Starting phenix.real_space_refine on Thu Jun 26 22:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dk6_30704/06_2025/7dk6_30704.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dk6_30704/06_2025/7dk6_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_30704/06_2025/7dk6_30704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dk6_30704/06_2025/7dk6_30704.map" model { file = "/net/cci-nas-00/data/ceres_data/7dk6_30704/06_2025/7dk6_30704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dk6_30704/06_2025/7dk6_30704.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 1.74s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.63, per 1000 atoms: 0.62 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: 7.83 Conformation dependent library (CDL) restraints added in 4.3 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: 5.40 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: 15.37 Time building geometry restraints manager: 9.44 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: 7.960 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: 0.070 Extract box with map and model: 1.460 Check model and map are aligned: 0.260 Set scattering table: 0.350 Process input model: 76.870 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.270 ------------------------------------------------------------------------------- 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 : 1.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP A 152 HIS 0.003 0.001 HIS A1048 PHE 0.014 0.001 PHE C 490 TYR 0.013 0.001 TYR C 873 ARG 0.003 0.000 ARG C 78 Details of bonding type rmsd hydrogen bonds : bond 0.24979 ( 1125) hydrogen bonds : angle 10.12582 ( 3246) SS BOND : bond 0.00145 ( 46) SS BOND : angle 0.55836 ( 92) covalent geometry : bond 0.00287 (32178) covalent geometry : angle 0.54244 (43798) *********************** 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 : 3.399 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: 0.2865 (t0) REVERT: A 224 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5561 (mt-10) REVERT: A 353 TRP cc_start: 0.3667 (p90) cc_final: 0.3351 (p90) REVERT: A 395 VAL cc_start: 0.6867 (t) cc_final: 0.6631 (t) REVERT: A 449 TYR cc_start: 0.2946 (m-80) cc_final: 0.2691 (m-80) REVERT: A 612 TYR cc_start: 0.6968 (m-80) cc_final: 0.6500 (m-80) REVERT: A 724 THR cc_start: 0.6869 (m) cc_final: 0.6014 (t) REVERT: A 736 VAL cc_start: 0.7880 (t) cc_final: 0.7544 (p) REVERT: A 805 ILE cc_start: 0.9427 (pt) cc_final: 0.9221 (pt) REVERT: A 901 GLN cc_start: 0.7896 (mt0) cc_final: 0.7512 (tt0) REVERT: A 907 ASN cc_start: 0.7780 (m-40) cc_final: 0.6953 (m-40) REVERT: A 960 ASN cc_start: 0.6634 (m-40) cc_final: 0.6431 (m-40) REVERT: A 998 THR cc_start: 0.8323 (p) cc_final: 0.8023 (t) REVERT: A 1007 TYR cc_start: 0.7768 (t80) cc_final: 0.6999 (t80) REVERT: A 1033 VAL cc_start: 0.8787 (t) cc_final: 0.8293 (t) REVERT: A 1041 ASP cc_start: 0.7022 (t0) cc_final: 0.6802 (t0) REVERT: A 1081 ILE cc_start: 0.8031 (pp) cc_final: 0.7693 (pp) REVERT: A 1115 ILE cc_start: 0.7269 (mt) cc_final: 0.6967 (mt) REVERT: B 141 LEU cc_start: 0.7347 (mt) cc_final: 0.7098 (mp) REVERT: B 572 THR cc_start: 0.7209 (p) cc_final: 0.6710 (m) REVERT: B 592 PHE cc_start: 0.5979 (t80) cc_final: 0.5177 (t80) REVERT: B 645 THR cc_start: 0.7829 (p) cc_final: 0.7117 (p) REVERT: B 736 VAL cc_start: 0.7747 (t) cc_final: 0.7373 (t) REVERT: B 753 LEU cc_start: 0.7413 (tp) cc_final: 0.6669 (tp) REVERT: B 803 SER cc_start: 0.7276 (p) cc_final: 0.7062 (m) REVERT: B 822 LEU cc_start: 0.8577 (mt) cc_final: 0.7706 (mt) REVERT: B 888 PHE cc_start: 0.8014 (p90) cc_final: 0.7796 (p90) REVERT: B 1027 THR cc_start: 0.8362 (m) cc_final: 0.7972 (t) REVERT: B 1051 SER cc_start: 0.8008 (m) cc_final: 0.7793 (p) REVERT: B 1054 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7539 (mm-40) REVERT: B 1061 VAL cc_start: 0.9041 (t) cc_final: 0.8703 (p) REVERT: B 1141 LEU cc_start: 0.5650 (mp) cc_final: 0.4580 (mp) REVERT: C 64 TRP cc_start: 0.3613 (t60) cc_final: 0.3401 (t60) REVERT: C 196 ASN cc_start: 0.7477 (t0) cc_final: 0.6742 (m-40) REVERT: C 197 ILE cc_start: 0.6720 (mt) cc_final: 0.6494 (pt) REVERT: C 805 ILE cc_start: 0.9104 (pt) cc_final: 0.8894 (pt) REVERT: C 864 LEU cc_start: 0.8152 (tp) cc_final: 0.7611 (tp) REVERT: C 882 ILE cc_start: 0.8570 (mt) cc_final: 0.7896 (mt) REVERT: C 907 ASN cc_start: 0.8030 (m-40) cc_final: 0.7763 (m-40) REVERT: C 916 LEU cc_start: 0.7437 (tt) cc_final: 0.7166 (tt) REVERT: C 993 ILE cc_start: 0.7259 (mt) cc_final: 0.6995 (mt) REVERT: C 1023 ASN cc_start: 0.7040 (m-40) cc_final: 0.6617 (t0) REVERT: a 52 TRP cc_start: 0.3491 (m-10) cc_final: 0.3274 (m-10) REVERT: a 90 THR cc_start: 0.2614 (m) cc_final: 0.2397 (t) REVERT: a 139 MET cc_start: -0.1767 (mmm) cc_final: -0.3345 (tmm) REVERT: a 159 ASN cc_start: 0.2313 (m-40) cc_final: 0.1459 (t0) REVERT: b 110 ILE cc_start: 0.6098 (mm) cc_final: 0.5591 (mm) REVERT: c 113 VAL cc_start: 0.4807 (t) cc_final: 0.4571 (t) REVERT: c 144 CYS cc_start: -0.0627 (OUTLIER) cc_final: -0.2179 (p) REVERT: d 218 CYS cc_start: 0.5939 (t) cc_final: 0.5571 (t) outliers start: 2 outliers final: 0 residues processed: 1115 average time/residue: 0.4894 time to fit residues: 858.4059 Evaluate side-chains 533 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 532 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 338 optimal weight: 0.9980 chunk 303 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 103 optimal weight: 0.0060 chunk 205 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 314 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 191 optimal weight: 0.2980 chunk 233 optimal weight: 0.0060 chunk 364 optimal weight: 6.9990 overall best weight: 0.4012 ------------------------------------------------------------------------------- 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 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 C 965 GLN C1005 GLN C1011 GLN C1023 ASN C1101 HIS a 73 ASN a 102 HIS a 200 ASN b 93 GLN b 160 GLN d 57 ASN d 94 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4277 r_free = 0.4277 target = 0.128734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.108761 restraints weight = 129642.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.110202 restraints weight = 77433.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.110786 restraints weight = 48456.476| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32224 Z= 0.131 Angle : 0.568 11.795 43890 Z= 0.295 Chirality : 0.045 0.244 4957 Planarity : 0.004 0.075 5679 Dihedral : 3.615 18.762 4321 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.23 % Allowed : 1.78 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.12), residues: 3992 helix: 0.18 (0.18), residues: 702 sheet: -1.03 (0.15), residues: 1027 loop : -1.95 (0.11), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 64 HIS 0.005 0.001 HIS d 202 PHE 0.035 0.002 PHE B 823 TYR 0.022 0.001 TYR d 32 ARG 0.009 0.001 ARG C 577 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 1125) hydrogen bonds : angle 7.03236 ( 3246) SS BOND : bond 0.00471 ( 46) SS BOND : angle 2.07964 ( 92) covalent geometry : bond 0.00297 (32178) covalent geometry : angle 0.56063 (43798) *********************** 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 759 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 751 time to evaluate : 3.431 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: A 41 LYS cc_start: 0.5841 (mttt) cc_final: 0.5623 (mppt) REVERT: A 44 ARG cc_start: 0.7167 (mtt-85) cc_final: 0.6581 (mtt-85) REVERT: A 119 ILE cc_start: 0.8434 (mt) cc_final: 0.7931 (mt) REVERT: A 191 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7253 (mp0) REVERT: A 224 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7862 (mt-10) REVERT: A 354 ASN cc_start: 0.7534 (m110) cc_final: 0.6763 (t0) REVERT: A 449 TYR cc_start: 0.4489 (m-80) cc_final: 0.4157 (m-80) REVERT: A 724 THR cc_start: 0.7098 (m) cc_final: 0.6860 (t) REVERT: A 759 PHE cc_start: 0.5927 (t80) cc_final: 0.5492 (t80) REVERT: A 1009 THR cc_start: 0.8971 (m) cc_final: 0.8513 (p) REVERT: B 156 GLU cc_start: 0.5548 (mm-30) cc_final: 0.5184 (mt-10) REVERT: B 351 TYR cc_start: 0.4140 (p90) cc_final: 0.3733 (p90) REVERT: B 535 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7318 (pttt) REVERT: B 572 THR cc_start: 0.8238 (p) cc_final: 0.7963 (m) REVERT: B 822 LEU cc_start: 0.9170 (mt) cc_final: 0.8725 (mt) REVERT: B 867 ASP cc_start: 0.7337 (p0) cc_final: 0.7075 (p0) REVERT: B 1010 GLN cc_start: 0.8107 (mm110) cc_final: 0.7425 (tm-30) REVERT: B 1054 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8065 (mm-40) REVERT: B 1061 VAL cc_start: 0.9288 (t) cc_final: 0.8933 (p) REVERT: C 196 ASN cc_start: 0.7919 (t0) cc_final: 0.7357 (m-40) REVERT: C 197 ILE cc_start: 0.7639 (mt) cc_final: 0.7353 (mt) REVERT: C 497 PHE cc_start: 0.4207 (m-10) cc_final: 0.3871 (m-10) REVERT: C 558 LYS cc_start: 0.6850 (mmtt) cc_final: 0.5785 (mtmt) REVERT: C 933 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8444 (tppt) REVERT: C 953 ASN cc_start: 0.7531 (m-40) cc_final: 0.7241 (m-40) REVERT: C 977 LEU cc_start: 0.8265 (mm) cc_final: 0.7865 (mm) REVERT: C 1023 ASN cc_start: 0.8273 (m110) cc_final: 0.7668 (t0) REVERT: C 1042 PHE cc_start: 0.8272 (t80) cc_final: 0.7596 (t80) REVERT: C 1092 GLU cc_start: 0.7132 (pp20) cc_final: 0.6851 (pp20) REVERT: a 106 PHE cc_start: 0.3278 (m-80) cc_final: 0.2439 (m-80) REVERT: a 139 MET cc_start: -0.1791 (mmm) cc_final: -0.3080 (tmm) REVERT: a 159 ASN cc_start: 0.4570 (m-40) cc_final: 0.3613 (t0) REVERT: b 72 ARG cc_start: 0.3955 (mmt180) cc_final: 0.3597 (mpt180) REVERT: c 94 TYR cc_start: 0.2854 (m-80) cc_final: 0.2284 (m-10) outliers start: 8 outliers final: 2 residues processed: 755 average time/residue: 0.4230 time to fit residues: 512.7221 Evaluate side-chains 468 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 466 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 248 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 250 optimal weight: 0.0370 chunk 200 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 334 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 81 ASN B 317 ASN B 774 GLN B 784 GLN B 901 GLN B 935 GLN B 954 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN b 41 GLN ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 160 GLN b 214 ASN c 39 GLN c 98 ASN c 200 ASN ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.125928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105986 restraints weight = 132043.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.107009 restraints weight = 80745.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.107606 restraints weight = 53291.523| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32224 Z= 0.158 Angle : 0.597 13.267 43890 Z= 0.308 Chirality : 0.045 0.249 4957 Planarity : 0.004 0.072 5679 Dihedral : 4.151 21.968 4321 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.11 % Allowed : 2.35 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.12), residues: 3992 helix: 0.30 (0.19), residues: 714 sheet: -0.67 (0.15), residues: 1026 loop : -1.68 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C1102 HIS 0.007 0.001 HIS d 202 PHE 0.036 0.002 PHE c 80 TYR 0.020 0.002 TYR d 32 ARG 0.013 0.001 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 1125) hydrogen bonds : angle 6.42392 ( 3246) SS BOND : bond 0.00518 ( 46) SS BOND : angle 1.56325 ( 92) covalent geometry : bond 0.00341 (32178) covalent geometry : angle 0.59297 (43798) *********************** 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 664 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 660 time to evaluate : 3.446 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: 0.7250 (p) cc_final: 0.7011 (m) REVERT: A 119 ILE cc_start: 0.8146 (mt) cc_final: 0.7793 (tt) REVERT: A 191 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7005 (mp0) REVERT: A 224 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 319 ARG cc_start: 0.5970 (tpt170) cc_final: 0.5741 (tpt170) REVERT: A 354 ASN cc_start: 0.7482 (m110) cc_final: 0.6825 (t0) REVERT: A 505 TYR cc_start: 0.4906 (m-80) cc_final: 0.4095 (m-10) REVERT: A 724 THR cc_start: 0.7754 (m) cc_final: 0.7544 (t) REVERT: A 962 LEU cc_start: 0.8510 (tp) cc_final: 0.7687 (tp) REVERT: A 976 VAL cc_start: 0.8347 (t) cc_final: 0.7500 (t) REVERT: B 32 PHE cc_start: 0.6571 (t80) cc_final: 0.6344 (t80) REVERT: B 535 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7378 (pttm) REVERT: B 572 THR cc_start: 0.8388 (p) cc_final: 0.8092 (m) REVERT: B 645 THR cc_start: 0.8267 (p) cc_final: 0.7843 (p) REVERT: B 736 VAL cc_start: 0.8091 (t) cc_final: 0.7883 (t) REVERT: B 739 THR cc_start: 0.8191 (p) cc_final: 0.7862 (p) REVERT: B 742 ILE cc_start: 0.9211 (mt) cc_final: 0.8492 (mt) REVERT: B 820 ASP cc_start: 0.6843 (t0) cc_final: 0.6517 (t0) REVERT: B 822 LEU cc_start: 0.9122 (mt) cc_final: 0.8769 (mt) REVERT: B 921 LYS cc_start: 0.7376 (ttpt) cc_final: 0.6952 (ttpp) REVERT: B 1028 LYS cc_start: 0.7899 (mttm) cc_final: 0.7571 (mttm) REVERT: B 1061 VAL cc_start: 0.9256 (t) cc_final: 0.8946 (p) REVERT: C 188 ASN cc_start: 0.6598 (m110) cc_final: 0.6361 (m110) REVERT: C 191 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6418 (mt-10) REVERT: C 238 PHE cc_start: 0.7778 (p90) cc_final: 0.7561 (p90) REVERT: C 506 GLN cc_start: 0.4757 (tp-100) cc_final: 0.3684 (tt0) REVERT: C 558 LYS cc_start: 0.6833 (mmtt) cc_final: 0.5748 (mtmt) REVERT: C 569 ILE cc_start: 0.7318 (pt) cc_final: 0.7064 (pt) REVERT: C 611 LEU cc_start: 0.9355 (tp) cc_final: 0.9051 (tt) REVERT: C 664 ILE cc_start: 0.8623 (mm) cc_final: 0.8291 (mm) REVERT: C 933 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8404 (tppt) REVERT: C 961 THR cc_start: 0.9080 (p) cc_final: 0.8879 (p) REVERT: C 1092 GLU cc_start: 0.7400 (pp20) cc_final: 0.6968 (pp20) REVERT: C 1112 PRO cc_start: 0.7779 (Cg_exo) cc_final: 0.7569 (Cg_endo) REVERT: a 106 PHE cc_start: 0.2629 (m-80) cc_final: 0.1639 (m-80) REVERT: a 139 MET cc_start: -0.1461 (mmm) cc_final: -0.2859 (tmm) REVERT: a 159 ASN cc_start: 0.4284 (m-40) cc_final: 0.3813 (m-40) REVERT: b 110 ILE cc_start: 0.7062 (mm) cc_final: 0.6292 (mt) REVERT: d 218 CYS cc_start: 0.4773 (t) cc_final: 0.4541 (t) outliers start: 4 outliers final: 0 residues processed: 661 average time/residue: 0.4136 time to fit residues: 442.0236 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 : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 11 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 285 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 355 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 365 optimal weight: 0.9990 chunk 380 optimal weight: 7.9990 chunk 256 optimal weight: 0.0470 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 953 ASN A 992 GLN B 317 ASN B 343 ASN B 388 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 777 ASN C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1054 GLN b 41 GLN ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.124210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103239 restraints weight = 132728.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.105101 restraints weight = 82222.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.105553 restraints weight = 48455.793| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32224 Z= 0.157 Angle : 0.579 14.065 43890 Z= 0.301 Chirality : 0.045 0.362 4957 Planarity : 0.005 0.125 5679 Dihedral : 4.274 23.782 4321 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.03 % Allowed : 2.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 3992 helix: 0.33 (0.18), residues: 725 sheet: -0.67 (0.15), residues: 1040 loop : -1.60 (0.12), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 64 HIS 0.005 0.001 HIS A 49 PHE 0.022 0.002 PHE B 823 TYR 0.028 0.002 TYR A 741 ARG 0.013 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 1125) hydrogen bonds : angle 6.19813 ( 3246) SS BOND : bond 0.00426 ( 46) SS BOND : angle 1.20985 ( 92) covalent geometry : bond 0.00343 (32178) covalent geometry : angle 0.57736 (43798) *********************** 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 619 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 618 time to evaluate : 3.670 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: A 119 ILE cc_start: 0.8083 (mt) cc_final: 0.7768 (tt) REVERT: A 191 GLU cc_start: 0.7591 (mt-10) cc_final: 0.6972 (mp0) REVERT: A 224 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 354 ASN cc_start: 0.7364 (m110) cc_final: 0.6778 (t0) REVERT: A 724 THR cc_start: 0.7758 (m) cc_final: 0.7547 (t) REVERT: A 758 SER cc_start: 0.8121 (t) cc_final: 0.7857 (t) REVERT: A 907 ASN cc_start: 0.8383 (m110) cc_final: 0.7765 (m-40) REVERT: A 1006 THR cc_start: 0.8947 (m) cc_final: 0.8742 (m) REVERT: A 1128 VAL cc_start: 0.8092 (m) cc_final: 0.7876 (t) REVERT: B 535 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7413 (pttm) REVERT: B 572 THR cc_start: 0.8536 (p) cc_final: 0.8304 (m) REVERT: B 645 THR cc_start: 0.8498 (p) cc_final: 0.8108 (p) REVERT: B 882 ILE cc_start: 0.8940 (mt) cc_final: 0.8734 (mm) REVERT: B 921 LYS cc_start: 0.7431 (ttpt) cc_final: 0.6969 (ttpp) REVERT: B 938 LEU cc_start: 0.7253 (mt) cc_final: 0.7001 (mt) REVERT: B 1001 LEU cc_start: 0.8536 (tp) cc_final: 0.8236 (tt) REVERT: B 1029 MET cc_start: 0.7555 (ttm) cc_final: 0.7299 (ttm) REVERT: B 1061 VAL cc_start: 0.9262 (t) cc_final: 0.9037 (p) REVERT: B 1110 TYR cc_start: 0.7990 (t80) cc_final: 0.7760 (t80) REVERT: C 170 TYR cc_start: 0.7468 (t80) cc_final: 0.6660 (t80) REVERT: C 191 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6290 (mt-10) REVERT: C 558 LYS cc_start: 0.6814 (mmtt) cc_final: 0.5817 (mtmt) REVERT: C 611 LEU cc_start: 0.9355 (tp) cc_final: 0.9143 (tt) REVERT: C 731 MET cc_start: 0.7932 (mtm) cc_final: 0.7711 (mtp) REVERT: C 917 TYR cc_start: 0.8331 (m-10) cc_final: 0.7919 (m-80) REVERT: C 933 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8472 (tptt) REVERT: C 977 LEU cc_start: 0.8134 (mm) cc_final: 0.7856 (mm) REVERT: C 1023 ASN cc_start: 0.8321 (m-40) cc_final: 0.7713 (t0) REVERT: C 1055 SER cc_start: 0.8558 (t) cc_final: 0.8302 (t) REVERT: C 1092 GLU cc_start: 0.7566 (pp20) cc_final: 0.7031 (pp20) REVERT: C 1112 PRO cc_start: 0.7795 (Cg_exo) cc_final: 0.7555 (Cg_endo) REVERT: a 106 PHE cc_start: 0.2922 (m-80) cc_final: 0.2190 (m-80) REVERT: a 139 MET cc_start: -0.1633 (mmm) cc_final: -0.3186 (tmm) REVERT: a 152 GLU cc_start: 0.4306 (mp0) cc_final: 0.2282 (tp30) REVERT: a 159 ASN cc_start: 0.4351 (m-40) cc_final: 0.3972 (m-40) REVERT: a 163 LEU cc_start: 0.3785 (mm) cc_final: 0.3458 (mt) REVERT: b 37 LEU cc_start: 0.4660 (mt) cc_final: 0.4220 (pt) REVERT: b 110 ILE cc_start: 0.6846 (mm) cc_final: 0.6345 (mt) REVERT: d 218 CYS cc_start: 0.4573 (t) cc_final: 0.4305 (t) outliers start: 1 outliers final: 0 residues processed: 619 average time/residue: 0.4308 time to fit residues: 441.9169 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 : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 332 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 386 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 372 optimal weight: 20.0000 chunk 296 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1119 ASN B 334 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 709 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 137 ASN C 207 HIS C 321 GLN C 450 ASN C 544 ASN C 655 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 GLN ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 160 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.119859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.099426 restraints weight = 132916.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.100823 restraints weight = 81729.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.101096 restraints weight = 59555.894| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 32224 Z= 0.264 Angle : 0.756 15.580 43890 Z= 0.397 Chirality : 0.050 0.333 4957 Planarity : 0.006 0.089 5679 Dihedral : 5.402 29.805 4321 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.12), residues: 3992 helix: -0.10 (0.18), residues: 728 sheet: -0.82 (0.16), residues: 1031 loop : -1.86 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP a 158 HIS 0.013 0.002 HIS c 203 PHE 0.044 0.003 PHE A 898 TYR 0.029 0.003 TYR A 741 ARG 0.014 0.001 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 1125) hydrogen bonds : angle 6.70691 ( 3246) SS BOND : bond 0.00608 ( 46) SS BOND : angle 1.38225 ( 92) covalent geometry : bond 0.00576 (32178) covalent geometry : angle 0.75435 (43798) *********************** 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 575 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 572 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.5983 (t70) cc_final: 0.5699 (t-170) REVERT: A 191 GLU cc_start: 0.7733 (mt-10) cc_final: 0.6753 (mp0) REVERT: A 224 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 354 ASN cc_start: 0.7207 (m110) cc_final: 0.6495 (t0) REVERT: A 408 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7610 (tpm170) REVERT: A 758 SER cc_start: 0.8207 (t) cc_final: 0.7992 (t) REVERT: A 907 ASN cc_start: 0.8395 (m110) cc_final: 0.8134 (m-40) REVERT: A 962 LEU cc_start: 0.9027 (tp) cc_final: 0.8825 (tp) REVERT: A 969 ASN cc_start: 0.8809 (p0) cc_final: 0.8256 (p0) REVERT: A 1055 SER cc_start: 0.8846 (t) cc_final: 0.8573 (p) REVERT: A 1081 ILE cc_start: 0.9163 (pt) cc_final: 0.8955 (pt) REVERT: A 1128 VAL cc_start: 0.8261 (m) cc_final: 0.8058 (t) REVERT: B 535 LYS cc_start: 0.8375 (mtmt) cc_final: 0.7693 (pttm) REVERT: B 572 THR cc_start: 0.8758 (p) cc_final: 0.8299 (m) REVERT: B 823 PHE cc_start: 0.7465 (m-80) cc_final: 0.7172 (m-80) REVERT: B 921 LYS cc_start: 0.7605 (ttpt) cc_final: 0.7112 (ttpp) REVERT: B 1061 VAL cc_start: 0.9371 (t) cc_final: 0.9150 (p) REVERT: C 38 TYR cc_start: 0.8502 (m-80) cc_final: 0.8298 (m-80) REVERT: C 170 TYR cc_start: 0.7736 (t80) cc_final: 0.7300 (t80) REVERT: C 188 ASN cc_start: 0.6773 (m110) cc_final: 0.6568 (m110) REVERT: C 191 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6375 (mt-10) REVERT: C 236 THR cc_start: 0.7456 (t) cc_final: 0.7186 (m) REVERT: C 238 PHE cc_start: 0.7981 (p90) cc_final: 0.7734 (p90) REVERT: C 275 PHE cc_start: 0.6898 (m-80) cc_final: 0.6675 (m-80) REVERT: C 933 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8487 (tptt) REVERT: C 1018 ILE cc_start: 0.8997 (tt) cc_final: 0.8783 (tt) REVERT: C 1023 ASN cc_start: 0.8456 (m-40) cc_final: 0.7764 (t0) REVERT: C 1055 SER cc_start: 0.8797 (t) cc_final: 0.8570 (t) REVERT: C 1092 GLU cc_start: 0.7399 (pp20) cc_final: 0.6907 (pp20) REVERT: a 82 MET cc_start: -0.0631 (pmm) cc_final: -0.0905 (pmm) REVERT: a 106 PHE cc_start: 0.2357 (m-80) cc_final: 0.1546 (m-80) REVERT: a 152 GLU cc_start: 0.5183 (mp0) cc_final: 0.2520 (tp30) REVERT: d 187 LYS cc_start: 0.6776 (pttp) cc_final: 0.6575 (mmmt) outliers start: 3 outliers final: 0 residues processed: 574 average time/residue: 0.4083 time to fit residues: 384.6082 Evaluate side-chains 394 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 228 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 323 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 313 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 901 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1071 GLN a 39 GLN b 41 GLN ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** 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 = 0.4181 r_free = 0.4181 target = 0.124159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.106339 restraints weight = 148882.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.106301 restraints weight = 108258.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.106406 restraints weight = 90547.569| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32224 Z= 0.164 Angle : 0.618 14.118 43890 Z= 0.322 Chirality : 0.046 0.379 4957 Planarity : 0.005 0.088 5679 Dihedral : 4.924 26.817 4321 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.03 % Allowed : 1.39 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 3992 helix: 0.15 (0.18), residues: 722 sheet: -0.85 (0.15), residues: 1069 loop : -1.75 (0.12), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 353 HIS 0.007 0.001 HIS A 49 PHE 0.034 0.002 PHE A 486 TYR 0.027 0.002 TYR A 741 ARG 0.009 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 1125) hydrogen bonds : angle 6.36803 ( 3246) SS BOND : bond 0.00481 ( 46) SS BOND : angle 1.40642 ( 92) covalent geometry : bond 0.00369 (32178) covalent geometry : angle 0.61574 (43798) *********************** 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 587 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 586 time to evaluate : 3.533 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: A 49 HIS cc_start: 0.5759 (t70) cc_final: 0.5514 (t-170) REVERT: A 191 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6648 (mp0) REVERT: A 224 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7320 (mt-10) REVERT: A 354 ASN cc_start: 0.7166 (m110) cc_final: 0.6904 (t0) REVERT: A 408 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7559 (tpm170) REVERT: A 486 PHE cc_start: 0.3982 (t80) cc_final: 0.3633 (t80) REVERT: A 758 SER cc_start: 0.7773 (t) cc_final: 0.7508 (t) REVERT: A 819 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 907 ASN cc_start: 0.7800 (m110) cc_final: 0.7589 (m-40) REVERT: A 1081 ILE cc_start: 0.8929 (pt) cc_final: 0.8714 (pt) REVERT: B 177 MET cc_start: 0.3159 (tpp) cc_final: 0.2915 (tpp) REVERT: B 820 ASP cc_start: 0.6847 (t0) cc_final: 0.6261 (t0) REVERT: B 905 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8246 (mtt180) REVERT: B 921 LYS cc_start: 0.7450 (ttpt) cc_final: 0.6972 (ttpp) REVERT: B 1050 MET cc_start: 0.6843 (ptt) cc_final: 0.6061 (ptt) REVERT: B 1061 VAL cc_start: 0.9135 (t) cc_final: 0.8891 (p) REVERT: C 38 TYR cc_start: 0.8470 (m-80) cc_final: 0.8179 (m-80) REVERT: C 170 TYR cc_start: 0.7207 (t80) cc_final: 0.6844 (t80) REVERT: C 191 GLU cc_start: 0.5928 (mt-10) cc_final: 0.5572 (mt-10) REVERT: C 611 LEU cc_start: 0.9306 (tp) cc_final: 0.8960 (tt) REVERT: C 763 LEU cc_start: 0.8205 (mt) cc_final: 0.7937 (mt) REVERT: C 864 LEU cc_start: 0.8752 (tp) cc_final: 0.8211 (tt) REVERT: C 875 SER cc_start: 0.8361 (p) cc_final: 0.8046 (m) REVERT: C 933 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8508 (tptt) REVERT: C 952 VAL cc_start: 0.8378 (t) cc_final: 0.8159 (t) REVERT: a 152 GLU cc_start: 0.4664 (mp0) cc_final: 0.2071 (tp30) REVERT: b 110 ILE cc_start: 0.6657 (mp) cc_final: 0.6410 (mp) REVERT: d 187 LYS cc_start: 0.6744 (pttp) cc_final: 0.6541 (mmmt) outliers start: 1 outliers final: 0 residues processed: 587 average time/residue: 0.3932 time to fit residues: 385.3667 Evaluate side-chains 396 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 185 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 370 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 234 optimal weight: 0.0370 chunk 337 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 360 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B1135 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 GLN ** 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** ** c 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.121881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.100982 restraints weight = 130898.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.102600 restraints weight = 82667.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.103623 restraints weight = 48894.744| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32224 Z= 0.133 Angle : 0.593 13.082 43890 Z= 0.306 Chirality : 0.045 0.282 4957 Planarity : 0.004 0.089 5679 Dihedral : 4.680 25.566 4321 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.11 % Allowed : 0.76 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3992 helix: 0.32 (0.19), residues: 712 sheet: -0.69 (0.16), residues: 1024 loop : -1.61 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.010 0.001 HIS d 193 PHE 0.048 0.002 PHE B 823 TYR 0.027 0.002 TYR A 741 ARG 0.008 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1125) hydrogen bonds : angle 6.16446 ( 3246) SS BOND : bond 0.00314 ( 46) SS BOND : angle 1.55992 ( 92) covalent geometry : bond 0.00303 (32178) covalent geometry : angle 0.58951 (43798) *********************** 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 581 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 577 time to evaluate : 3.531 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: 0.7267 (p) cc_final: 0.6919 (m) REVERT: A 49 HIS cc_start: 0.5856 (t70) cc_final: 0.5638 (t-170) REVERT: A 191 GLU cc_start: 0.7899 (mt-10) cc_final: 0.6835 (mp0) REVERT: A 224 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7654 (mt-10) REVERT: A 299 THR cc_start: 0.8840 (m) cc_final: 0.8625 (p) REVERT: A 354 ASN cc_start: 0.7131 (m110) cc_final: 0.6879 (t0) REVERT: A 408 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7561 (mmm160) REVERT: A 486 PHE cc_start: 0.4044 (t80) cc_final: 0.3700 (t80) REVERT: A 598 ILE cc_start: 0.8928 (mp) cc_final: 0.8479 (mm) REVERT: A 758 SER cc_start: 0.8062 (t) cc_final: 0.7847 (t) REVERT: A 1081 ILE cc_start: 0.9088 (pt) cc_final: 0.8859 (pt) REVERT: B 177 MET cc_start: 0.2921 (tpp) cc_final: 0.2657 (tpp) REVERT: B 595 VAL cc_start: 0.8071 (t) cc_final: 0.7865 (t) REVERT: B 712 ILE cc_start: 0.8805 (tt) cc_final: 0.8599 (tt) REVERT: B 820 ASP cc_start: 0.7352 (t0) cc_final: 0.6804 (t0) REVERT: B 921 LYS cc_start: 0.7445 (ttpt) cc_final: 0.7016 (ttpp) REVERT: B 1050 MET cc_start: 0.6903 (ptt) cc_final: 0.6575 (ptt) REVERT: B 1077 THR cc_start: 0.7710 (t) cc_final: 0.7282 (t) REVERT: C 38 TYR cc_start: 0.8546 (m-80) cc_final: 0.8249 (m-80) REVERT: C 170 TYR cc_start: 0.7554 (t80) cc_final: 0.7194 (t80) REVERT: C 191 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6114 (mt-10) REVERT: C 497 PHE cc_start: 0.4167 (m-10) cc_final: 0.3031 (m-80) REVERT: C 611 LEU cc_start: 0.9302 (tp) cc_final: 0.9018 (tt) REVERT: C 735 SER cc_start: 0.8643 (m) cc_final: 0.8436 (m) REVERT: C 864 LEU cc_start: 0.8809 (tp) cc_final: 0.8597 (tt) REVERT: C 875 SER cc_start: 0.8456 (p) cc_final: 0.8084 (m) REVERT: C 933 LYS cc_start: 0.8957 (ttpt) cc_final: 0.8506 (tptt) REVERT: C 1006 THR cc_start: 0.8396 (m) cc_final: 0.8114 (m) REVERT: C 1023 ASN cc_start: 0.8625 (m-40) cc_final: 0.7981 (t0) REVERT: C 1055 SER cc_start: 0.8462 (t) cc_final: 0.8204 (t) REVERT: a 107 TRP cc_start: 0.5547 (m100) cc_final: 0.5158 (m100) REVERT: a 139 MET cc_start: -0.0640 (tpt) cc_final: -0.2343 (tmm) REVERT: b 110 ILE cc_start: 0.6685 (mp) cc_final: 0.6321 (mp) outliers start: 4 outliers final: 2 residues processed: 580 average time/residue: 0.4263 time to fit residues: 409.3806 Evaluate side-chains 408 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 406 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 335 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 chunk 178 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 230 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN b 41 GLN ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN b 214 ASN ** c 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 128 GLN d 193 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.121463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.101202 restraints weight = 129935.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.102706 restraints weight = 79040.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.103010 restraints weight = 49261.605| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.6788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32224 Z= 0.140 Angle : 0.595 12.474 43890 Z= 0.306 Chirality : 0.045 0.277 4957 Planarity : 0.004 0.091 5679 Dihedral : 4.621 25.495 4321 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.06 % Allowed : 0.65 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3992 helix: 0.44 (0.19), residues: 697 sheet: -0.69 (0.16), residues: 1034 loop : -1.56 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 353 HIS 0.006 0.001 HIS A 49 PHE 0.027 0.002 PHE c 80 TYR 0.033 0.002 TYR B 674 ARG 0.008 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 1125) hydrogen bonds : angle 6.10579 ( 3246) SS BOND : bond 0.00497 ( 46) SS BOND : angle 1.25243 ( 92) covalent geometry : bond 0.00313 (32178) covalent geometry : angle 0.59279 (43798) *********************** 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 558 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 556 time to evaluate : 3.451 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 42 VAL cc_start: 0.7171 (p) cc_final: 0.6820 (m) REVERT: A 49 HIS cc_start: 0.5812 (t70) cc_final: 0.5597 (t-170) REVERT: A 191 GLU cc_start: 0.7716 (mt-10) cc_final: 0.6629 (mp0) REVERT: A 354 ASN cc_start: 0.7154 (m110) cc_final: 0.6921 (t0) REVERT: A 408 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7590 (mmm160) REVERT: A 486 PHE cc_start: 0.3934 (t80) cc_final: 0.3380 (t80) REVERT: A 598 ILE cc_start: 0.8843 (mp) cc_final: 0.8384 (mm) REVERT: A 758 SER cc_start: 0.7821 (t) cc_final: 0.7592 (t) REVERT: A 1081 ILE cc_start: 0.9005 (pt) cc_final: 0.8792 (pt) REVERT: B 177 MET cc_start: 0.3171 (tpp) cc_final: 0.2789 (tpp) REVERT: B 535 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7648 (pttm) REVERT: B 712 ILE cc_start: 0.8739 (tt) cc_final: 0.8478 (tt) REVERT: B 921 LYS cc_start: 0.7459 (ttpt) cc_final: 0.6984 (ttpp) REVERT: B 1077 THR cc_start: 0.7596 (t) cc_final: 0.7247 (t) REVERT: C 38 TYR cc_start: 0.8444 (m-80) cc_final: 0.8145 (m-80) REVERT: C 170 TYR cc_start: 0.7291 (t80) cc_final: 0.6957 (t80) REVERT: C 191 GLU cc_start: 0.6220 (mt-10) cc_final: 0.5723 (mt-10) REVERT: C 497 PHE cc_start: 0.3969 (m-10) cc_final: 0.2969 (m-80) REVERT: C 611 LEU cc_start: 0.9312 (tp) cc_final: 0.9061 (tt) REVERT: C 735 SER cc_start: 0.8524 (m) cc_final: 0.8297 (m) REVERT: C 864 LEU cc_start: 0.8892 (tp) cc_final: 0.8620 (tp) REVERT: C 875 SER cc_start: 0.8134 (p) cc_final: 0.7609 (m) REVERT: C 933 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8496 (tptt) REVERT: C 1006 THR cc_start: 0.8516 (m) cc_final: 0.8314 (m) REVERT: C 1014 ARG cc_start: 0.6906 (mtm-85) cc_final: 0.6584 (mtt90) REVERT: C 1023 ASN cc_start: 0.8184 (m-40) cc_final: 0.7463 (t0) REVERT: C 1055 SER cc_start: 0.8357 (t) cc_final: 0.8080 (t) REVERT: a 82 MET cc_start: -0.0529 (pmm) cc_final: -0.0735 (pmm) REVERT: a 139 MET cc_start: -0.0363 (tpt) cc_final: -0.2675 (tmm) REVERT: a 152 GLU cc_start: 0.4906 (mp0) cc_final: 0.2235 (tp30) outliers start: 2 outliers final: 1 residues processed: 557 average time/residue: 0.4087 time to fit residues: 380.4955 Evaluate side-chains 396 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 104 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 297 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 chunk 361 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 GLN b 93 GLN c 39 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.121552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.101393 restraints weight = 128242.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.102556 restraints weight = 82504.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102806 restraints weight = 51839.258| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.6931 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= 0.133 Angle : 0.586 12.037 43890 Z= 0.303 Chirality : 0.045 0.263 4957 Planarity : 0.004 0.090 5679 Dihedral : 4.625 25.586 4321 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3992 helix: 0.45 (0.19), residues: 697 sheet: -0.64 (0.16), residues: 1036 loop : -1.54 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.009 0.001 HIS B 207 PHE 0.033 0.002 PHE C 592 TYR 0.025 0.002 TYR B 674 ARG 0.008 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 1125) hydrogen bonds : angle 6.10518 ( 3246) SS BOND : bond 0.00295 ( 46) SS BOND : angle 1.25454 ( 92) covalent geometry : bond 0.00298 (32178) covalent geometry : angle 0.58348 (43798) *********************** 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 548 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 546 time to evaluate : 3.742 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: 0.7225 (p) cc_final: 0.6857 (m) REVERT: A 49 HIS cc_start: 0.5566 (t70) cc_final: 0.5338 (t-170) REVERT: A 191 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6590 (mp0) REVERT: A 354 ASN cc_start: 0.7174 (m110) cc_final: 0.6864 (t0) REVERT: A 408 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7557 (mmm160) REVERT: A 598 ILE cc_start: 0.8911 (mp) cc_final: 0.8511 (mm) REVERT: A 758 SER cc_start: 0.7760 (t) cc_final: 0.7544 (t) REVERT: B 177 MET cc_start: 0.2887 (tpp) cc_final: 0.2643 (tpp) REVERT: B 535 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7840 (pttp) REVERT: B 712 ILE cc_start: 0.8688 (tt) cc_final: 0.8470 (tt) REVERT: B 820 ASP cc_start: 0.6482 (t0) cc_final: 0.5884 (t0) REVERT: B 1077 THR cc_start: 0.7745 (t) cc_final: 0.7371 (t) REVERT: C 54 LEU cc_start: 0.7279 (mt) cc_final: 0.6778 (tp) REVERT: C 170 TYR cc_start: 0.7153 (t80) cc_final: 0.6902 (t80) REVERT: C 191 GLU cc_start: 0.6265 (mt-10) cc_final: 0.5789 (mt-10) REVERT: C 497 PHE cc_start: 0.3677 (m-10) cc_final: 0.3142 (m-80) REVERT: C 611 LEU cc_start: 0.9288 (tp) cc_final: 0.9077 (tt) REVERT: C 875 SER cc_start: 0.8115 (p) cc_final: 0.7572 (m) REVERT: C 933 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8452 (tptt) REVERT: C 1006 THR cc_start: 0.8441 (m) cc_final: 0.7853 (m) REVERT: C 1014 ARG cc_start: 0.6963 (mtm-85) cc_final: 0.6493 (mtt90) REVERT: C 1023 ASN cc_start: 0.8235 (m-40) cc_final: 0.7638 (t0) REVERT: C 1055 SER cc_start: 0.8393 (t) cc_final: 0.8111 (t) REVERT: C 1075 PHE cc_start: 0.7613 (m-80) cc_final: 0.7365 (m-80) REVERT: a 139 MET cc_start: -0.0230 (tpt) cc_final: -0.2606 (tmm) outliers start: 2 outliers final: 2 residues processed: 548 average time/residue: 0.4059 time to fit residues: 368.0508 Evaluate side-chains 397 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 140 optimal weight: 4.9990 chunk 387 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 318 optimal weight: 0.0570 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 919 ASN B 360 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 160 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.121517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.101428 restraints weight = 130482.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.102678 restraints weight = 85731.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.102855 restraints weight = 59271.637| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32224 Z= 0.142 Angle : 0.597 11.982 43890 Z= 0.309 Chirality : 0.045 0.272 4957 Planarity : 0.005 0.091 5679 Dihedral : 4.661 25.423 4321 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 3992 helix: 0.47 (0.19), residues: 699 sheet: -0.62 (0.16), residues: 1044 loop : -1.60 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 52 HIS 0.020 0.001 HIS C1048 PHE 0.031 0.002 PHE C 592 TYR 0.027 0.002 TYR B 674 ARG 0.010 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 1125) hydrogen bonds : angle 6.11007 ( 3246) SS BOND : bond 0.00311 ( 46) SS BOND : angle 1.25504 ( 92) covalent geometry : bond 0.00321 (32178) covalent geometry : angle 0.59458 (43798) ********************** 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 542 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7311 (p) cc_final: 0.6924 (m) REVERT: A 191 GLU cc_start: 0.8119 (mt-10) cc_final: 0.6767 (mp0) REVERT: A 354 ASN cc_start: 0.7091 (m110) cc_final: 0.6829 (t0) REVERT: A 408 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7535 (mmm160) REVERT: A 598 ILE cc_start: 0.8983 (mp) cc_final: 0.8567 (mm) REVERT: B 535 LYS cc_start: 0.8380 (mtmt) cc_final: 0.7888 (pttp) REVERT: B 1077 THR cc_start: 0.7927 (t) cc_final: 0.7466 (t) REVERT: C 170 TYR cc_start: 0.7532 (t80) cc_final: 0.7244 (t80) REVERT: C 191 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6272 (mt-10) REVERT: C 275 PHE cc_start: 0.7997 (m-10) cc_final: 0.7675 (m-80) REVERT: C 497 PHE cc_start: 0.4139 (m-10) cc_final: 0.3435 (m-80) REVERT: C 569 ILE cc_start: 0.6829 (pt) cc_final: 0.6617 (mp) REVERT: C 611 LEU cc_start: 0.9281 (tp) cc_final: 0.9016 (tt) REVERT: C 731 MET cc_start: 0.7994 (mtm) cc_final: 0.7762 (mtm) REVERT: C 875 SER cc_start: 0.8394 (p) cc_final: 0.7948 (m) REVERT: C 933 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8458 (tptt) REVERT: C 1014 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6803 (mtt90) REVERT: C 1023 ASN cc_start: 0.8112 (m-40) cc_final: 0.7561 (t0) REVERT: C 1055 SER cc_start: 0.8534 (t) cc_final: 0.8284 (t) REVERT: C 1075 PHE cc_start: 0.7670 (m-80) cc_final: 0.7426 (m-80) REVERT: a 139 MET cc_start: -0.0194 (tpt) cc_final: -0.2459 (tmm) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.3893 time to fit residues: 355.7026 Evaluate side-chains 385 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 378 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 302 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 317 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 935 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 710 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.121863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.101127 restraints weight = 129954.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102725 restraints weight = 81165.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.103030 restraints weight = 59787.601| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32224 Z= 0.129 Angle : 0.582 11.653 43890 Z= 0.301 Chirality : 0.044 0.267 4957 Planarity : 0.004 0.090 5679 Dihedral : 4.569 24.947 4321 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3992 helix: 0.63 (0.19), residues: 691 sheet: -0.55 (0.16), residues: 1037 loop : -1.55 (0.12), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 353 HIS 0.008 0.001 HIS C1048 PHE 0.035 0.002 PHE A 898 TYR 0.024 0.002 TYR B 674 ARG 0.009 0.001 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1125) hydrogen bonds : angle 6.00667 ( 3246) SS BOND : bond 0.00308 ( 46) SS BOND : angle 1.16469 ( 92) covalent geometry : bond 0.00289 (32178) covalent geometry : angle 0.57970 (43798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12189.69 seconds wall clock time: 211 minutes 22.26 seconds (12682.26 seconds total)