6183 (t80) REVERT: C 754 LEU cc_start: 0.8158 (mm) cc_final: 0.7913 (mt) REVERT: C 883 THR cc_start: 0.8563 (m) cc_final: 0.8125 (t) outliers start: 31 outliers final: 27 residues processed: 421 average time/residue: 1.0464 time to fit residues: 647.7577 Evaluate side-chains 440 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 413 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.8980 chunk 293 optimal weight: 0.0770 chunk 267 optimal weight: 1.9990 chunk 285 optimal weight: 0.0770 chunk 171 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 258 optimal weight: 20.0000 chunk 270 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 25506 Z= 0.162 Angle : 0.457 5.195 34695 Z= 0.240 Chirality : 0.042 0.175 3921 Planarity : 0.004 0.129 4506 Dihedral : 3.935 18.100 3417 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.08 % Allowed : 9.20 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3150 helix: 2.05 (0.20), residues: 680 sheet: -0.02 (0.17), residues: 748 loop : -0.72 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 64 HIS 0.002 0.001 HIS A1058 PHE 0.014 0.001 PHE C 92 TYR 0.021 0.001 TYR A1138 ARG 0.011 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 413 time to evaluate : 4.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 VAL cc_start: 0.8168 (t) cc_final: 0.7958 (p) REVERT: A 1028 LYS cc_start: 0.8384 (mttt) cc_final: 0.8180 (mttm) REVERT: A 1084 ASP cc_start: 0.5916 (p0) cc_final: 0.5683 (p0) REVERT: A 1086 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7721 (ptpp) REVERT: B 302 THR cc_start: 0.7859 (m) cc_final: 0.7503 (t) REVERT: B 1107 ARG cc_start: 0.7234 (tpt170) cc_final: 0.6957 (tpt170) REVERT: C 754 LEU cc_start: 0.8137 (mm) cc_final: 0.7878 (mt) REVERT: C 883 THR cc_start: 0.8565 (m) cc_final: 0.8110 (t) outliers start: 30 outliers final: 23 residues processed: 421 average time/residue: 1.0265 time to fit residues: 634.6547 Evaluate side-chains 426 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 403 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.0570 chunk 302 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 20.0000 chunk 26 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25506 Z= 0.208 Angle : 0.463 5.186 34695 Z= 0.244 Chirality : 0.042 0.172 3921 Planarity : 0.004 0.132 4506 Dihedral : 3.934 18.085 3417 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.94 % Rotamer: Outliers : 0.93 % Allowed : 9.41 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3150 helix: 2.06 (0.20), residues: 680 sheet: -0.03 (0.17), residues: 752 loop : -0.70 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.005 0.001 HIS C 207 PHE 0.018 0.001 PHE B 800 TYR 0.021 0.001 TYR A1138 ARG 0.012 0.000 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 409 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 VAL cc_start: 0.8191 (t) cc_final: 0.7972 (p) REVERT: A 1084 ASP cc_start: 0.5999 (p0) cc_final: 0.5769 (p0) REVERT: A 1086 LYS cc_start: 0.8056 (ptpp) cc_final: 0.7756 (ptpp) REVERT: B 302 THR cc_start: 0.7903 (m) cc_final: 0.7534 (t) REVERT: C 92 PHE cc_start: 0.6674 (t80) cc_final: 0.6178 (t80) REVERT: C 754 LEU cc_start: 0.8140 (mm) cc_final: 0.7892 (mt) REVERT: C 883 THR cc_start: 0.8564 (m) cc_final: 0.8104 (t) outliers start: 26 outliers final: 24 residues processed: 417 average time/residue: 1.0460 time to fit residues: 641.4031 Evaluate side-chains 428 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 404 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 1.9990 chunk 268 optimal weight: 0.4980 chunk 77 optimal weight: 0.3980 chunk 232 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN B 317 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.202123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151154 restraints weight = 101491.171| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.68 r_work: 0.3526 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 25506 Z= 0.380 Angle : 0.533 5.645 34695 Z= 0.286 Chirality : 0.044 0.174 3921 Planarity : 0.004 0.113 4506 Dihedral : 4.249 19.449 3417 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 1.15 % Allowed : 9.34 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3150 helix: 1.67 (0.20), residues: 681 sheet: -0.16 (0.17), residues: 756 loop : -0.88 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.008 0.001 HIS A1058 PHE 0.031 0.002 PHE B 800 TYR 0.023 0.002 TYR A 756 ARG 0.011 0.001 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13120.34 seconds wall clock time: 230 minutes 50.72 seconds (13850.72 seconds total)