Starting phenix.real_space_refine on Thu Mar 21 00:22:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/03_2024/7n9t_24262.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/03_2024/7n9t_24262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/03_2024/7n9t_24262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/03_2024/7n9t_24262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/03_2024/7n9t_24262.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/03_2024/7n9t_24262.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 18345 2.51 5 N 4848 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 28884 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8747 Classifications: {'peptide': 1123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1067} Chain: "B" Number of atoms: 8747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8747 Classifications: {'peptide': 1123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1067} Chain: "C" Number of atoms: 8747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8747 Classifications: {'peptide': 1123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1067} Chain: "D" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 881 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "E" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 881 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 881 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Residues with excluded nonbonded symmetry interactions: 357 residue: pdb=" N HIS D 1 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS D 1 " occ=0.00 residue: pdb=" N VAL D 2 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL D 2 " occ=0.00 residue: pdb=" N GLN D 3 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN D 3 " occ=0.00 residue: pdb=" N LEU D 4 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU D 4 " occ=0.00 residue: pdb=" N VAL D 5 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL D 5 " occ=0.00 residue: pdb=" N GLU D 6 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU D 6 " occ=0.00 residue: pdb=" N SER D 7 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER D 7 " occ=0.00 residue: pdb=" N GLY D 8 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 8 " occ=0.00 residue: pdb=" N GLY D 9 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 9 " occ=0.00 residue: pdb=" N GLY D 10 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 10 " occ=0.00 residue: pdb=" N LEU D 11 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU D 11 " occ=0.00 residue: pdb=" N VAL D 12 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL D 12 " occ=0.00 ... (remaining 345 not shown) Time building chain proxies: 15.02, per 1000 atoms: 0.52 Number of scatterers: 28884 At special positions: 0 Unit cell: (159.43, 158.36, 197.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5556 8.00 N 4848 7.00 C 18345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, 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 480 " - pdb=" SG CYS A 488 " 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 480 " - pdb=" SG CYS B 488 " 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 480 " - pdb=" SG CYS C 488 " 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: 12.06 Conformation dependent library (CDL) restraints added in 5.2 seconds 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6924 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 60 sheets defined 21.6% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.349A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.763A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.482A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.660A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.048A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 854 removed outlier: 3.827A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.554A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.941A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.608A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.959A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.879A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.350A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.764A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.483A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.661A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.048A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 849 through 854 removed outlier: 3.827A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.555A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.941A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.607A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.959A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.879A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.350A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.765A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.483A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.660A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.048A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 854 removed outlier: 3.827A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.554A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.941A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.606A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.958A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.880A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'F' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.218A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.491A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.815A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 229 removed outlier: 7.851A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.052A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 122 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 314 removed outlier: 3.636A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.682A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 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 539 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.589A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.672A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.191A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 719 removed outlier: 6.020A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 719 removed outlier: 6.020A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.219A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.492A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.814A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 225 through 229 removed outlier: 7.851A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 192 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.051A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 118 through 122 Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 314 removed outlier: 3.636A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.683A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 577 removed outlier: 3.588A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.671A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.019A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.019A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.218A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.492A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.815A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 225 through 229 removed outlier: 7.852A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 192 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 92 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.053A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 118 through 122 Processing sheet with id=AE8, first strand: chain 'C' and resid 312 through 314 removed outlier: 3.636A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.683A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AF4, first strand: chain 'C' and resid 575 through 577 removed outlier: 3.589A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.671A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 719 removed outlier: 6.019A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 712 through 719 removed outlier: 6.019A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG1, first strand: chain 'D' and resid 57 through 59 removed outlier: 7.203A pdb=" N ARG D 45 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ALA D 40 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 67 through 72 Processing sheet with id=AG3, first strand: chain 'E' and resid 57 through 59 removed outlier: 7.204A pdb=" N ARG E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ALA E 40 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 67 through 72 Processing sheet with id=AG5, first strand: chain 'F' and resid 57 through 59 removed outlier: 7.204A pdb=" N ARG F 45 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ALA F 40 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 67 through 72 872 hydrogen bonds defined for protein. 2364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.96 Time building geometry restraints manager: 12.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9423 1.35 - 1.46: 7255 1.46 - 1.58: 12710 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 29565 Sorted by residual: bond pdb=" CA PHE B 186 " pdb=" CB PHE B 186 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.62e-02 3.81e+03 4.95e+00 bond pdb=" CA PHE C 186 " pdb=" CB PHE C 186 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.62e-02 3.81e+03 4.91e+00 bond pdb=" CA PHE A 186 " pdb=" CB PHE A 186 " ideal model delta sigma weight residual 1.524 1.559 -0.036 1.62e-02 3.81e+03 4.82e+00 bond pdb=" CB MET B 153 " pdb=" CG MET B 153 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.92e+00 bond pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.85e+00 ... (remaining 29560 not shown) Histogram of bond angle deviations from ideal: 100.51 - 109.10: 2068 109.10 - 117.70: 19865 117.70 - 126.29: 17832 126.29 - 134.88: 456 134.88 - 143.48: 30 Bond angle restraints: 40251 Sorted by residual: angle pdb=" C HIS C 245 " pdb=" N ARG C 246 " pdb=" CA ARG C 246 " ideal model delta sigma weight residual 120.60 143.48 -22.88 1.60e+00 3.91e-01 2.04e+02 angle pdb=" C HIS B 245 " pdb=" N ARG B 246 " pdb=" CA ARG B 246 " ideal model delta sigma weight residual 120.60 143.47 -22.87 1.60e+00 3.91e-01 2.04e+02 angle pdb=" C HIS A 245 " pdb=" N ARG A 246 " pdb=" CA ARG A 246 " ideal model delta sigma weight residual 120.60 143.44 -22.84 1.60e+00 3.91e-01 2.04e+02 angle pdb=" C GLY B 842 " pdb=" N ASP B 843 " pdb=" CA ASP B 843 " ideal model delta sigma weight residual 122.74 142.67 -19.93 1.44e+00 4.82e-01 1.92e+02 angle pdb=" C GLY A 842 " pdb=" N ASP A 843 " pdb=" CA ASP A 843 " ideal model delta sigma weight residual 122.74 142.66 -19.92 1.44e+00 4.82e-01 1.91e+02 ... (remaining 40246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 16278 17.29 - 34.59: 967 34.59 - 51.88: 250 51.88 - 69.18: 52 69.18 - 86.47: 21 Dihedral angle restraints: 17568 sinusoidal: 6753 harmonic: 10815 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 135.01 -42.01 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 134.99 -41.99 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 134.98 -41.98 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 17565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 4427 0.343 - 0.685: 67 0.685 - 1.028: 12 1.028 - 1.371: 3 1.371 - 1.713: 9 Chirality restraints: 4518 Sorted by residual: chirality pdb=" CG LEU C 629 " pdb=" CB LEU C 629 " pdb=" CD1 LEU C 629 " pdb=" CD2 LEU C 629 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.34e+01 chirality pdb=" CG LEU B 629 " pdb=" CB LEU B 629 " pdb=" CD1 LEU B 629 " pdb=" CD2 LEU B 629 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 chirality pdb=" CG LEU A 629 " pdb=" CB LEU A 629 " pdb=" CD1 LEU A 629 " pdb=" CD2 LEU A 629 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 ... (remaining 4515 not shown) Planarity restraints: 5250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 792 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO B 793 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 793 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 793 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 792 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO A 793 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 792 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO C 793 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 793 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 793 " -0.034 5.00e-02 4.00e+02 ... (remaining 5247 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 308 2.61 - 3.18: 25313 3.18 - 3.75: 40237 3.75 - 4.33: 53804 4.33 - 4.90: 89377 Nonbonded interactions: 209039 Sorted by model distance: nonbonded pdb=" OG1 THR B 645 " pdb=" O GLY B 648 " model vdw 2.032 2.440 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.032 2.440 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.033 2.440 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.067 2.440 nonbonded pdb=" OD1 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.067 2.440 ... (remaining 209034 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=0.91 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: 2.470 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: 0.030 Extract box with map and model: 11.490 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 74.340 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.180 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 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 0.059 29565 Z= 0.191 Angle : 0.952 23.001 40251 Z= 0.544 Chirality : 0.116 1.713 4518 Planarity : 0.003 0.060 5250 Dihedral : 12.538 86.470 10545 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 2.91 % Allowed : 1.78 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3714 helix: 2.29 (0.21), residues: 672 sheet: 0.25 (0.20), residues: 708 loop : -0.65 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP F 36 HIS 0.002 0.000 HIS B1048 PHE 0.011 0.001 PHE B 927 TYR 0.005 0.000 TYR B 873 ARG 0.005 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 375 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6647 (mmt-90) cc_final: 0.5740 (mtt180) REVERT: A 805 ILE cc_start: 0.5616 (OUTLIER) cc_final: 0.5340 (tt) REVERT: A 844 MET cc_start: 0.2160 (mpp) cc_final: 0.1737 (mpp) REVERT: A 1104 VAL cc_start: 0.6541 (p) cc_final: 0.5629 (m) REVERT: B 55 PHE cc_start: 0.5124 (m-10) cc_final: 0.4600 (m-10) REVERT: B 92 PHE cc_start: 0.7839 (t80) cc_final: 0.6928 (m-80) REVERT: B 153 MET cc_start: -0.1803 (OUTLIER) cc_final: -0.2483 (ppp) REVERT: B 567 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6698 (mmt-90) REVERT: B 568 ASP cc_start: 0.6761 (t0) cc_final: 0.6418 (t0) REVERT: B 844 MET cc_start: 0.3263 (mpp) cc_final: 0.2807 (mpp) REVERT: B 974 SER cc_start: 0.8065 (t) cc_final: 0.7831 (p) REVERT: C 153 MET cc_start: -0.0302 (OUTLIER) cc_final: -0.0733 (mtm) REVERT: C 195 LYS cc_start: 0.7927 (pttt) cc_final: 0.7246 (ptmt) REVERT: C 560 LEU cc_start: 0.1726 (mm) cc_final: 0.1254 (mm) REVERT: C 835 MET cc_start: 0.0349 (mmp) cc_final: -0.0239 (ptp) REVERT: C 844 MET cc_start: 0.3047 (mpp) cc_final: 0.2608 (mpp) REVERT: C 931 ILE cc_start: 0.6939 (mm) cc_final: 0.6447 (mm) REVERT: C 1084 ASP cc_start: 0.6146 (OUTLIER) cc_final: 0.5567 (p0) REVERT: D 34 MET cc_start: -0.0604 (tmm) cc_final: -0.1140 (tmm) REVERT: E 34 MET cc_start: 0.0674 (tmm) cc_final: 0.0049 (tmm) REVERT: E 61 ASP cc_start: 0.1453 (m-30) cc_final: 0.1047 (p0) REVERT: F 118 SER cc_start: 0.1542 (t) cc_final: 0.1245 (p) outliers start: 93 outliers final: 19 residues processed: 434 average time/residue: 0.3959 time to fit residues: 273.7928 Evaluate side-chains 223 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.5980 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 149 optimal weight: 20.0000 chunk 289 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 335 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 606 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 913 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 196 ASN B 613 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 87 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 913 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29565 Z= 0.248 Angle : 0.580 8.576 40251 Z= 0.302 Chirality : 0.046 0.196 4518 Planarity : 0.004 0.047 5250 Dihedral : 4.238 56.921 4075 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.63 % Allowed : 6.29 % Favored : 92.08 % 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: 0.11 (0.14), residues: 3714 helix: 2.36 (0.20), residues: 660 sheet: 0.47 (0.20), residues: 705 loop : -0.76 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS B1083 PHE 0.027 0.002 PHE B 817 TYR 0.022 0.001 TYR A 904 ARG 0.015 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6638 (mmt-90) cc_final: 0.5804 (mtt180) REVERT: A 55 PHE cc_start: 0.7193 (m-10) cc_final: 0.6723 (m-10) REVERT: B 567 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6682 (mmt180) REVERT: B 568 ASP cc_start: 0.7049 (t0) cc_final: 0.6784 (t0) REVERT: B 614 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: B 759 PHE cc_start: 0.5021 (OUTLIER) cc_final: 0.4645 (t80) REVERT: B 844 MET cc_start: 0.3398 (mpp) cc_final: 0.3041 (mpp) REVERT: C 105 ILE cc_start: 0.5752 (mt) cc_final: 0.5484 (mm) REVERT: C 195 LYS cc_start: 0.7518 (pttt) cc_final: 0.7165 (ptmt) REVERT: C 808 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6366 (p0) REVERT: C 844 MET cc_start: 0.3262 (mpp) cc_final: 0.2688 (mpp) outliers start: 52 outliers final: 27 residues processed: 244 average time/residue: 0.3526 time to fit residues: 144.4593 Evaluate side-chains 192 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 278 optimal weight: 0.0570 chunk 228 optimal weight: 0.3980 chunk 92 optimal weight: 0.0000 chunk 335 optimal weight: 0.7980 chunk 362 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 269 optimal weight: 30.0000 overall best weight: 0.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 774 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A1142 GLN B 196 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 644 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN C1083 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29565 Z= 0.138 Angle : 0.483 9.838 40251 Z= 0.249 Chirality : 0.042 0.140 4518 Planarity : 0.003 0.045 5250 Dihedral : 3.656 57.558 4040 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.38 % Allowed : 7.73 % Favored : 90.89 % 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: 3714 helix: 2.25 (0.20), residues: 669 sheet: 0.50 (0.20), residues: 711 loop : -0.74 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 36 HIS 0.004 0.001 HIS B1083 PHE 0.019 0.001 PHE A1121 TYR 0.010 0.001 TYR B 789 ARG 0.002 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6642 (mmt-90) cc_final: 0.5995 (mtt180) REVERT: A 322 PRO cc_start: 0.5222 (Cg_endo) cc_final: 0.4966 (Cg_exo) REVERT: B 567 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6626 (mmt180) REVERT: B 844 MET cc_start: 0.3012 (mpp) cc_final: 0.2671 (mpp) REVERT: C 105 ILE cc_start: 0.5817 (mt) cc_final: 0.5512 (mm) REVERT: C 195 LYS cc_start: 0.7199 (pttt) cc_final: 0.6934 (ptmt) REVERT: C 844 MET cc_start: 0.3183 (mpp) cc_final: 0.2433 (mpp) outliers start: 44 outliers final: 19 residues processed: 217 average time/residue: 0.3428 time to fit residues: 126.1536 Evaluate side-chains 180 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 174 optimal weight: 0.0870 chunk 37 optimal weight: 4.9990 chunk 160 optimal weight: 0.0470 chunk 225 optimal weight: 0.8980 chunk 336 optimal weight: 0.3980 chunk 356 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 774 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29565 Z= 0.135 Angle : 0.474 10.723 40251 Z= 0.243 Chirality : 0.042 0.148 4518 Planarity : 0.003 0.049 5250 Dihedral : 3.556 58.446 4040 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.13 % Allowed : 8.95 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3714 helix: 2.28 (0.20), residues: 654 sheet: 0.53 (0.18), residues: 783 loop : -0.69 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 436 HIS 0.003 0.000 HIS A1083 PHE 0.020 0.001 PHE A1121 TYR 0.014 0.001 TYR B 741 ARG 0.003 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6705 (mmt-90) cc_final: 0.6052 (mtt180) REVERT: A 776 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8637 (ttmm) REVERT: A 1031 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: B 153 MET cc_start: -0.1073 (ppp) cc_final: -0.2609 (ptt) REVERT: B 567 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6277 (mmt180) REVERT: C 105 ILE cc_start: 0.6129 (mt) cc_final: 0.5861 (mm) REVERT: C 170 TYR cc_start: 0.4924 (t80) cc_final: 0.4349 (t80) REVERT: C 844 MET cc_start: 0.3029 (mpp) cc_final: 0.2204 (mpp) outliers start: 36 outliers final: 28 residues processed: 210 average time/residue: 0.3485 time to fit residues: 124.1325 Evaluate side-chains 191 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 313 TYR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 246 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 320 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 641 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A 965 GLN A1135 ASN B 87 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1135 ASN C 87 ASN C 641 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 29565 Z= 0.412 Angle : 0.661 10.335 40251 Z= 0.353 Chirality : 0.047 0.192 4518 Planarity : 0.005 0.057 5250 Dihedral : 4.613 58.082 4040 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.72 % Allowed : 10.55 % Favored : 87.73 % 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: -0.45 (0.13), residues: 3714 helix: 1.59 (0.20), residues: 633 sheet: 0.32 (0.18), residues: 720 loop : -1.08 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.005 0.001 HIS B 207 PHE 0.037 0.002 PHE B1089 TYR 0.031 0.002 TYR B 204 ARG 0.005 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 175 time to evaluate : 3.423 Fit side-chains REVERT: A 195 LYS cc_start: 0.7766 (pttt) cc_final: 0.7156 (pttp) REVERT: A 238 PHE cc_start: 0.3856 (OUTLIER) cc_final: 0.3114 (p90) REVERT: A 1031 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: B 153 MET cc_start: -0.1275 (ppp) cc_final: -0.2588 (ptt) REVERT: B 223 LEU cc_start: 0.5752 (mp) cc_final: 0.5454 (mp) REVERT: B 955 ASN cc_start: 0.8084 (m110) cc_final: 0.7861 (m-40) REVERT: C 105 ILE cc_start: 0.6898 (mt) cc_final: 0.6610 (mm) REVERT: C 195 LYS cc_start: 0.7782 (pttt) cc_final: 0.7446 (ptmt) REVERT: C 776 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8928 (ttmm) REVERT: C 817 PHE cc_start: 0.6879 (m-80) cc_final: 0.6667 (m-80) REVERT: C 844 MET cc_start: 0.2990 (mpp) cc_final: 0.2033 (mpp) REVERT: C 1019 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7675 (tpt170) outliers start: 55 outliers final: 28 residues processed: 216 average time/residue: 0.3472 time to fit residues: 127.6332 Evaluate side-chains 170 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 5.9990 chunk 321 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 209 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 357 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 804 GLN A1005 GLN B 52 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 965 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29565 Z= 0.168 Angle : 0.503 8.592 40251 Z= 0.262 Chirality : 0.043 0.169 4518 Planarity : 0.004 0.069 5250 Dihedral : 3.898 47.400 4034 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.41 % Allowed : 11.42 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3714 helix: 1.83 (0.20), residues: 639 sheet: 0.38 (0.18), residues: 729 loop : -1.00 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 64 HIS 0.002 0.000 HIS A1064 PHE 0.022 0.001 PHE A1121 TYR 0.017 0.001 TYR C 160 ARG 0.003 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 150 time to evaluate : 3.091 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.5169 (m-80) REVERT: A 238 PHE cc_start: 0.4101 (OUTLIER) cc_final: 0.3613 (p90) REVERT: A 1031 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: B 844 MET cc_start: 0.2669 (mpp) cc_final: 0.2114 (mpp) REVERT: B 856 ASN cc_start: 0.7699 (t0) cc_final: 0.7229 (t0) REVERT: C 105 ILE cc_start: 0.6781 (mt) cc_final: 0.6514 (mm) REVERT: C 195 LYS cc_start: 0.7566 (pttt) cc_final: 0.7300 (ptmt) REVERT: C 269 TYR cc_start: 0.6506 (m-80) cc_final: 0.6243 (m-80) REVERT: C 573 THR cc_start: 0.9000 (m) cc_final: 0.8774 (m) REVERT: C 740 MET cc_start: 0.7340 (tmm) cc_final: 0.6858 (tmm) REVERT: C 844 MET cc_start: 0.2839 (mpp) cc_final: 0.1652 (mpp) outliers start: 45 outliers final: 27 residues processed: 182 average time/residue: 0.3466 time to fit residues: 109.0941 Evaluate side-chains 161 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 202 optimal weight: 0.7980 chunk 300 optimal weight: 0.0000 chunk 199 optimal weight: 0.9990 chunk 355 optimal weight: 4.9990 chunk 222 optimal weight: 0.0170 chunk 216 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 overall best weight: 0.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 207 HIS B 641 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29565 Z= 0.149 Angle : 0.484 8.818 40251 Z= 0.249 Chirality : 0.042 0.137 4518 Planarity : 0.004 0.060 5250 Dihedral : 3.598 38.049 4032 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.53 % Allowed : 11.55 % Favored : 86.92 % 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: 3714 helix: 2.03 (0.20), residues: 639 sheet: 0.47 (0.18), residues: 744 loop : -0.92 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 152 HIS 0.002 0.000 HIS A1064 PHE 0.033 0.001 PHE A 592 TYR 0.013 0.001 TYR A 269 ARG 0.003 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 148 time to evaluate : 2.998 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.5233 (m-80) REVERT: A 238 PHE cc_start: 0.4213 (OUTLIER) cc_final: 0.3748 (p90) REVERT: A 804 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7838 (tp40) REVERT: A 1031 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: B 153 MET cc_start: -0.1191 (ppp) cc_final: -0.4379 (pmm) REVERT: B 844 MET cc_start: 0.2855 (mpp) cc_final: 0.2380 (mpp) REVERT: B 856 ASN cc_start: 0.7450 (t0) cc_final: 0.6775 (t0) REVERT: C 105 ILE cc_start: 0.6729 (mt) cc_final: 0.6498 (mm) REVERT: C 195 LYS cc_start: 0.7512 (pttt) cc_final: 0.7250 (ptmt) REVERT: C 573 THR cc_start: 0.9058 (m) cc_final: 0.8841 (m) REVERT: C 740 MET cc_start: 0.7494 (tmm) cc_final: 0.6814 (tmm) REVERT: C 844 MET cc_start: 0.2857 (mpp) cc_final: 0.1718 (mpp) outliers start: 49 outliers final: 29 residues processed: 185 average time/residue: 0.3424 time to fit residues: 109.4478 Evaluate side-chains 165 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 0.0980 chunk 142 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29565 Z= 0.165 Angle : 0.492 8.960 40251 Z= 0.252 Chirality : 0.042 0.155 4518 Planarity : 0.004 0.055 5250 Dihedral : 3.574 30.340 4032 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.38 % Allowed : 11.74 % Favored : 86.89 % 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: -0.08 (0.14), residues: 3714 helix: 2.10 (0.20), residues: 639 sheet: 0.50 (0.18), residues: 738 loop : -0.89 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 64 HIS 0.004 0.000 HIS B 207 PHE 0.045 0.001 PHE A 592 TYR 0.013 0.001 TYR A 269 ARG 0.003 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 3.057 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: A 238 PHE cc_start: 0.4487 (OUTLIER) cc_final: 0.4016 (p90) REVERT: A 318 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5535 (p90) REVERT: A 1031 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: B 153 MET cc_start: -0.1405 (ppp) cc_final: -0.3294 (ptt) REVERT: B 844 MET cc_start: 0.2944 (mpp) cc_final: 0.2540 (mpp) REVERT: B 856 ASN cc_start: 0.7485 (t0) cc_final: 0.6800 (t0) REVERT: C 105 ILE cc_start: 0.6755 (mt) cc_final: 0.6450 (mm) REVERT: C 740 MET cc_start: 0.7578 (tmm) cc_final: 0.6857 (tmm) REVERT: C 844 MET cc_start: 0.2872 (mpp) cc_final: 0.1707 (mpp) outliers start: 44 outliers final: 31 residues processed: 176 average time/residue: 0.3436 time to fit residues: 104.8591 Evaluate side-chains 165 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 4.9990 chunk 340 optimal weight: 20.0000 chunk 310 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 144 optimal weight: 30.0000 chunk 260 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 299 optimal weight: 0.0770 chunk 313 optimal weight: 0.6980 chunk 330 optimal weight: 6.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 804 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29565 Z= 0.265 Angle : 0.560 11.612 40251 Z= 0.290 Chirality : 0.044 0.205 4518 Planarity : 0.004 0.051 5250 Dihedral : 3.959 21.954 4032 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.35 % Allowed : 12.14 % Favored : 86.51 % 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: -0.33 (0.14), residues: 3714 helix: 1.85 (0.21), residues: 645 sheet: 0.35 (0.19), residues: 738 loop : -1.06 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1102 HIS 0.003 0.001 HIS C 207 PHE 0.046 0.002 PHE A 817 TYR 0.014 0.001 TYR C 160 ARG 0.004 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.4518 (OUTLIER) cc_final: 0.3907 (p90) REVERT: B 153 MET cc_start: -0.1699 (ppp) cc_final: -0.4803 (pmm) REVERT: B 844 MET cc_start: 0.3120 (mpp) cc_final: 0.2843 (mpp) REVERT: B 856 ASN cc_start: 0.7620 (t0) cc_final: 0.7220 (t0) REVERT: C 740 MET cc_start: 0.7784 (tmm) cc_final: 0.7045 (tmm) REVERT: C 835 MET cc_start: -0.0148 (mmp) cc_final: -0.0947 (ppp) REVERT: C 844 MET cc_start: 0.2799 (mpp) cc_final: 0.1577 (mpp) outliers start: 43 outliers final: 32 residues processed: 175 average time/residue: 0.4046 time to fit residues: 120.7106 Evaluate side-chains 159 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 0.9980 chunk 350 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 243 optimal weight: 0.0980 chunk 367 optimal weight: 30.0000 chunk 338 optimal weight: 20.0000 chunk 292 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29565 Z= 0.162 Angle : 0.507 10.224 40251 Z= 0.259 Chirality : 0.042 0.146 4518 Planarity : 0.004 0.054 5250 Dihedral : 3.679 19.920 4030 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.10 % Allowed : 12.55 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3714 helix: 2.11 (0.21), residues: 636 sheet: 0.40 (0.19), residues: 741 loop : -0.96 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.002 0.000 HIS A1064 PHE 0.056 0.001 PHE A 592 TYR 0.019 0.001 TYR B 200 ARG 0.009 0.000 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 3.286 Fit side-chains revert: symmetry clash REVERT: A 223 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5257 (mp) REVERT: A 238 PHE cc_start: 0.4630 (OUTLIER) cc_final: 0.4094 (p90) REVERT: A 1031 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 153 MET cc_start: -0.1491 (ppp) cc_final: -0.4580 (pmm) REVERT: B 844 MET cc_start: 0.2734 (mpp) cc_final: 0.2521 (mpp) REVERT: B 856 ASN cc_start: 0.7518 (t0) cc_final: 0.7254 (t0) REVERT: C 740 MET cc_start: 0.7643 (tmm) cc_final: 0.6983 (tmm) REVERT: C 835 MET cc_start: 0.0056 (mmp) cc_final: -0.0771 (ppp) REVERT: C 844 MET cc_start: 0.2799 (mpp) cc_final: 0.1506 (mpp) outliers start: 35 outliers final: 27 residues processed: 165 average time/residue: 0.3497 time to fit residues: 99.0624 Evaluate side-chains 157 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 10.0000 chunk 311 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 269 optimal weight: 30.0000 chunk 43 optimal weight: 0.5980 chunk 81 optimal weight: 0.0770 chunk 293 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 301 optimal weight: 0.0870 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.174802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121182 restraints weight = 60689.030| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.63 r_work: 0.3492 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29565 Z= 0.137 Angle : 0.496 11.661 40251 Z= 0.252 Chirality : 0.042 0.152 4518 Planarity : 0.004 0.054 5250 Dihedral : 3.516 18.688 4030 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.06 % Allowed : 12.68 % Favored : 86.26 % 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: 3714 helix: 2.25 (0.21), residues: 639 sheet: 0.50 (0.19), residues: 741 loop : -0.88 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.003 0.000 HIS F 94 PHE 0.056 0.001 PHE A 817 TYR 0.020 0.001 TYR B 200 ARG 0.008 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5352.96 seconds wall clock time: 97 minutes 38.51 seconds (5858.51 seconds total)