Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 20:32:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljr_23400/04_2023/7ljr_23400.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljr_23400/04_2023/7ljr_23400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljr_23400/04_2023/7ljr_23400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljr_23400/04_2023/7ljr_23400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljr_23400/04_2023/7ljr_23400.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljr_23400/04_2023/7ljr_23400.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.046 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 112 5.16 5 C 16767 2.51 5 N 4376 2.21 5 O 5036 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 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 69": "NH1" <-> "NH2" Residue "S GLU 101": "OE1" <-> "OE2" Residue "S TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 123": "OD1" <-> "OD2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 177": "OE1" <-> "OE2" Residue "S GLU 241": "OE1" <-> "OE2" Residue "T ARG 43": "NH1" <-> "NH2" Residue "T TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 65": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T ARG 97": "NH1" <-> "NH2" Residue "T TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 115": "NH1" <-> "NH2" Residue "T GLU 124": "OE1" <-> "OE2" Residue "T GLU 142": "OE1" <-> "OE2" Residue "T TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 161": "NH1" <-> "NH2" Residue "T GLU 162": "OE1" <-> "OE2" Residue "T GLU 184": "OE1" <-> "OE2" Residue "T GLU 206": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 26291 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7597 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "S" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1694 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1573 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 195} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 13.41, per 1000 atoms: 0.51 Number of scatterers: 26291 At special positions: 0 Unit cell: (133.308, 156.584, 221.122, 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 112 16.00 O 5036 8.00 N 4376 7.00 C 16767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 10.64 Conformation dependent library (CDL) restraints added in 4.0 seconds 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6330 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 50 sheets defined 24.8% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.675A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.856A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.467A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.067A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.635A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.118A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.689A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.703A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.759A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.118A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 4.209A pdb=" N LEU A1145 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 756 removed outlier: 4.446A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.600A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.452A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.812A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.554A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.339A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.473A pdb=" N PHE C 342 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.794A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.791A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.361A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.954A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.019A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.505A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.636A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.986A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1145 Processing helix chain 'S' and resid 44 through 50 removed outlier: 4.483A pdb=" N PHE S 48 " --> pdb=" O GLY S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 110 Processing helix chain 'S' and resid 120 through 124 removed outlier: 3.544A pdb=" N ASP S 123 " --> pdb=" O TYR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 158 No H-bonds generated for 'chain 'S' and resid 156 through 158' Processing helix chain 'S' and resid 185 through 187 No H-bonds generated for 'chain 'S' and resid 185 through 187' Processing helix chain 'S' and resid 216 through 218 No H-bonds generated for 'chain 'S' and resid 216 through 218' Processing helix chain 'S' and resid 230 through 233 Processing helix chain 'T' and resid 140 through 147 Processing helix chain 'T' and resid 202 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.983A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.582A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.802A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.893A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.171A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.654A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.277A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.882A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.913A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.850A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.850A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.539A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.476A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.069A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.983A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.212A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.609A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 377 through 379 removed outlier: 3.812A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 656 removed outlier: 4.305A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.858A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.685A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.210A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.410A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 50 through 55 removed outlier: 7.169A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.221A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.262A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AD9, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.891A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.458A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.645A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.645A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.350A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.214A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 38 through 42 Processing sheet with id=AE7, first strand: chain 'S' and resid 77 through 79 removed outlier: 5.258A pdb=" N TRP S 66 " --> pdb=" O ARG S 57 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG S 57 " --> pdb=" O TRP S 66 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 149 through 153 removed outlier: 4.970A pdb=" N ALA S 166 " --> pdb=" O VAL S 213 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL S 213 " --> pdb=" O ALA S 166 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY S 168 " --> pdb=" O VAL S 211 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 211 " --> pdb=" O GLY S 168 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU S 170 " --> pdb=" O SER S 209 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER S 209 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LYS S 172 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU S 207 " --> pdb=" O LYS S 172 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 160 through 161 removed outlier: 3.511A pdb=" N THR S 164 " --> pdb=" O SER S 161 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA S 166 " --> pdb=" O VAL S 213 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL S 213 " --> pdb=" O ALA S 166 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY S 168 " --> pdb=" O VAL S 211 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 211 " --> pdb=" O GLY S 168 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU S 170 " --> pdb=" O SER S 209 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER S 209 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LYS S 172 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU S 207 " --> pdb=" O LYS S 172 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 182 through 183 Processing sheet with id=AF2, first strand: chain 'T' and resid 29 through 32 Processing sheet with id=AF3, first strand: chain 'T' and resid 65 through 68 removed outlier: 6.589A pdb=" N TRP T 55 " --> pdb=" O LEU T 67 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLN T 109 " --> pdb=" O LEU T 53 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP T 55 " --> pdb=" O TYR T 107 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR T 107 " --> pdb=" O TRP T 55 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN T 57 " --> pdb=" O VAL T 105 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL T 105 " --> pdb=" O GLN T 57 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 133 through 137 removed outlier: 5.043A pdb=" N TYR T 192 " --> pdb=" O ASN T 157 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER T 181 " --> pdb=" O SER T 195 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 172 through 174 1056 hydrogen bonds defined for protein. 2829 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.34 Time building geometry restraints manager: 11.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6970 1.33 - 1.46: 5231 1.46 - 1.58: 14538 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26877 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.42e+01 bond pdb=" N VAL A 130 " pdb=" CA VAL A 130 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.04e-02 9.25e+03 1.29e+01 bond pdb=" CA ALA C 411 " pdb=" C ALA C 411 " ideal model delta sigma weight residual 1.519 1.557 -0.038 1.09e-02 8.42e+03 1.23e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.14e+01 bond pdb=" CZ ARG B 454 " pdb=" NH2 ARG B 454 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.06e+01 ... (remaining 26872 not shown) Histogram of bond angle deviations from ideal: 95.50 - 103.48: 300 103.48 - 111.47: 9652 111.47 - 119.46: 12002 119.46 - 127.45: 14396 127.45 - 135.43: 207 Bond angle restraints: 36557 Sorted by residual: angle pdb=" CA PHE B 515 " pdb=" CB PHE B 515 " pdb=" CG PHE B 515 " ideal model delta sigma weight residual 113.80 124.63 -10.83 1.00e+00 1.00e+00 1.17e+02 angle pdb=" CA PHE S 129 " pdb=" CB PHE S 129 " pdb=" CG PHE S 129 " ideal model delta sigma weight residual 113.80 121.25 -7.45 1.00e+00 1.00e+00 5.55e+01 angle pdb=" CA PRO T 27 " pdb=" N PRO T 27 " pdb=" CD PRO T 27 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" CA ASP C 737 " pdb=" CB ASP C 737 " pdb=" CG ASP C 737 " ideal model delta sigma weight residual 112.60 106.23 6.37 1.00e+00 1.00e+00 4.05e+01 angle pdb=" CA PHE B 392 " pdb=" CB PHE B 392 " pdb=" CG PHE B 392 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.52e+01 ... (remaining 36552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14672 17.91 - 35.82: 1000 35.82 - 53.73: 164 53.73 - 71.64: 47 71.64 - 89.56: 38 Dihedral angle restraints: 15921 sinusoidal: 6099 harmonic: 9822 Sorted by residual: dihedral pdb=" CA LYS B 113 " pdb=" C LYS B 113 " pdb=" N THR B 114 " pdb=" CA THR B 114 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALA C 522 " pdb=" C ALA C 522 " pdb=" N THR C 523 " pdb=" CA THR C 523 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA LYS B 97 " pdb=" C LYS B 97 " pdb=" N SER B 98 " pdb=" CA SER B 98 " ideal model delta harmonic sigma weight residual 180.00 -150.04 -29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 15918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2636 0.085 - 0.169: 1274 0.169 - 0.254: 215 0.254 - 0.339: 37 0.339 - 0.424: 12 Chirality restraints: 4174 Sorted by residual: chirality pdb=" CA ARG C 983 " pdb=" N ARG C 983 " pdb=" C ARG C 983 " pdb=" CB ARG C 983 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TYR S 120 " pdb=" N TYR S 120 " pdb=" C TYR S 120 " pdb=" CB TYR S 120 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 4171 not shown) Planarity restraints: 4724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 917 " 0.236 2.00e-02 2.50e+03 1.33e-01 3.56e+02 pdb=" CG TYR A 917 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 917 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TYR A 917 " -0.136 2.00e-02 2.50e+03 pdb=" CE1 TYR A 917 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR A 917 " -0.067 2.00e-02 2.50e+03 pdb=" CZ TYR A 917 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 917 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.170 2.00e-02 2.50e+03 9.62e-02 2.31e+02 pdb=" CG TRP A 886 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.108 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " -0.141 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.093 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 707 " 0.200 2.00e-02 2.50e+03 1.07e-01 2.29e+02 pdb=" CG TYR B 707 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR B 707 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR B 707 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR B 707 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR B 707 " -0.053 2.00e-02 2.50e+03 pdb=" CZ TYR B 707 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 707 " 0.154 2.00e-02 2.50e+03 ... (remaining 4721 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 13393 2.99 - 3.47: 27658 3.47 - 3.94: 45086 3.94 - 4.42: 50828 4.42 - 4.90: 84002 Nonbonded interactions: 220967 Sorted by model distance: nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.509 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.517 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.520 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE1 GLU C 918 " model vdw 2.521 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.525 2.440 ... (remaining 220962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 444 or resid 447 through 452 or (resid 453 and \ (name N or name CA or name C or name O or name CB )) or resid 454 or resid 462 t \ hrough 468 or resid 489 through 501 or resid 503 through 1147)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 452 or (resid 453 and (name N or name CA or nam \ e C or name O or name CB )) or resid 454 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.100 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 69.500 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 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 : 0.013 0.046 26877 Z= 0.832 Angle : 1.827 11.874 36557 Z= 1.215 Chirality : 0.095 0.424 4174 Planarity : 0.015 0.133 4724 Dihedral : 13.960 89.556 9591 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.15 % Favored : 90.03 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3310 helix: -0.87 (0.17), residues: 660 sheet: -0.28 (0.23), residues: 469 loop : -1.70 (0.12), residues: 2181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 10 residues processed: 265 average time/residue: 0.4526 time to fit residues: 183.4945 Evaluate side-chains 103 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2583 time to fit residues: 8.8827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 305 optimal weight: 30.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 655 HIS A 914 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 360 ASN B 450 ASN B 762 GLN C 61 ASN C 66 HIS ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1119 ASN S 54 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 26877 Z= 0.201 Angle : 0.667 15.889 36557 Z= 0.360 Chirality : 0.045 0.169 4174 Planarity : 0.004 0.061 4724 Dihedral : 6.760 29.930 3601 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.08 % Favored : 94.77 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3310 helix: 0.67 (0.20), residues: 661 sheet: -0.32 (0.19), residues: 657 loop : -1.37 (0.13), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 178 average time/residue: 0.4026 time to fit residues: 115.8077 Evaluate side-chains 127 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 3.050 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3437 time to fit residues: 16.6060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 675 GLN A 901 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 901 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 26877 Z= 0.470 Angle : 0.753 18.197 36557 Z= 0.397 Chirality : 0.048 0.190 4174 Planarity : 0.005 0.051 4724 Dihedral : 6.487 28.433 3601 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.92 % Favored : 92.93 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3310 helix: 0.18 (0.19), residues: 661 sheet: -0.81 (0.19), residues: 716 loop : -1.44 (0.14), residues: 1933 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 141 average time/residue: 0.4340 time to fit residues: 99.9577 Evaluate side-chains 106 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 3.090 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2795 time to fit residues: 13.5004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 145 optimal weight: 0.0970 chunk 205 optimal weight: 20.0000 chunk 306 optimal weight: 8.9990 chunk 324 optimal weight: 20.0000 chunk 160 optimal weight: 0.8980 chunk 290 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 493 GLN B 134 GLN B 137 ASN B 360 ASN B 675 GLN B 969 ASN C 580 GLN C 762 GLN C 914 ASN ** S 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 228 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 26877 Z= 0.159 Angle : 0.581 19.292 36557 Z= 0.305 Chirality : 0.044 0.161 4174 Planarity : 0.004 0.050 4724 Dihedral : 5.694 25.436 3601 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3310 helix: 0.94 (0.20), residues: 651 sheet: -0.83 (0.18), residues: 756 loop : -1.19 (0.14), residues: 1903 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 11 residues processed: 153 average time/residue: 0.4094 time to fit residues: 102.2557 Evaluate side-chains 106 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 3.037 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2863 time to fit residues: 9.7658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 291 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 110 GLN T 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 26877 Z= 0.241 Angle : 0.590 18.485 36557 Z= 0.308 Chirality : 0.044 0.187 4174 Planarity : 0.004 0.049 4724 Dihedral : 5.530 24.800 3601 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.72 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.99 (0.14), residues: 3310 helix: 1.05 (0.20), residues: 645 sheet: -0.82 (0.18), residues: 762 loop : -1.20 (0.14), residues: 1903 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 122 average time/residue: 0.3952 time to fit residues: 80.6863 Evaluate side-chains 106 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2582 time to fit residues: 9.4212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 0.0670 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 chunk 325 optimal weight: 40.0000 chunk 269 optimal weight: 0.6980 chunk 150 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 498 GLN B 675 GLN B 762 GLN B1088 HIS C 498 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 26877 Z= 0.140 Angle : 0.550 18.163 36557 Z= 0.284 Chirality : 0.043 0.212 4174 Planarity : 0.004 0.048 4724 Dihedral : 5.147 23.879 3601 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.59 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.69 (0.15), residues: 3310 helix: 1.36 (0.20), residues: 646 sheet: -0.59 (0.19), residues: 743 loop : -1.05 (0.14), residues: 1921 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 131 average time/residue: 0.3990 time to fit residues: 87.5370 Evaluate side-chains 97 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 3.024 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2336 time to fit residues: 5.4480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 0.0670 chunk 181 optimal weight: 0.8980 chunk 323 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN C 914 ASN C 949 GLN C 955 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 26877 Z= 0.258 Angle : 0.578 18.152 36557 Z= 0.300 Chirality : 0.043 0.170 4174 Planarity : 0.004 0.054 4724 Dihedral : 5.199 23.616 3601 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.92 % Favored : 93.96 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.77 (0.15), residues: 3310 helix: 1.22 (0.20), residues: 645 sheet: -0.62 (0.19), residues: 765 loop : -1.08 (0.14), residues: 1900 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.4184 time to fit residues: 75.4967 Evaluate side-chains 100 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 2.871 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2533 time to fit residues: 8.1563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 205 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 949 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 208 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 26877 Z= 0.308 Angle : 0.610 18.755 36557 Z= 0.316 Chirality : 0.044 0.265 4174 Planarity : 0.004 0.053 4724 Dihedral : 5.308 24.585 3601 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.44 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.93 (0.15), residues: 3310 helix: 1.02 (0.20), residues: 646 sheet: -0.74 (0.19), residues: 759 loop : -1.15 (0.14), residues: 1905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 97 average time/residue: 0.4068 time to fit residues: 67.9918 Evaluate side-chains 86 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 3.545 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3047 time to fit residues: 8.0855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 301 optimal weight: 40.0000 chunk 181 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 300 optimal weight: 0.0070 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 913 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 26877 Z= 0.181 Angle : 0.548 18.860 36557 Z= 0.283 Chirality : 0.043 0.204 4174 Planarity : 0.004 0.054 4724 Dihedral : 5.059 23.441 3601 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.87 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.76 (0.15), residues: 3310 helix: 1.31 (0.20), residues: 646 sheet: -0.68 (0.18), residues: 767 loop : -1.08 (0.14), residues: 1897 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 92 average time/residue: 0.3856 time to fit residues: 61.1544 Evaluate side-chains 88 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 3.032 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2701 time to fit residues: 6.6192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 3.9990 chunk 319 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 chunk 308 optimal weight: 50.0000 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 26877 Z= 0.324 Angle : 0.619 18.719 36557 Z= 0.319 Chirality : 0.044 0.216 4174 Planarity : 0.004 0.063 4724 Dihedral : 5.243 24.615 3601 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.94 (0.14), residues: 3310 helix: 1.07 (0.20), residues: 646 sheet: -0.79 (0.19), residues: 751 loop : -1.17 (0.14), residues: 1913 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 87 average time/residue: 0.3749 time to fit residues: 57.5129 Evaluate side-chains 86 residues out of total 2947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 3.031 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3321 time to fit residues: 5.5826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.0970 chunk 283 optimal weight: 0.0060 chunk 81 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 266 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 949 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.104407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.080880 restraints weight = 108204.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.078474 restraints weight = 66039.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.079335 restraints weight = 70617.900| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 26877 Z= 0.163 Angle : 0.546 18.152 36557 Z= 0.281 Chirality : 0.043 0.160 4174 Planarity : 0.004 0.054 4724 Dihedral : 4.950 23.073 3601 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.89 % Favored : 93.99 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % 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: -0.72 (0.15), residues: 3310 helix: 1.40 (0.20), residues: 646 sheet: -0.68 (0.19), residues: 766 loop : -1.06 (0.14), residues: 1898 =============================================================================== Job complete usr+sys time: 3667.80 seconds wall clock time: 70 minutes 2.60 seconds (4202.60 seconds total)