Starting phenix.real_space_refine on Sat Aug 10 10:04:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/08_2024/7n9t_24262.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/08_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_24262/08_2024/7n9t_24262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/08_2024/7n9t_24262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/08_2024/7n9t_24262.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9t_24262/08_2024/7n9t_24262.cif" } 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 15.76, per 1000 atoms: 0.55 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: 10.52 Conformation dependent library (CDL) restraints added in 5.4 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: 3.81 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: 11.43 Time building geometry restraints manager: 11.73 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 3.040 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.032 3.040 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.033 3.040 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.067 3.040 nonbonded pdb=" OD1 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.067 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.440 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: 0.050 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 75.110 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.010 ------------------------------------------------------------------------------- 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 : 3.250 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: 0.3830 time to fit residues: 264.6727 Evaluate side-chains 223 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 2.846 ------------------------------------------------------------------------------- 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: 0.9980 chunk 279 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 613 GLN A 690 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 613 GLN B 690 GLN B 777 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 87 ASN C 644 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29565 Z= 0.305 Angle : 0.660 8.897 40251 Z= 0.347 Chirality : 0.048 0.227 4518 Planarity : 0.005 0.052 5250 Dihedral : 4.597 58.355 4075 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.63 % Allowed : 6.38 % Favored : 91.99 % 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: -0.14 (0.14), residues: 3714 helix: 1.88 (0.20), residues: 642 sheet: 0.34 (0.19), residues: 756 loop : -0.85 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1102 HIS 0.005 0.001 HIS A1083 PHE 0.036 0.002 PHE B1089 TYR 0.031 0.002 TYR C 904 ARG 0.007 0.001 ARG C 815 *********************** 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 264 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 212 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6516 (mmt-90) cc_final: 0.5770 (mtt180) REVERT: A 195 LYS cc_start: 0.6716 (pttt) cc_final: 0.6122 (pttp) REVERT: A 238 PHE cc_start: 0.4114 (OUTLIER) cc_final: 0.3679 (p90) REVERT: A 322 PRO cc_start: 0.5227 (Cg_exo) cc_final: 0.5013 (Cg_endo) REVERT: A 835 MET cc_start: 0.1774 (OUTLIER) cc_final: -0.2279 (mmm) REVERT: A 844 MET cc_start: 0.2156 (mpp) cc_final: 0.1739 (mpp) REVERT: A 953 ASN cc_start: 0.7805 (m-40) cc_final: 0.7599 (m-40) REVERT: B 153 MET cc_start: -0.2635 (pmm) cc_final: -0.3429 (ptt) REVERT: B 567 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6786 (mpt180) REVERT: B 759 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.5026 (t80) REVERT: B 844 MET cc_start: 0.3223 (mpp) cc_final: 0.2766 (mpp) REVERT: C 105 ILE cc_start: 0.5778 (mt) cc_final: 0.5497 (mm) REVERT: C 195 LYS cc_start: 0.7534 (pttt) cc_final: 0.7233 (ptmt) REVERT: C 844 MET cc_start: 0.3230 (mpp) cc_final: 0.2646 (mpp) REVERT: D 80 MET cc_start: -0.0303 (tpt) cc_final: -0.0509 (tpt) REVERT: E 34 MET cc_start: 0.1310 (tmm) cc_final: 0.1080 (tmm) outliers start: 52 outliers final: 26 residues processed: 248 average time/residue: 0.3377 time to fit residues: 140.9213 Evaluate side-chains 182 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 2.784 ------------------------------------------------------------------------------- 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 697 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL 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 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 615 VAL 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 1130 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL 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: 0.9980 chunk 103 optimal weight: 0.7980 chunk 278 optimal weight: 0.5980 chunk 228 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 335 optimal weight: 0.0970 chunk 362 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 chunk 332 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 901 GLN A 913 GLN A1005 GLN A1142 GLN B 644 GLN B 913 GLN B1135 ASN C 641 ASN C 644 GLN C 690 GLN C 751 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3632 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= 0.151 Angle : 0.498 8.529 40251 Z= 0.259 Chirality : 0.043 0.145 4518 Planarity : 0.004 0.047 5250 Dihedral : 3.797 59.514 4040 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.28 % Allowed : 8.42 % Favored : 90.30 % 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: -0.05 (0.14), residues: 3714 helix: 2.23 (0.20), residues: 627 sheet: 0.39 (0.19), residues: 747 loop : -0.84 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 36 HIS 0.003 0.000 HIS B1083 PHE 0.021 0.001 PHE A 133 TYR 0.012 0.001 TYR B 789 ARG 0.003 0.000 ARG E 19 *********************** 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 219 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 2.999 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6418 (mmt-90) cc_final: 0.5998 (mtt180) REVERT: A 195 LYS cc_start: 0.6881 (pttt) cc_final: 0.6449 (pttp) REVERT: A 238 PHE cc_start: 0.4178 (OUTLIER) cc_final: 0.3899 (p90) REVERT: A 835 MET cc_start: 0.1691 (OUTLIER) cc_final: -0.2232 (mmm) REVERT: A 1031 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: B 153 MET cc_start: -0.3137 (pmm) cc_final: -0.3842 (ptt) REVERT: B 567 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6748 (mpt180) REVERT: B 844 MET cc_start: 0.3145 (mpp) cc_final: 0.2598 (mpp) REVERT: C 614 ASP cc_start: 0.7669 (t0) cc_final: 0.7350 (t0) REVERT: C 817 PHE cc_start: 0.6691 (m-80) cc_final: 0.6464 (m-80) REVERT: C 844 MET cc_start: 0.3312 (mpp) cc_final: 0.2561 (mpp) REVERT: C 1017 GLU cc_start: 0.7363 (tp30) cc_final: 0.7120 (mm-30) outliers start: 41 outliers final: 19 residues processed: 205 average time/residue: 0.3392 time to fit residues: 118.8020 Evaluate side-chains 171 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE 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 697 MET Chi-restraints excluded: chain A residue 835 MET 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 47 VAL 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 576 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1005 GLN 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: 0.7980 chunk 252 optimal weight: 0.0170 chunk 174 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 chunk 160 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 336 optimal weight: 40.0000 chunk 356 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 954 GLN B 52 GLN C 87 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN C1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29565 Z= 0.180 Angle : 0.502 8.388 40251 Z= 0.262 Chirality : 0.043 0.160 4518 Planarity : 0.004 0.066 5250 Dihedral : 3.620 56.188 4034 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.35 % Allowed : 9.39 % Favored : 89.26 % 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: -0.06 (0.14), residues: 3714 helix: 2.22 (0.20), residues: 624 sheet: 0.40 (0.18), residues: 792 loop : -0.87 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.003 0.000 HIS A1064 PHE 0.023 0.001 PHE A 133 TYR 0.015 0.001 TYR B 160 ARG 0.006 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 214 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 3.010 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6567 (mmt-90) cc_final: 0.6021 (mtt180) REVERT: A 195 LYS cc_start: 0.7129 (pttt) cc_final: 0.6644 (pttp) REVERT: A 238 PHE cc_start: 0.4200 (OUTLIER) cc_final: 0.3718 (p90) REVERT: A 835 MET cc_start: 0.1730 (OUTLIER) cc_final: -0.2081 (mmm) REVERT: A 979 ASP cc_start: 0.8384 (t0) cc_final: 0.8069 (t0) REVERT: A 1031 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: B 153 MET cc_start: -0.3338 (pmm) cc_final: -0.3943 (ptt) REVERT: B 567 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6213 (mmt180) REVERT: B 844 MET cc_start: 0.2922 (mpp) cc_final: 0.2347 (mpp) REVERT: C 170 TYR cc_start: 0.5220 (t80) cc_final: 0.4440 (t80) REVERT: C 195 LYS cc_start: 0.7377 (pttt) cc_final: 0.6890 (pttp) REVERT: C 614 ASP cc_start: 0.7666 (t0) cc_final: 0.7125 (t0) REVERT: C 835 MET cc_start: -0.0374 (mmp) cc_final: -0.0971 (ptp) REVERT: C 844 MET cc_start: 0.3136 (mpp) cc_final: 0.2274 (mpp) outliers start: 43 outliers final: 29 residues processed: 200 average time/residue: 0.3659 time to fit residues: 123.8263 Evaluate side-chains 178 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 835 MET 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 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 675 GLN 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 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 265 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 320 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 134 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 955 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29565 Z= 0.268 Angle : 0.556 7.922 40251 Z= 0.292 Chirality : 0.044 0.163 4518 Planarity : 0.004 0.055 5250 Dihedral : 3.985 44.115 4034 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.75 % Allowed : 10.42 % Favored : 87.82 % 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: 1.83 (0.20), residues: 642 sheet: 0.27 (0.18), residues: 747 loop : -1.02 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1102 HIS 0.004 0.001 HIS A1064 PHE 0.035 0.002 PHE A 592 TYR 0.021 0.001 TYR C 160 ARG 0.006 0.000 ARG A 983 *********************** 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 219 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.4243 (OUTLIER) cc_final: 0.3589 (p90) REVERT: A 835 MET cc_start: 0.1753 (OUTLIER) cc_final: -0.2121 (mmm) REVERT: A 979 ASP cc_start: 0.8571 (t0) cc_final: 0.8337 (t0) REVERT: A 1031 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: B 153 MET cc_start: -0.2858 (pmm) cc_final: -0.3576 (ptt) REVERT: B 223 LEU cc_start: 0.5456 (mp) cc_final: 0.5137 (mt) REVERT: B 856 ASN cc_start: 0.7389 (t0) cc_final: 0.7059 (t0) REVERT: C 195 LYS cc_start: 0.7542 (pttt) cc_final: 0.7090 (pttp) REVERT: C 844 MET cc_start: 0.2937 (mpp) cc_final: 0.1762 (mpp) REVERT: C 1017 GLU cc_start: 0.7495 (tp30) cc_final: 0.7251 (mm-30) outliers start: 56 outliers final: 34 residues processed: 202 average time/residue: 0.3501 time to fit residues: 120.1877 Evaluate side-chains 171 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 VAL 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 552 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 835 MET 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 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 645 THR 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 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 286 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 736 VAL 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 D residue 119 SER 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: 6.9990 chunk 321 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 209 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 357 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1142 GLN B 641 ASN C 804 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29565 Z= 0.227 Angle : 0.521 9.807 40251 Z= 0.271 Chirality : 0.043 0.153 4518 Planarity : 0.004 0.053 5250 Dihedral : 3.763 22.313 4030 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.69 % Allowed : 11.02 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3714 helix: 1.90 (0.20), residues: 639 sheet: 0.35 (0.19), residues: 729 loop : -1.02 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1102 HIS 0.003 0.001 HIS B 207 PHE 0.022 0.001 PHE C1121 TYR 0.016 0.001 TYR C 160 ARG 0.005 0.000 ARG A 983 *********************** 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 207 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 153 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5270 (m-80) REVERT: A 238 PHE cc_start: 0.4419 (OUTLIER) cc_final: 0.3831 (p90) REVERT: A 568 ASP cc_start: 0.6973 (t0) cc_final: 0.6632 (p0) REVERT: A 835 MET cc_start: 0.1788 (OUTLIER) cc_final: -0.2098 (mmm) REVERT: A 1031 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: B 153 MET cc_start: -0.2708 (pmm) cc_final: -0.3407 (ptt) REVERT: C 195 LYS cc_start: 0.7376 (pttt) cc_final: 0.6898 (ptmt) REVERT: C 844 MET cc_start: 0.2829 (mpp) cc_final: 0.1702 (mpp) REVERT: C 1017 GLU cc_start: 0.7439 (tp30) cc_final: 0.7218 (mm-30) outliers start: 54 outliers final: 36 residues processed: 194 average time/residue: 0.3438 time to fit residues: 114.6553 Evaluate side-chains 172 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL 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 747 THR Chi-restraints excluded: chain A residue 835 MET 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 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 732 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 645 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 2.9990 chunk 40 optimal weight: 0.0170 chunk 203 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 202 optimal weight: 0.5980 chunk 300 optimal weight: 0.0170 chunk 199 optimal weight: 0.4980 chunk 355 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 675 GLN C 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29565 Z= 0.176 Angle : 0.498 8.640 40251 Z= 0.259 Chirality : 0.043 0.164 4518 Planarity : 0.004 0.052 5250 Dihedral : 3.654 19.576 4030 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.72 % Allowed : 11.64 % Favored : 86.64 % 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: -0.26 (0.14), residues: 3714 helix: 2.03 (0.20), residues: 636 sheet: 0.34 (0.19), residues: 729 loop : -1.01 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.002 0.000 HIS C1064 PHE 0.020 0.001 PHE A 817 TYR 0.013 0.001 TYR C 160 ARG 0.003 0.000 ARG C 995 *********************** 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 194 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 139 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5373 (m-80) REVERT: A 238 PHE cc_start: 0.4672 (OUTLIER) cc_final: 0.4057 (p90) REVERT: A 277 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9040 (mt) REVERT: A 835 MET cc_start: 0.1717 (OUTLIER) cc_final: -0.2146 (mmm) REVERT: A 957 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: A 1031 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: B 153 MET cc_start: -0.2755 (pmm) cc_final: -0.3334 (ptt) REVERT: B 568 ASP cc_start: 0.7123 (t0) cc_final: 0.6651 (p0) REVERT: C 195 LYS cc_start: 0.7412 (pttt) cc_final: 0.6941 (pttp) REVERT: C 835 MET cc_start: 0.0015 (mmp) cc_final: -0.0632 (ptp) REVERT: C 844 MET cc_start: 0.2925 (mpp) cc_final: 0.1660 (mpp) REVERT: C 1017 GLU cc_start: 0.7448 (tp30) cc_final: 0.7222 (mm-30) outliers start: 55 outliers final: 40 residues processed: 181 average time/residue: 0.3395 time to fit residues: 107.4975 Evaluate side-chains 176 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 VAL 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 277 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 957 GLN 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 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 615 VAL 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 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 645 THR 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 D residue 119 SER 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: 2.9990 chunk 142 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 279 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 856 ASN C 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29565 Z= 0.272 Angle : 0.561 10.150 40251 Z= 0.292 Chirality : 0.044 0.186 4518 Planarity : 0.004 0.057 5250 Dihedral : 3.947 26.053 4030 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.82 % Allowed : 11.86 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 3714 helix: 1.84 (0.20), residues: 636 sheet: 0.23 (0.19), residues: 705 loop : -1.13 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1102 HIS 0.003 0.001 HIS C1064 PHE 0.026 0.001 PHE A 817 TYR 0.027 0.001 TYR C 741 ARG 0.005 0.000 ARG C 190 *********************** 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 206 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 148 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.4701 (OUTLIER) cc_final: 0.4026 (p90) REVERT: A 580 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: A 835 MET cc_start: 0.1875 (OUTLIER) cc_final: -0.2110 (mmm) REVERT: A 1031 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: B 153 MET cc_start: -0.2677 (pmm) cc_final: -0.3392 (ptt) REVERT: B 844 MET cc_start: 0.3050 (mpp) cc_final: 0.2492 (mpp) REVERT: C 153 MET cc_start: -0.0414 (pmm) cc_final: -0.0719 (pmm) REVERT: C 195 LYS cc_start: 0.7598 (pttt) cc_final: 0.7049 (pttp) REVERT: C 835 MET cc_start: -0.0087 (mmp) cc_final: -0.0917 (ppp) REVERT: C 844 MET cc_start: 0.2875 (mpp) cc_final: 0.1560 (mpp) outliers start: 58 outliers final: 40 residues processed: 190 average time/residue: 0.3509 time to fit residues: 115.3337 Evaluate side-chains 169 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL 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 580 GLN Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 835 MET 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 47 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 615 VAL 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 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 753 LEU 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 D residue 119 SER 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6951 > 50: distance: 23 - 74: 32.636 distance: 26 - 71: 29.474 distance: 37 - 45: 20.386 distance: 45 - 46: 24.771 distance: 46 - 47: 41.734 distance: 46 - 49: 4.391 distance: 47 - 48: 21.246 distance: 47 - 53: 42.639 distance: 49 - 50: 29.148 distance: 50 - 51: 7.199 distance: 50 - 52: 10.304 distance: 53 - 54: 9.622 distance: 54 - 55: 20.242 distance: 55 - 56: 17.352 distance: 55 - 57: 45.213 distance: 57 - 58: 7.325 distance: 58 - 59: 33.276 distance: 58 - 61: 37.318 distance: 59 - 60: 14.404 distance: 59 - 66: 13.854 distance: 61 - 62: 4.293 distance: 62 - 63: 8.150 distance: 63 - 64: 8.309 distance: 64 - 65: 39.575 distance: 67 - 68: 51.035 distance: 67 - 70: 41.383 distance: 68 - 69: 11.450 distance: 68 - 71: 28.586 distance: 71 - 72: 50.096 distance: 72 - 73: 30.674 distance: 72 - 75: 40.147 distance: 73 - 74: 40.590 distance: 73 - 81: 35.632 distance: 75 - 76: 30.072 distance: 76 - 77: 47.677 distance: 76 - 78: 21.972 distance: 77 - 79: 27.787 distance: 78 - 80: 35.334 distance: 79 - 80: 30.841 distance: 81 - 82: 41.439 distance: 81 - 173: 33.989 distance: 82 - 83: 58.147 distance: 82 - 85: 53.837 distance: 83 - 84: 14.186 distance: 83 - 92: 49.622 distance: 84 - 170: 34.070 distance: 85 - 86: 30.167 distance: 86 - 87: 32.455 distance: 86 - 88: 36.862 distance: 87 - 89: 51.045 distance: 88 - 90: 15.941 distance: 89 - 91: 32.058 distance: 90 - 91: 48.542 distance: 92 - 93: 49.451 distance: 92 - 98: 41.834 distance: 93 - 94: 38.766 distance: 93 - 96: 57.719 distance: 94 - 95: 39.794 distance: 96 - 97: 40.148 distance: 97 - 98: 50.666 distance: 99 - 100: 39.205 distance: 100 - 101: 39.347 distance: 100 - 103: 45.793 distance: 101 - 102: 35.033 distance: 101 - 110: 22.629 distance: 103 - 104: 22.907 distance: 105 - 106: 10.807 distance: 106 - 107: 9.942 distance: 107 - 108: 24.608 distance: 107 - 109: 8.904 distance: 111 - 112: 18.260 distance: 111 - 114: 16.762 distance: 112 - 113: 40.888 distance: 112 - 119: 35.669 distance: 114 - 115: 28.056 distance: 115 - 116: 27.371 distance: 116 - 117: 27.214 distance: 116 - 118: 25.016 distance: 119 - 120: 18.116 distance: 120 - 121: 11.064 distance: 121 - 122: 31.694 distance: 121 - 123: 15.663 distance: 123 - 139: 3.216