Starting phenix.real_space_refine on Fri Mar 6 12:43:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dk6_30704/03_2026/7dk6_30704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dk6_30704/03_2026/7dk6_30704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dk6_30704/03_2026/7dk6_30704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dk6_30704/03_2026/7dk6_30704.map" model { file = "/net/cci-nas-00/data/ceres_data/7dk6_30704/03_2026/7dk6_30704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dk6_30704/03_2026/7dk6_30704.cif" } resolution = 4.3 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 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= 0.006 sd= 0.079 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 144 5.16 5 C 19977 2.51 5 N 5259 2.21 5 O 6068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31448 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8295 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 51, 'TRANS': 1008} Chain breaks: 6 Chain: "B" Number of atoms: 8295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8295 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 51, 'TRANS': 1008} Chain breaks: 6 Chain: "C" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8280 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "a" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Chain: "c" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "d" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1686 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 8, 'TRANS': 204} Time building chain proxies: 6.73, per 1000 atoms: 0.21 Number of scatterers: 31448 At special positions: 0 Unit cell: (143.82, 159.12, 237.66, 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 144 16.00 O 6068 8.00 N 5259 7.00 C 19977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 95 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 95 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 199 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS d 138 " - pdb=" SG CYS d 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7566 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 66 sheets defined 19.8% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.560A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.599A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.634A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.502A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 4.499A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.539A 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 912 through 919 removed outlier: 4.043A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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: 3.662A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.978A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.553A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.606A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.162A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.533A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (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 908 removed outlier: 3.668A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.250A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) 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 966 removed outlier: 3.904A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.231A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.697A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.542A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.625A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.782A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.524A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.637A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.639A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 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 968 removed outlier: 4.027A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.663A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.849A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.667A pdb=" N TYR a 32 " --> pdb=" O LEU a 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 90 removed outlier: 3.762A pdb=" N THR a 90 " --> pdb=" O THR a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 190 through 192 No H-bonds generated for 'chain 'a' and resid 190 through 192' Processing helix chain 'b' and resid 125 through 132 removed outlier: 3.650A pdb=" N GLY b 132 " --> pdb=" O GLN b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 191 Processing helix chain 'c' and resid 86 through 90 removed outlier: 3.738A pdb=" N THR c 90 " --> pdb=" O THR c 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 132 Processing helix chain 'd' and resid 187 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.066A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.655A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.517A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.333A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.397A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.380A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 327 removed outlier: 5.200A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.600A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.203A 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 711 through 728 removed outlier: 3.503A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.246A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 5.117A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.966A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.384A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.532A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.331A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 154 through 157 removed outlier: 6.483A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 259 " --> pdb=" O HIS B 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.501A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.551A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.539A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.537A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.945A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.983A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.121A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.514A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.424A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.415A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.624A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.339A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.527A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.573A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'a' and resid 6 through 7 Processing sheet with id=AF1, first strand: chain 'a' and resid 57 through 59 removed outlier: 5.828A pdb=" N TRP a 47 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG a 38 " --> pdb=" O TRP a 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL a 34 " --> pdb=" O MET a 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA a 96 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE a 106 " --> pdb=" O LYS a 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 57 through 59 removed outlier: 5.828A pdb=" N TRP a 47 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG a 38 " --> pdb=" O TRP a 47 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL a 34 " --> pdb=" O MET a 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA a 96 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL a 113 " --> pdb=" O ALA a 91 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR a 111 " --> pdb=" O TYR a 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 124 through 128 removed outlier: 5.907A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 124 through 128 removed outlier: 5.907A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 155 through 158 Processing sheet with id=AF6, first strand: chain 'b' and resid 5 through 7 Processing sheet with id=AF7, first strand: chain 'b' and resid 10 through 14 removed outlier: 6.360A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LYS b 111 " --> pdb=" O LEU b 11 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL b 13 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS b 38 " --> pdb=" O GLN b 93 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE b 52 " --> pdb=" O TRP b 39 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN b 41 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU b 50 " --> pdb=" O GLN b 41 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 120 through 122 removed outlier: 5.124A pdb=" N SER b 135 " --> pdb=" O LEU b 185 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU b 185 " --> pdb=" O SER b 135 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL b 137 " --> pdb=" O LEU b 183 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU b 183 " --> pdb=" O VAL b 137 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE b 139 " --> pdb=" O SER b 181 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER b 181 " --> pdb=" O PHE b 139 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN b 141 " --> pdb=" O MET b 179 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET b 179 " --> pdb=" O ASN b 141 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU b 164 " --> pdb=" O THR b 182 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 120 through 122 removed outlier: 5.124A pdb=" N SER b 135 " --> pdb=" O LEU b 185 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU b 185 " --> pdb=" O SER b 135 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL b 137 " --> pdb=" O LEU b 183 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU b 183 " --> pdb=" O VAL b 137 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE b 139 " --> pdb=" O SER b 181 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER b 181 " --> pdb=" O PHE b 139 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN b 141 " --> pdb=" O MET b 179 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET b 179 " --> pdb=" O ASN b 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER b 178 " --> pdb=" O THR b 168 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 148 through 150 Processing sheet with id=AG2, first strand: chain 'b' and resid 195 through 197 Processing sheet with id=AG3, first strand: chain 'c' and resid 6 through 7 removed outlier: 3.815A pdb=" N VAL c 78 " --> pdb=" O CYS c 22 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'c' and resid 57 through 59 removed outlier: 4.014A pdb=" N GLU c 46 " --> pdb=" O ARG c 38 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP c 36 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA c 96 " --> pdb=" O HIS c 35 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE c 106 " --> pdb=" O LYS c 97 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 57 through 59 removed outlier: 4.014A pdb=" N GLU c 46 " --> pdb=" O ARG c 38 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP c 36 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA c 96 " --> pdb=" O HIS c 35 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 124 through 128 removed outlier: 4.025A pdb=" N LYS c 147 " --> pdb=" O SER c 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 124 through 128 removed outlier: 4.025A pdb=" N LYS c 147 " --> pdb=" O SER c 124 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU c 178 " --> pdb=" O GLN c 175 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR c 180 " --> pdb=" O VAL c 173 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 155 through 158 Processing sheet with id=AG9, first strand: chain 'd' and resid 6 through 7 Processing sheet with id=AH1, first strand: chain 'd' and resid 10 through 13 removed outlier: 3.505A pdb=" N HIS d 38 " --> pdb=" O GLN d 93 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE d 52 " --> pdb=" O TRP d 39 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN d 41 " --> pdb=" O LEU d 50 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU d 50 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 120 through 122 removed outlier: 3.602A pdb=" N SER d 120 " --> pdb=" O PHE d 139 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR d 177 " --> pdb=" O ASN d 142 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER d 178 " --> pdb=" O THR d 168 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 148 through 154 removed outlier: 3.546A pdb=" N THR d 197 " --> pdb=" O LYS d 153 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS d 211 " --> pdb=" O CYS d 198 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3246 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: 8.16 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10134 1.34 - 1.46: 7634 1.46 - 1.58: 14224 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 32178 Sorted by residual: bond pdb=" C PHE B 497 " pdb=" N GLN B 498 " ideal model delta sigma weight residual 1.329 1.364 -0.036 1.35e-02 5.49e+03 6.95e+00 bond pdb=" C THR B 599 " pdb=" N PRO B 600 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.44e-02 4.82e+03 3.59e+00 bond pdb=" N GLN c 1 " pdb=" CA GLN c 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N ASN b 1 " pdb=" CA ASN b 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 32173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 42719 1.33 - 2.65: 810 2.65 - 3.98: 131 3.98 - 5.30: 131 5.30 - 6.63: 7 Bond angle restraints: 43798 Sorted by residual: angle pdb=" C GLU b 27 " pdb=" N SER b 28 " pdb=" CA SER b 28 " ideal model delta sigma weight residual 121.70 128.33 -6.63 1.80e+00 3.09e-01 1.36e+01 angle pdb=" C GLU d 27 " pdb=" N SER d 28 " pdb=" CA SER d 28 " ideal model delta sigma weight residual 121.70 127.62 -5.92 1.80e+00 3.09e-01 1.08e+01 angle pdb=" C ILE B 326 " pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta sigma weight residual 120.49 124.17 -3.68 1.38e+00 5.25e-01 7.12e+00 angle pdb=" C GLY A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta sigma weight residual 120.35 124.05 -3.70 1.39e+00 5.18e-01 7.10e+00 angle pdb=" C GLU c 152 " pdb=" N PRO c 153 " pdb=" CA PRO c 153 " ideal model delta sigma weight residual 127.00 132.97 -5.97 2.40e+00 1.74e-01 6.19e+00 ... (remaining 43793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 18737 17.99 - 35.99: 368 35.99 - 53.98: 66 53.98 - 71.97: 11 71.97 - 89.96: 10 Dihedral angle restraints: 19192 sinusoidal: 7439 harmonic: 11753 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 142.84 -49.84 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 142.74 -49.74 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual 180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 19189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3299 0.034 - 0.067: 1126 0.067 - 0.101: 234 0.101 - 0.135: 285 0.135 - 0.168: 13 Chirality restraints: 4957 Sorted by residual: chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ILE B 896 " pdb=" N ILE B 896 " pdb=" C ILE B 896 " pdb=" CB ILE B 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 4954 not shown) Planarity restraints: 5679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY a 8 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO a 9 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO a 9 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO a 9 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU a 152 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO a 153 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO a 153 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 153 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B 579 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.017 5.00e-02 4.00e+02 ... (remaining 5676 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 444 2.66 - 3.22: 28974 3.22 - 3.78: 47414 3.78 - 4.34: 69447 4.34 - 4.90: 113094 Nonbonded interactions: 259373 Sorted by model distance: nonbonded pdb=" O GLN B 755 " pdb=" OG SER C 968 " model vdw 2.096 3.040 nonbonded pdb=" OG1 THR a 136 " pdb=" O MET a 139 " model vdw 2.101 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.102 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR C 912 " pdb=" OD1 ASN C 914 " model vdw 2.115 3.040 ... (remaining 259368 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' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147)) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147)) selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'b' selection = chain 'd' } 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: 4.030 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.100 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4535 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 0.039 32224 Z= 0.145 Angle : 0.542 6.626 43890 Z= 0.294 Chirality : 0.043 0.168 4957 Planarity : 0.002 0.037 5679 Dihedral : 7.786 89.963 11488 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.06 % Allowed : 0.74 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.11), residues: 3992 helix: -1.48 (0.14), residues: 701 sheet: -1.92 (0.14), residues: 1066 loop : -2.44 (0.11), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 78 TYR 0.013 0.001 TYR C 873 PHE 0.014 0.001 PHE C 490 TRP 0.009 0.001 TRP A 152 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00287 (32178) covalent geometry : angle 0.54244 (43798) SS BOND : bond 0.00145 ( 46) SS BOND : angle 0.55836 ( 92) hydrogen bonds : bond 0.24979 ( 1125) hydrogen bonds : angle 10.12582 ( 3246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1114 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.3413 (t0) cc_final: 0.2819 (t0) REVERT: A 224 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5558 (mt-10) REVERT: A 353 TRP cc_start: 0.3667 (p90) cc_final: 0.3301 (p90) REVERT: A 395 VAL cc_start: 0.6867 (t) cc_final: 0.6651 (t) REVERT: A 449 TYR cc_start: 0.2946 (m-80) cc_final: 0.2649 (m-80) REVERT: A 612 TYR cc_start: 0.6968 (m-80) cc_final: 0.6505 (m-80) REVERT: A 724 THR cc_start: 0.6869 (m) cc_final: 0.5989 (t) REVERT: A 736 VAL cc_start: 0.7880 (t) cc_final: 0.7564 (p) REVERT: A 805 ILE cc_start: 0.9427 (pt) cc_final: 0.9222 (pt) REVERT: A 901 GLN cc_start: 0.7896 (mt0) cc_final: 0.7537 (tt0) REVERT: A 907 ASN cc_start: 0.7780 (m-40) cc_final: 0.6938 (m-40) REVERT: A 998 THR cc_start: 0.8323 (p) cc_final: 0.8022 (t) REVERT: A 1007 TYR cc_start: 0.7767 (t80) cc_final: 0.6999 (t80) REVERT: A 1033 VAL cc_start: 0.8787 (t) cc_final: 0.8323 (t) REVERT: A 1041 ASP cc_start: 0.7022 (t0) cc_final: 0.6794 (t0) REVERT: A 1081 ILE cc_start: 0.8031 (pp) cc_final: 0.7634 (pp) REVERT: B 141 LEU cc_start: 0.7347 (mt) cc_final: 0.7103 (mp) REVERT: B 572 THR cc_start: 0.7209 (p) cc_final: 0.6731 (m) REVERT: B 592 PHE cc_start: 0.5979 (t80) cc_final: 0.5173 (t80) REVERT: B 645 THR cc_start: 0.7829 (p) cc_final: 0.7133 (p) REVERT: B 736 VAL cc_start: 0.7747 (t) cc_final: 0.7362 (t) REVERT: B 753 LEU cc_start: 0.7413 (tp) cc_final: 0.6667 (tp) REVERT: B 822 LEU cc_start: 0.8577 (mt) cc_final: 0.7685 (mt) REVERT: B 888 PHE cc_start: 0.8014 (p90) cc_final: 0.7804 (p90) REVERT: B 1027 THR cc_start: 0.8362 (m) cc_final: 0.7966 (t) REVERT: B 1051 SER cc_start: 0.8008 (m) cc_final: 0.7794 (p) REVERT: B 1054 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7541 (mm-40) REVERT: B 1061 VAL cc_start: 0.9041 (t) cc_final: 0.8707 (p) REVERT: B 1141 LEU cc_start: 0.5650 (mp) cc_final: 0.4932 (mt) REVERT: C 64 TRP cc_start: 0.3613 (t60) cc_final: 0.3379 (t60) REVERT: C 196 ASN cc_start: 0.7477 (t0) cc_final: 0.6793 (m-40) REVERT: C 197 ILE cc_start: 0.6720 (mt) cc_final: 0.6508 (pt) REVERT: C 864 LEU cc_start: 0.8153 (tp) cc_final: 0.7561 (tp) REVERT: C 882 ILE cc_start: 0.8570 (mt) cc_final: 0.7885 (mt) REVERT: C 907 ASN cc_start: 0.8030 (m-40) cc_final: 0.7799 (m-40) REVERT: C 993 ILE cc_start: 0.7259 (mt) cc_final: 0.6981 (mt) REVERT: C 1023 ASN cc_start: 0.7040 (m-40) cc_final: 0.6621 (t0) REVERT: a 52 TRP cc_start: 0.3491 (m-10) cc_final: 0.3288 (m-10) REVERT: a 90 THR cc_start: 0.2614 (m) cc_final: 0.2392 (t) REVERT: a 139 MET cc_start: -0.1767 (mmm) cc_final: -0.3329 (tmm) REVERT: a 159 ASN cc_start: 0.2313 (m-40) cc_final: 0.1452 (t0) REVERT: b 110 ILE cc_start: 0.6098 (mm) cc_final: 0.5594 (mm) REVERT: c 113 VAL cc_start: 0.4807 (t) cc_final: 0.4563 (t) REVERT: c 144 CYS cc_start: -0.0627 (OUTLIER) cc_final: -0.2183 (p) REVERT: d 218 CYS cc_start: 0.5939 (t) cc_final: 0.5567 (t) outliers start: 2 outliers final: 0 residues processed: 1115 average time/residue: 0.2006 time to fit residues: 355.0606 Evaluate side-chains 524 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 969 ASN A1058 HIS B 125 ASN B 149 ASN B 188 ASN B 388 ASN B 606 ASN B 751 ASN B 901 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1010 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 544 ASN C 779 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1005 GLN C1011 GLN C1023 ASN C1101 HIS a 73 ASN a 102 HIS a 200 ASN ** b 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN b 160 GLN c 98 ASN d 57 ASN ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.127176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.107038 restraints weight = 131347.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.108509 restraints weight = 80095.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.108971 restraints weight = 49918.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.109263 restraints weight = 41088.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.109419 restraints weight = 37216.689| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32224 Z= 0.155 Angle : 0.586 11.145 43890 Z= 0.305 Chirality : 0.045 0.266 4957 Planarity : 0.004 0.079 5679 Dihedral : 3.696 19.611 4321 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.12), residues: 3992 helix: 0.11 (0.18), residues: 709 sheet: -1.07 (0.15), residues: 999 loop : -1.96 (0.11), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 577 TYR 0.022 0.002 TYR B 38 PHE 0.034 0.002 PHE B 823 TRP 0.019 0.001 TRP C 64 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00349 (32178) covalent geometry : angle 0.57768 (43798) SS BOND : bond 0.00513 ( 46) SS BOND : angle 2.22146 ( 92) hydrogen bonds : bond 0.05174 ( 1125) hydrogen bonds : angle 7.07443 ( 3246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 729 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7314 (mtt-85) cc_final: 0.6546 (mtt-85) REVERT: A 119 ILE cc_start: 0.8469 (mt) cc_final: 0.8039 (mt) REVERT: A 191 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7151 (mp0) REVERT: A 224 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7866 (mt-10) REVERT: A 354 ASN cc_start: 0.7536 (m110) cc_final: 0.6728 (t0) REVERT: A 724 THR cc_start: 0.7160 (m) cc_final: 0.6939 (t) REVERT: A 759 PHE cc_start: 0.6108 (t80) cc_final: 0.5358 (t80) REVERT: A 1009 THR cc_start: 0.9025 (m) cc_final: 0.8638 (p) REVERT: B 104 TRP cc_start: 0.5024 (m-90) cc_final: 0.4755 (m-90) REVERT: B 156 GLU cc_start: 0.5520 (mm-30) cc_final: 0.5205 (mt-10) REVERT: B 194 PHE cc_start: 0.5931 (m-10) cc_final: 0.5692 (m-10) REVERT: B 535 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7457 (pttt) REVERT: B 572 THR cc_start: 0.8390 (p) cc_final: 0.8157 (m) REVERT: B 645 THR cc_start: 0.8264 (p) cc_final: 0.7914 (p) REVERT: B 735 SER cc_start: 0.7445 (t) cc_final: 0.6419 (t) REVERT: B 822 LEU cc_start: 0.9148 (mt) cc_final: 0.8712 (mt) REVERT: B 921 LYS cc_start: 0.7719 (ptmt) cc_final: 0.6797 (mtmm) REVERT: B 1010 GLN cc_start: 0.8135 (mm110) cc_final: 0.7544 (tm-30) REVERT: B 1054 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8293 (mm-40) REVERT: B 1061 VAL cc_start: 0.9348 (t) cc_final: 0.9010 (p) REVERT: C 191 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6460 (mt-10) REVERT: C 196 ASN cc_start: 0.8018 (t0) cc_final: 0.7409 (m-40) REVERT: C 197 ILE cc_start: 0.7654 (mt) cc_final: 0.7377 (mt) REVERT: C 402 ILE cc_start: 0.8066 (tp) cc_final: 0.7783 (tp) REVERT: C 497 PHE cc_start: 0.4448 (m-10) cc_final: 0.4089 (m-10) REVERT: C 558 LYS cc_start: 0.6710 (mmtt) cc_final: 0.5822 (mtmt) REVERT: C 611 LEU cc_start: 0.9387 (tp) cc_final: 0.9112 (tt) REVERT: C 777 ASN cc_start: 0.8839 (m-40) cc_final: 0.8599 (m-40) REVERT: C 782 PHE cc_start: 0.7723 (m-80) cc_final: 0.7406 (m-10) REVERT: C 882 ILE cc_start: 0.8765 (mt) cc_final: 0.8552 (mt) REVERT: C 933 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8484 (tppt) REVERT: C 953 ASN cc_start: 0.7704 (m-40) cc_final: 0.7404 (m-40) REVERT: C 977 LEU cc_start: 0.8318 (mm) cc_final: 0.7903 (mm) REVERT: C 1023 ASN cc_start: 0.8323 (m110) cc_final: 0.7638 (t0) REVERT: C 1092 GLU cc_start: 0.7126 (pp20) cc_final: 0.6800 (pp20) REVERT: C 1112 PRO cc_start: 0.7785 (Cg_exo) cc_final: 0.7579 (Cg_endo) REVERT: a 106 PHE cc_start: 0.2705 (m-80) cc_final: 0.1817 (m-80) REVERT: a 139 MET cc_start: -0.1819 (mmm) cc_final: -0.3095 (tmm) REVERT: a 159 ASN cc_start: 0.4361 (m-40) cc_final: 0.3382 (t0) REVERT: b 110 ILE cc_start: 0.7190 (mm) cc_final: 0.6206 (mt) REVERT: c 46 GLU cc_start: 0.5455 (mm-30) cc_final: 0.5001 (mm-30) REVERT: c 94 TYR cc_start: 0.2846 (m-80) cc_final: 0.2241 (m-10) outliers start: 5 outliers final: 0 residues processed: 729 average time/residue: 0.1851 time to fit residues: 220.3630 Evaluate side-chains 448 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 48 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 263 optimal weight: 0.5980 chunk 397 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A1058 HIS B 81 ASN B 317 ASN B 774 GLN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 901 GLN B 935 GLN B 954 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN a 102 HIS b 41 GLN b 160 GLN b 214 ASN c 39 GLN c 200 ASN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.124726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.104190 restraints weight = 131584.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.105621 restraints weight = 79668.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.106125 restraints weight = 52014.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.107074 restraints weight = 38836.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.106879 restraints weight = 34810.270| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 32224 Z= 0.172 Angle : 0.602 11.146 43890 Z= 0.313 Chirality : 0.045 0.254 4957 Planarity : 0.005 0.113 5679 Dihedral : 4.153 20.857 4321 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.08 % Allowed : 2.44 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.12), residues: 3992 helix: 0.32 (0.19), residues: 727 sheet: -0.85 (0.15), residues: 1028 loop : -1.75 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 273 TYR 0.024 0.002 TYR B 313 PHE 0.037 0.002 PHE c 80 TRP 0.028 0.002 TRP B 64 HIS 0.007 0.001 HIS d 202 Details of bonding type rmsd covalent geometry : bond 0.00384 (32178) covalent geometry : angle 0.59646 (43798) SS BOND : bond 0.00465 ( 46) SS BOND : angle 1.92087 ( 92) hydrogen bonds : bond 0.04420 ( 1125) hydrogen bonds : angle 6.56267 ( 3246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 652 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7263 (p) cc_final: 0.7058 (m) REVERT: A 58 PHE cc_start: 0.6377 (m-10) cc_final: 0.6164 (m-10) REVERT: A 119 ILE cc_start: 0.8122 (mt) cc_final: 0.7819 (tt) REVERT: A 191 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7020 (mp0) REVERT: A 224 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 354 ASN cc_start: 0.7553 (m110) cc_final: 0.6813 (t0) REVERT: A 867 ASP cc_start: 0.6945 (t0) cc_final: 0.6717 (t0) REVERT: A 976 VAL cc_start: 0.8456 (t) cc_final: 0.7539 (t) REVERT: A 1009 THR cc_start: 0.8907 (m) cc_final: 0.8706 (p) REVERT: A 1081 ILE cc_start: 0.9026 (pt) cc_final: 0.8814 (pt) REVERT: B 535 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7533 (pttm) REVERT: B 645 THR cc_start: 0.8206 (p) cc_final: 0.7798 (p) REVERT: B 739 THR cc_start: 0.8221 (p) cc_final: 0.7923 (p) REVERT: B 742 ILE cc_start: 0.9289 (mt) cc_final: 0.8590 (mt) REVERT: B 819 GLU cc_start: 0.5493 (mt-10) cc_final: 0.5055 (mt-10) REVERT: B 867 ASP cc_start: 0.7168 (p0) cc_final: 0.6948 (p0) REVERT: B 900 MET cc_start: 0.8013 (mmm) cc_final: 0.7534 (mmp) REVERT: B 921 LYS cc_start: 0.7738 (ptmt) cc_final: 0.7261 (ttpp) REVERT: B 1054 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8392 (mm-40) REVERT: B 1061 VAL cc_start: 0.9295 (t) cc_final: 0.9020 (p) REVERT: C 196 ASN cc_start: 0.8136 (t0) cc_final: 0.7484 (m-40) REVERT: C 197 ILE cc_start: 0.7571 (mt) cc_final: 0.7219 (mt) REVERT: C 238 PHE cc_start: 0.7901 (p90) cc_final: 0.7563 (p90) REVERT: C 275 PHE cc_start: 0.6680 (m-80) cc_final: 0.6464 (m-80) REVERT: C 506 GLN cc_start: 0.4762 (tp-100) cc_final: 0.3681 (tt0) REVERT: C 619 GLU cc_start: 0.6446 (tm-30) cc_final: 0.5873 (tm-30) REVERT: C 882 ILE cc_start: 0.8934 (mt) cc_final: 0.8658 (mt) REVERT: C 933 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8498 (tptt) REVERT: C 1023 ASN cc_start: 0.8197 (m110) cc_final: 0.7820 (t0) REVERT: C 1092 GLU cc_start: 0.7442 (pp20) cc_final: 0.6959 (pp20) REVERT: C 1112 PRO cc_start: 0.7946 (Cg_exo) cc_final: 0.7520 (Cg_endo) REVERT: a 106 PHE cc_start: 0.2577 (m-80) cc_final: 0.1665 (m-80) REVERT: a 139 MET cc_start: -0.1509 (mmm) cc_final: -0.2935 (tmm) REVERT: a 159 ASN cc_start: 0.3960 (m-40) cc_final: 0.3498 (m-40) REVERT: a 211 ASP cc_start: 0.6888 (m-30) cc_final: 0.4962 (p0) REVERT: b 110 ILE cc_start: 0.7016 (mm) cc_final: 0.6462 (mp) REVERT: c 82 MET cc_start: -0.5168 (mmp) cc_final: -0.5436 (mmm) REVERT: d 218 CYS cc_start: 0.4330 (t) cc_final: 0.4024 (t) outliers start: 3 outliers final: 0 residues processed: 653 average time/residue: 0.1885 time to fit residues: 201.2355 Evaluate side-chains 423 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 286 optimal weight: 0.7980 chunk 273 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 108 optimal weight: 0.4980 chunk 292 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 207 HIS A 774 GLN A 907 ASN A 919 ASN A 953 ASN B 388 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 901 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 544 ASN C 856 ASN C 907 ASN C 965 GLN C1054 GLN b 41 GLN b 160 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.124089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103533 restraints weight = 132337.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.104996 restraints weight = 81196.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.105603 restraints weight = 51660.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.106928 restraints weight = 36849.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.106720 restraints weight = 31272.787| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32224 Z= 0.146 Angle : 0.573 13.897 43890 Z= 0.297 Chirality : 0.045 0.380 4957 Planarity : 0.004 0.092 5679 Dihedral : 4.253 21.269 4321 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.52 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.12), residues: 3992 helix: 0.38 (0.19), residues: 725 sheet: -0.80 (0.15), residues: 1061 loop : -1.61 (0.12), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 273 TYR 0.021 0.002 TYR B 313 PHE 0.026 0.002 PHE C 306 TRP 0.030 0.002 TRP B 64 HIS 0.006 0.001 HIS d 202 Details of bonding type rmsd covalent geometry : bond 0.00324 (32178) covalent geometry : angle 0.57154 (43798) SS BOND : bond 0.00463 ( 46) SS BOND : angle 1.16753 ( 92) hydrogen bonds : bond 0.04047 ( 1125) hydrogen bonds : angle 6.24494 ( 3246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 610 time to evaluate : 1.163 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: A 42 VAL cc_start: 0.7387 (p) cc_final: 0.7034 (m) REVERT: A 119 ILE cc_start: 0.8222 (mt) cc_final: 0.7881 (tt) REVERT: A 191 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6778 (mp0) REVERT: A 224 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 293 LEU cc_start: 0.7642 (tp) cc_final: 0.7394 (tp) REVERT: A 354 ASN cc_start: 0.7441 (m110) cc_final: 0.6781 (t0) REVERT: A 758 SER cc_start: 0.8089 (t) cc_final: 0.7878 (t) REVERT: A 867 ASP cc_start: 0.6723 (t0) cc_final: 0.6518 (t0) REVERT: A 907 ASN cc_start: 0.8318 (m110) cc_final: 0.7563 (m-40) REVERT: A 969 ASN cc_start: 0.8146 (m-40) cc_final: 0.7676 (m110) REVERT: A 1049 LEU cc_start: 0.8911 (mt) cc_final: 0.8165 (mt) REVERT: B 535 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7424 (pttm) REVERT: B 599 THR cc_start: 0.8083 (p) cc_final: 0.7699 (p) REVERT: B 645 THR cc_start: 0.8368 (p) cc_final: 0.7987 (p) REVERT: B 921 LYS cc_start: 0.7734 (ptmt) cc_final: 0.7273 (ttpp) REVERT: B 1029 MET cc_start: 0.7528 (ttm) cc_final: 0.7280 (ttm) REVERT: B 1054 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8585 (mm-40) REVERT: B 1061 VAL cc_start: 0.9347 (t) cc_final: 0.9092 (p) REVERT: C 191 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6399 (mt-10) REVERT: C 238 PHE cc_start: 0.7807 (p90) cc_final: 0.7590 (p90) REVERT: C 408 ARG cc_start: 0.6744 (mpt180) cc_final: 0.6534 (mpt180) REVERT: C 558 LYS cc_start: 0.6660 (mmtt) cc_final: 0.5679 (mtmt) REVERT: C 619 GLU cc_start: 0.6193 (tm-30) cc_final: 0.5823 (tm-30) REVERT: C 777 ASN cc_start: 0.8750 (m-40) cc_final: 0.8516 (m110) REVERT: C 917 TYR cc_start: 0.8296 (m-80) cc_final: 0.7926 (m-80) REVERT: C 933 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8470 (tptt) REVERT: C 977 LEU cc_start: 0.8075 (mm) cc_final: 0.7797 (mm) REVERT: C 1023 ASN cc_start: 0.8258 (m110) cc_final: 0.7669 (t0) REVERT: C 1055 SER cc_start: 0.8583 (t) cc_final: 0.8381 (t) REVERT: C 1092 GLU cc_start: 0.7474 (pp20) cc_final: 0.6896 (pp20) REVERT: C 1112 PRO cc_start: 0.7789 (Cg_exo) cc_final: 0.7548 (Cg_endo) REVERT: a 106 PHE cc_start: 0.2800 (m-80) cc_final: 0.2075 (m-80) REVERT: a 139 MET cc_start: -0.1583 (mmm) cc_final: -0.3157 (tmm) REVERT: a 152 GLU cc_start: 0.4222 (mp0) cc_final: 0.2202 (tp30) REVERT: a 159 ASN cc_start: 0.4074 (m-40) cc_final: 0.3664 (m-40) REVERT: a 211 ASP cc_start: 0.6548 (m-30) cc_final: 0.4743 (p0) REVERT: b 72 ARG cc_start: 0.3939 (mmt180) cc_final: 0.3643 (mmt180) REVERT: b 110 ILE cc_start: 0.6982 (mm) cc_final: 0.6574 (mp) REVERT: d 179 MET cc_start: 0.0713 (mtt) cc_final: -0.0123 (ppp) REVERT: d 218 CYS cc_start: 0.4352 (t) cc_final: 0.4105 (t) outliers start: 2 outliers final: 1 residues processed: 612 average time/residue: 0.1732 time to fit residues: 177.1407 Evaluate side-chains 422 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 275 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 308 optimal weight: 0.1980 chunk 184 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 487 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 804 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 450 ASN C 544 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.124294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102666 restraints weight = 130664.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104278 restraints weight = 76337.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.105297 restraints weight = 50162.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.105944 restraints weight = 36339.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.106308 restraints weight = 28859.409| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32224 Z= 0.125 Angle : 0.546 11.322 43890 Z= 0.282 Chirality : 0.044 0.328 4957 Planarity : 0.004 0.087 5679 Dihedral : 4.186 19.260 4321 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.06 % Allowed : 1.39 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 3992 helix: 0.50 (0.19), residues: 724 sheet: -0.74 (0.15), residues: 1084 loop : -1.49 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 65 TYR 0.019 0.001 TYR B 904 PHE 0.031 0.002 PHE c 80 TRP 0.024 0.002 TRP C 886 HIS 0.004 0.001 HIS d 202 Details of bonding type rmsd covalent geometry : bond 0.00281 (32178) covalent geometry : angle 0.54521 (43798) SS BOND : bond 0.00350 ( 46) SS BOND : angle 0.93276 ( 92) hydrogen bonds : bond 0.03728 ( 1125) hydrogen bonds : angle 6.03663 ( 3246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 607 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.8091 (mt) cc_final: 0.7807 (tt) REVERT: A 191 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6845 (mp0) REVERT: A 224 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 310 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7503 (ptmm) REVERT: A 354 ASN cc_start: 0.7477 (m110) cc_final: 0.6811 (t0) REVERT: A 598 ILE cc_start: 0.9053 (mp) cc_final: 0.8786 (mp) REVERT: A 758 SER cc_start: 0.7690 (t) cc_final: 0.7403 (t) REVERT: A 869 MET cc_start: 0.7412 (mtm) cc_final: 0.7109 (mtm) REVERT: A 962 LEU cc_start: 0.8356 (tp) cc_final: 0.7671 (tp) REVERT: A 969 ASN cc_start: 0.7824 (m-40) cc_final: 0.7419 (m110) REVERT: A 1081 ILE cc_start: 0.8962 (pt) cc_final: 0.8759 (pt) REVERT: A 1128 VAL cc_start: 0.8058 (m) cc_final: 0.7786 (t) REVERT: B 535 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7409 (pttm) REVERT: B 599 THR cc_start: 0.7990 (p) cc_final: 0.7753 (p) REVERT: B 645 THR cc_start: 0.8312 (p) cc_final: 0.7957 (p) REVERT: B 819 GLU cc_start: 0.5518 (mt-10) cc_final: 0.4898 (mt-10) REVERT: B 921 LYS cc_start: 0.7672 (ptmt) cc_final: 0.7201 (ttpp) REVERT: B 938 LEU cc_start: 0.7145 (mt) cc_final: 0.6821 (mt) REVERT: B 1001 LEU cc_start: 0.8418 (tp) cc_final: 0.8053 (tt) REVERT: B 1061 VAL cc_start: 0.9297 (t) cc_final: 0.9032 (p) REVERT: C 28 TYR cc_start: 0.6465 (m-10) cc_final: 0.6220 (m-80) REVERT: C 38 TYR cc_start: 0.8423 (m-80) cc_final: 0.8100 (m-10) REVERT: C 170 TYR cc_start: 0.7146 (t80) cc_final: 0.6352 (t80) REVERT: C 191 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6189 (mt-10) REVERT: C 215 ASP cc_start: 0.8203 (m-30) cc_final: 0.7844 (m-30) REVERT: C 558 LYS cc_start: 0.6667 (mmtt) cc_final: 0.5661 (mtmt) REVERT: C 619 GLU cc_start: 0.6241 (tm-30) cc_final: 0.5902 (tm-30) REVERT: C 904 TYR cc_start: 0.7760 (m-10) cc_final: 0.7453 (m-10) REVERT: C 933 LYS cc_start: 0.8963 (ttpt) cc_final: 0.8494 (tptt) REVERT: C 1023 ASN cc_start: 0.7707 (m110) cc_final: 0.7368 (t0) REVERT: C 1055 SER cc_start: 0.8565 (t) cc_final: 0.8315 (t) REVERT: C 1112 PRO cc_start: 0.7700 (Cg_exo) cc_final: 0.7378 (Cg_endo) REVERT: a 106 PHE cc_start: 0.2604 (m-80) cc_final: 0.2150 (m-80) REVERT: a 139 MET cc_start: -0.1601 (mmm) cc_final: -0.3148 (tmm) REVERT: a 152 GLU cc_start: 0.4062 (mp0) cc_final: 0.1959 (tp30) REVERT: a 159 ASN cc_start: 0.4147 (m-40) cc_final: 0.3796 (m-40) REVERT: a 163 LEU cc_start: 0.4040 (mm) cc_final: 0.3645 (mt) REVERT: b 72 ARG cc_start: 0.3906 (mmt180) cc_final: 0.3637 (mmt180) REVERT: b 108 LEU cc_start: 0.6490 (tp) cc_final: 0.5676 (mp) REVERT: b 110 ILE cc_start: 0.6967 (mm) cc_final: 0.6660 (mp) REVERT: c 82 MET cc_start: -0.4565 (mmp) cc_final: -0.4931 (mmm) REVERT: d 179 MET cc_start: 0.1163 (mtt) cc_final: 0.0132 (ppp) REVERT: d 218 CYS cc_start: 0.4667 (t) cc_final: 0.4319 (t) outliers start: 2 outliers final: 0 residues processed: 608 average time/residue: 0.1751 time to fit residues: 178.4068 Evaluate side-chains 418 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 346 optimal weight: 0.9990 chunk 379 optimal weight: 10.0000 chunk 394 optimal weight: 3.9990 chunk 369 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 116 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 388 ASN A 907 ASN A 953 ASN A1119 ASN B 493 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 655 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 GLN b 46 GLN b 160 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.118946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.098955 restraints weight = 132844.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.099846 restraints weight = 84996.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.100401 restraints weight = 62192.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.101450 restraints weight = 43577.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.101495 restraints weight = 33385.348| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 32224 Z= 0.292 Angle : 0.775 12.448 43890 Z= 0.407 Chirality : 0.049 0.285 4957 Planarity : 0.006 0.093 5679 Dihedral : 5.502 25.545 4321 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.06 % Allowed : 2.10 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.12), residues: 3992 helix: -0.21 (0.18), residues: 734 sheet: -0.86 (0.15), residues: 1059 loop : -1.82 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 408 TYR 0.037 0.003 TYR A 741 PHE 0.030 0.003 PHE A 338 TRP 0.023 0.003 TRP a 158 HIS 0.011 0.002 HIS c 203 Details of bonding type rmsd covalent geometry : bond 0.00639 (32178) covalent geometry : angle 0.77275 (43798) SS BOND : bond 0.00527 ( 46) SS BOND : angle 1.44177 ( 92) hydrogen bonds : bond 0.04927 ( 1125) hydrogen bonds : angle 6.74661 ( 3246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 557 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7750 (mt-10) cc_final: 0.6752 (mp0) REVERT: A 224 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 354 ASN cc_start: 0.7514 (m110) cc_final: 0.6686 (t0) REVERT: A 408 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7606 (tpm170) REVERT: A 598 ILE cc_start: 0.9135 (mp) cc_final: 0.8733 (mm) REVERT: A 756 TYR cc_start: 0.7124 (m-80) cc_final: 0.6831 (m-80) REVERT: A 819 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 907 ASN cc_start: 0.8261 (m110) cc_final: 0.7992 (m-40) REVERT: A 962 LEU cc_start: 0.9058 (tp) cc_final: 0.8693 (tp) REVERT: A 969 ASN cc_start: 0.8371 (m-40) cc_final: 0.8163 (m-40) REVERT: A 1081 ILE cc_start: 0.9126 (pt) cc_final: 0.8912 (pt) REVERT: B 101 ILE cc_start: 0.7652 (tt) cc_final: 0.7429 (tt) REVERT: B 535 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7707 (pttm) REVERT: B 819 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6535 (mt-10) REVERT: B 820 ASP cc_start: 0.7368 (t0) cc_final: 0.6610 (t0) REVERT: B 921 LYS cc_start: 0.7890 (ptmt) cc_final: 0.7420 (ttpp) REVERT: C 170 TYR cc_start: 0.7664 (t80) cc_final: 0.7134 (t80) REVERT: C 191 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6549 (mt-10) REVERT: C 269 TYR cc_start: 0.7476 (m-10) cc_final: 0.7082 (m-10) REVERT: C 735 SER cc_start: 0.8002 (t) cc_final: 0.7712 (m) REVERT: C 861 LEU cc_start: 0.8791 (mt) cc_final: 0.8575 (mp) REVERT: C 875 SER cc_start: 0.8543 (p) cc_final: 0.8297 (m) REVERT: C 882 ILE cc_start: 0.9083 (mp) cc_final: 0.8858 (mp) REVERT: C 933 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8542 (tptt) REVERT: C 1054 GLN cc_start: 0.8247 (mp-120) cc_final: 0.7832 (mm-40) REVERT: C 1055 SER cc_start: 0.9077 (t) cc_final: 0.8861 (t) REVERT: C 1092 GLU cc_start: 0.7356 (pp20) cc_final: 0.6883 (pp20) REVERT: a 152 GLU cc_start: 0.4982 (mp0) cc_final: 0.2681 (tp30) outliers start: 2 outliers final: 0 residues processed: 559 average time/residue: 0.1752 time to fit residues: 163.0421 Evaluate side-chains 393 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 166 optimal weight: 2.9990 chunk 383 optimal weight: 9.9990 chunk 390 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 chunk 68 optimal weight: 0.0770 chunk 255 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1011 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 218 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B 901 GLN B1135 ASN C 544 ASN C 556 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 HIS ** b 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.120142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.100519 restraints weight = 133875.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.101527 restraints weight = 80490.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.101960 restraints weight = 55000.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.102389 restraints weight = 44293.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.102530 restraints weight = 40964.776| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32224 Z= 0.195 Angle : 0.656 12.276 43890 Z= 0.344 Chirality : 0.047 0.304 4957 Planarity : 0.005 0.091 5679 Dihedral : 5.139 23.452 4321 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.03 % Allowed : 1.33 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.13), residues: 3992 helix: -0.06 (0.18), residues: 721 sheet: -0.81 (0.16), residues: 1045 loop : -1.77 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1039 TYR 0.020 0.002 TYR B 904 PHE 0.034 0.002 PHE B 823 TRP 0.019 0.002 TRP C 886 HIS 0.010 0.001 HIS d 193 Details of bonding type rmsd covalent geometry : bond 0.00439 (32178) covalent geometry : angle 0.65372 (43798) SS BOND : bond 0.00473 ( 46) SS BOND : angle 1.45093 ( 92) hydrogen bonds : bond 0.04258 ( 1125) hydrogen bonds : angle 6.51406 ( 3246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 550 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7877 (mt-10) cc_final: 0.6814 (mp0) REVERT: A 224 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7782 (mt-10) REVERT: A 299 THR cc_start: 0.8827 (m) cc_final: 0.8603 (p) REVERT: A 354 ASN cc_start: 0.7546 (m110) cc_final: 0.6658 (t0) REVERT: A 408 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7613 (tpm170) REVERT: A 568 ASP cc_start: 0.8318 (p0) cc_final: 0.8038 (p0) REVERT: A 598 ILE cc_start: 0.9148 (mp) cc_final: 0.8765 (mm) REVERT: A 756 TYR cc_start: 0.7047 (m-80) cc_final: 0.6679 (m-80) REVERT: A 819 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 901 GLN cc_start: 0.8074 (tt0) cc_final: 0.7759 (tt0) REVERT: A 1049 LEU cc_start: 0.9242 (mt) cc_final: 0.9000 (mt) REVERT: A 1081 ILE cc_start: 0.9138 (pt) cc_final: 0.8936 (pt) REVERT: B 820 ASP cc_start: 0.7444 (t0) cc_final: 0.7086 (t0) REVERT: B 921 LYS cc_start: 0.7822 (ptmt) cc_final: 0.7375 (ttpp) REVERT: B 1019 ARG cc_start: 0.7864 (ptp-110) cc_final: 0.7283 (ptp90) REVERT: C 38 TYR cc_start: 0.8561 (m-80) cc_final: 0.8280 (m-80) REVERT: C 170 TYR cc_start: 0.7693 (t80) cc_final: 0.7259 (t80) REVERT: C 191 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6400 (mt-10) REVERT: C 275 PHE cc_start: 0.7262 (m-80) cc_final: 0.6882 (m-80) REVERT: C 592 PHE cc_start: 0.7724 (t80) cc_final: 0.7468 (t80) REVERT: C 611 LEU cc_start: 0.9349 (tp) cc_final: 0.9141 (tt) REVERT: C 864 LEU cc_start: 0.8813 (tp) cc_final: 0.8390 (tt) REVERT: C 875 SER cc_start: 0.8427 (p) cc_final: 0.8180 (m) REVERT: C 933 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8480 (tptt) REVERT: C 1018 ILE cc_start: 0.9186 (tt) cc_final: 0.8924 (tt) REVERT: C 1054 GLN cc_start: 0.8395 (mp-120) cc_final: 0.7800 (mm-40) REVERT: C 1055 SER cc_start: 0.8929 (t) cc_final: 0.8705 (t) REVERT: C 1092 GLU cc_start: 0.7335 (pp20) cc_final: 0.6884 (pp20) REVERT: a 51 MET cc_start: 0.2750 (ptp) cc_final: 0.2402 (ptm) REVERT: a 139 MET cc_start: -0.1637 (mmm) cc_final: -0.3280 (tmm) REVERT: b 108 LEU cc_start: 0.6900 (tp) cc_final: 0.6074 (mp) REVERT: c 38 ARG cc_start: 0.4540 (ptt180) cc_final: 0.3809 (ptm-80) outliers start: 1 outliers final: 1 residues processed: 551 average time/residue: 0.1787 time to fit residues: 164.5400 Evaluate side-chains 398 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 400 optimal weight: 0.7980 chunk 229 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 308 optimal weight: 0.7980 chunk 187 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 339 optimal weight: 0.0670 chunk 368 optimal weight: 0.9990 chunk 377 optimal weight: 7.9990 chunk 162 optimal weight: 0.0670 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1011 GLN A1036 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1135 ASN b 41 GLN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 128 GLN ** d 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.122143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.102233 restraints weight = 130128.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.103260 restraints weight = 84051.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.103385 restraints weight = 60955.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.103907 restraints weight = 47975.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.103969 restraints weight = 41504.774| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32224 Z= 0.120 Angle : 0.586 10.621 43890 Z= 0.302 Chirality : 0.045 0.290 4957 Planarity : 0.004 0.091 5679 Dihedral : 4.576 21.371 4321 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.08 % Allowed : 0.48 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 3992 helix: 0.42 (0.19), residues: 702 sheet: -0.71 (0.16), residues: 1055 loop : -1.64 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 815 TYR 0.030 0.001 TYR A 741 PHE 0.036 0.002 PHE c 80 TRP 0.023 0.001 TRP A 353 HIS 0.005 0.001 HIS a 35 Details of bonding type rmsd covalent geometry : bond 0.00272 (32178) covalent geometry : angle 0.58358 (43798) SS BOND : bond 0.00316 ( 46) SS BOND : angle 1.28978 ( 92) hydrogen bonds : bond 0.03703 ( 1125) hydrogen bonds : angle 6.09263 ( 3246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 596 time to evaluate : 0.997 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: A 191 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6859 (mp0) REVERT: A 224 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 297 SER cc_start: 0.8764 (m) cc_final: 0.8459 (m) REVERT: A 353 TRP cc_start: 0.4172 (p90) cc_final: 0.3684 (p90) REVERT: A 354 ASN cc_start: 0.7427 (m110) cc_final: 0.6748 (t0) REVERT: A 408 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7453 (ttp80) REVERT: A 568 ASP cc_start: 0.8323 (p0) cc_final: 0.8039 (p0) REVERT: A 756 TYR cc_start: 0.6714 (m-80) cc_final: 0.6372 (m-80) REVERT: A 758 SER cc_start: 0.7853 (t) cc_final: 0.7574 (t) REVERT: A 819 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 969 ASN cc_start: 0.8046 (m-40) cc_final: 0.7388 (m110) REVERT: A 1013 ILE cc_start: 0.9108 (mt) cc_final: 0.8900 (mm) REVERT: A 1081 ILE cc_start: 0.9065 (pt) cc_final: 0.8678 (pt) REVERT: B 101 ILE cc_start: 0.7976 (tt) cc_final: 0.7667 (tt) REVERT: B 535 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7788 (pttp) REVERT: B 819 GLU cc_start: 0.6342 (mt-10) cc_final: 0.5769 (mt-10) REVERT: B 820 ASP cc_start: 0.7106 (t0) cc_final: 0.6415 (t0) REVERT: B 921 LYS cc_start: 0.7694 (ptmt) cc_final: 0.7195 (ttpp) REVERT: B 1019 ARG cc_start: 0.7783 (ptp-110) cc_final: 0.7272 (ptp90) REVERT: B 1050 MET cc_start: 0.6747 (ptp) cc_final: 0.6461 (ptm) REVERT: B 1077 THR cc_start: 0.7576 (t) cc_final: 0.7227 (t) REVERT: C 170 TYR cc_start: 0.7453 (t80) cc_final: 0.7042 (t80) REVERT: C 191 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6109 (mt-10) REVERT: C 238 PHE cc_start: 0.7399 (p90) cc_final: 0.7091 (p90) REVERT: C 275 PHE cc_start: 0.7201 (m-80) cc_final: 0.6952 (m-80) REVERT: C 864 LEU cc_start: 0.8657 (tp) cc_final: 0.8224 (tt) REVERT: C 875 SER cc_start: 0.8307 (p) cc_final: 0.7843 (m) REVERT: C 933 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8371 (tptt) REVERT: C 1023 ASN cc_start: 0.7654 (m110) cc_final: 0.7443 (m110) REVERT: C 1061 VAL cc_start: 0.8865 (t) cc_final: 0.8619 (t) REVERT: a 139 MET cc_start: -0.1838 (mmm) cc_final: -0.3326 (tmm) REVERT: a 152 GLU cc_start: 0.4805 (mp0) cc_final: 0.2231 (tp30) REVERT: b 108 LEU cc_start: 0.6695 (tp) cc_final: 0.5931 (mp) REVERT: c 38 ARG cc_start: 0.4366 (ptt180) cc_final: 0.3605 (ptm-80) REVERT: c 82 MET cc_start: -0.4649 (mmp) cc_final: -0.5090 (mmm) outliers start: 3 outliers final: 0 residues processed: 598 average time/residue: 0.1825 time to fit residues: 179.2873 Evaluate side-chains 419 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 268 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 363 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 295 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 398 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 145 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN b 41 GLN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.121984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101945 restraints weight = 129357.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.103070 restraints weight = 79672.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.103336 restraints weight = 63565.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.103761 restraints weight = 47604.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.104020 restraints weight = 41595.822| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.6864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32224 Z= 0.125 Angle : 0.594 11.218 43890 Z= 0.306 Chirality : 0.045 0.312 4957 Planarity : 0.004 0.091 5679 Dihedral : 4.523 19.997 4321 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.06 % Allowed : 0.34 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 3992 helix: 0.51 (0.19), residues: 690 sheet: -0.64 (0.16), residues: 1061 loop : -1.57 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 983 TYR 0.031 0.002 TYR A 741 PHE 0.029 0.002 PHE C 592 TRP 0.028 0.001 TRP a 52 HIS 0.022 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00285 (32178) covalent geometry : angle 0.59215 (43798) SS BOND : bond 0.00327 ( 46) SS BOND : angle 1.27251 ( 92) hydrogen bonds : bond 0.03688 ( 1125) hydrogen bonds : angle 6.03718 ( 3246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 553 time to evaluate : 1.169 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: A 42 VAL cc_start: 0.7345 (p) cc_final: 0.6938 (m) REVERT: A 191 GLU cc_start: 0.7650 (mt-10) cc_final: 0.6671 (mp0) REVERT: A 294 ASP cc_start: 0.7468 (p0) cc_final: 0.7266 (m-30) REVERT: A 353 TRP cc_start: 0.4113 (p90) cc_final: 0.3371 (p90) REVERT: A 354 ASN cc_start: 0.7365 (m110) cc_final: 0.6735 (t0) REVERT: A 408 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7448 (ttp80) REVERT: A 568 ASP cc_start: 0.8348 (p0) cc_final: 0.8052 (p0) REVERT: A 598 ILE cc_start: 0.9114 (mp) cc_final: 0.8735 (mm) REVERT: A 756 TYR cc_start: 0.6911 (m-80) cc_final: 0.6553 (m-10) REVERT: A 819 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7658 (mt-10) REVERT: A 855 PHE cc_start: 0.4346 (m-80) cc_final: 0.4010 (m-80) REVERT: A 969 ASN cc_start: 0.8047 (m-40) cc_final: 0.7336 (m110) REVERT: A 1013 ILE cc_start: 0.9041 (mt) cc_final: 0.8836 (mm) REVERT: A 1049 LEU cc_start: 0.9142 (mt) cc_final: 0.8798 (mt) REVERT: B 101 ILE cc_start: 0.7976 (tt) cc_final: 0.7752 (tt) REVERT: B 535 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7819 (pttp) REVERT: B 819 GLU cc_start: 0.6177 (mt-10) cc_final: 0.5694 (mt-10) REVERT: B 820 ASP cc_start: 0.7175 (t0) cc_final: 0.6408 (t0) REVERT: B 874 THR cc_start: 0.8340 (p) cc_final: 0.8133 (p) REVERT: B 921 LYS cc_start: 0.7643 (ptmt) cc_final: 0.7206 (ttpp) REVERT: C 170 TYR cc_start: 0.7458 (t80) cc_final: 0.7035 (t80) REVERT: C 191 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6108 (mt-10) REVERT: C 275 PHE cc_start: 0.7212 (m-80) cc_final: 0.6998 (m-80) REVERT: C 875 SER cc_start: 0.8191 (p) cc_final: 0.7759 (m) REVERT: C 933 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8345 (tptt) REVERT: C 1023 ASN cc_start: 0.7539 (m110) cc_final: 0.7335 (m110) REVERT: C 1055 SER cc_start: 0.8694 (t) cc_final: 0.8459 (t) REVERT: a 82 MET cc_start: -0.0888 (pmm) cc_final: -0.1102 (pmm) REVERT: a 139 MET cc_start: -0.1743 (mmm) cc_final: -0.3266 (tmm) REVERT: a 152 GLU cc_start: 0.4861 (mp0) cc_final: 0.2177 (tp30) REVERT: a 181 LEU cc_start: 0.4738 (tp) cc_final: 0.4506 (mt) REVERT: b 108 LEU cc_start: 0.6688 (tp) cc_final: 0.5936 (mp) REVERT: b 110 ILE cc_start: 0.6575 (mp) cc_final: 0.6297 (mp) REVERT: c 38 ARG cc_start: 0.4421 (ptt180) cc_final: 0.3671 (ptm-80) outliers start: 2 outliers final: 1 residues processed: 555 average time/residue: 0.1732 time to fit residues: 160.0173 Evaluate side-chains 419 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 326 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 213 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 chunk 400 optimal weight: 9.9990 chunk 336 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A 907 ASN A 919 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1119 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.121372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.101970 restraints weight = 130470.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.102962 restraints weight = 80587.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.103191 restraints weight = 56384.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.103517 restraints weight = 50468.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.103685 restraints weight = 43797.418| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.7064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32224 Z= 0.146 Angle : 0.614 10.954 43890 Z= 0.317 Chirality : 0.046 0.299 4957 Planarity : 0.004 0.092 5679 Dihedral : 4.663 21.663 4321 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3992 helix: 0.35 (0.19), residues: 690 sheet: -0.65 (0.16), residues: 1064 loop : -1.58 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 815 TYR 0.030 0.002 TYR A 741 PHE 0.027 0.002 PHE C 592 TRP 0.023 0.002 TRP C 64 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00332 (32178) covalent geometry : angle 0.61200 (43798) SS BOND : bond 0.00337 ( 46) SS BOND : angle 1.26232 ( 92) hydrogen bonds : bond 0.03789 ( 1125) hydrogen bonds : angle 6.05550 ( 3246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.003 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: A 42 VAL cc_start: 0.7299 (p) cc_final: 0.6899 (m) REVERT: A 191 GLU cc_start: 0.7858 (mt-10) cc_final: 0.6712 (mp0) REVERT: A 353 TRP cc_start: 0.4228 (p90) cc_final: 0.3458 (p90) REVERT: A 354 ASN cc_start: 0.7305 (m110) cc_final: 0.6840 (t0) REVERT: A 408 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7533 (tpm170) REVERT: A 568 ASP cc_start: 0.8320 (p0) cc_final: 0.8065 (p0) REVERT: A 598 ILE cc_start: 0.9179 (mp) cc_final: 0.8820 (mm) REVERT: A 756 TYR cc_start: 0.6927 (m-80) cc_final: 0.6570 (m-80) REVERT: A 855 PHE cc_start: 0.4659 (m-80) cc_final: 0.4334 (m-80) REVERT: A 867 ASP cc_start: 0.7147 (t0) cc_final: 0.6910 (t0) REVERT: B 535 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7885 (pttp) REVERT: B 819 GLU cc_start: 0.6456 (mt-10) cc_final: 0.5952 (mt-10) REVERT: B 820 ASP cc_start: 0.7529 (t0) cc_final: 0.6656 (t0) REVERT: B 874 THR cc_start: 0.8359 (p) cc_final: 0.8133 (p) REVERT: B 921 LYS cc_start: 0.7711 (ptmt) cc_final: 0.7304 (ttpp) REVERT: B 1077 THR cc_start: 0.7773 (t) cc_final: 0.7514 (t) REVERT: C 170 TYR cc_start: 0.7604 (t80) cc_final: 0.7198 (t80) REVERT: C 191 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6254 (mt-10) REVERT: C 497 PHE cc_start: 0.4250 (m-10) cc_final: 0.3364 (m-80) REVERT: C 875 SER cc_start: 0.8366 (p) cc_final: 0.7917 (m) REVERT: C 933 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8245 (tppt) REVERT: C 1055 SER cc_start: 0.8821 (t) cc_final: 0.8579 (t) REVERT: a 64 MET cc_start: 0.5295 (mmp) cc_final: 0.4510 (mtm) REVERT: a 82 MET cc_start: -0.1215 (pmm) cc_final: -0.1425 (pmm) REVERT: a 139 MET cc_start: -0.1756 (mmm) cc_final: -0.3309 (tmm) REVERT: b 108 LEU cc_start: 0.6786 (tp) cc_final: 0.6071 (mp) REVERT: c 38 ARG cc_start: 0.4596 (ptt180) cc_final: 0.3847 (ptm-80) REVERT: c 80 PHE cc_start: 0.0867 (t80) cc_final: -0.0432 (t80) REVERT: d 142 ASN cc_start: 0.3999 (m110) cc_final: 0.3085 (t0) outliers start: 0 outliers final: 0 residues processed: 558 average time/residue: 0.1762 time to fit residues: 164.5320 Evaluate side-chains 407 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 201 optimal weight: 0.0030 chunk 181 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 315 optimal weight: 3.9990 chunk 302 optimal weight: 0.5980 chunk 243 optimal weight: 0.4980 chunk 281 optimal weight: 0.9980 chunk 366 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 375 optimal weight: 5.9990 chunk 267 optimal weight: 0.0370 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 214 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.122668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.102766 restraints weight = 130429.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.104191 restraints weight = 83056.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.104572 restraints weight = 53808.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.104821 restraints weight = 43630.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105000 restraints weight = 42367.833| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.7089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32224 Z= 0.115 Angle : 0.580 11.011 43890 Z= 0.299 Chirality : 0.045 0.296 4957 Planarity : 0.004 0.089 5679 Dihedral : 4.459 21.806 4321 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.06 % Allowed : 0.17 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3992 helix: 0.52 (0.19), residues: 696 sheet: -0.59 (0.16), residues: 1065 loop : -1.53 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.030 0.002 TYR A 741 PHE 0.026 0.002 PHE C 592 TRP 0.016 0.001 TRP C 886 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00261 (32178) covalent geometry : angle 0.57769 (43798) SS BOND : bond 0.00354 ( 46) SS BOND : angle 1.19575 ( 92) hydrogen bonds : bond 0.03578 ( 1125) hydrogen bonds : angle 5.88375 ( 3246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5999.12 seconds wall clock time: 104 minutes 29.49 seconds (6269.49 seconds total)