Starting phenix.real_space_refine on Fri Nov 15 08:58:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/11_2024/8g46_29714.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/11_2024/8g46_29714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/11_2024/8g46_29714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/11_2024/8g46_29714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/11_2024/8g46_29714.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g46_29714/11_2024/8g46_29714.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.071 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 57 5.16 5 C 5415 2.51 5 N 1433 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8603 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 782, 6150 Classifications: {'peptide': 782} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 755} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 782, 6150 Classifications: {'peptide': 782} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 755} Chain breaks: 6 bond proxies already assigned to first conformer: 6221 Chain: "B" Number of atoms: 1260 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 158, 1246 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 17, 'TRANS': 140} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 158, 1246 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 17, 'TRANS': 140} Chain breaks: 1 bond proxies already assigned to first conformer: 1266 Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 859 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'YK3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6635 SG CYS B 100 40.352 30.235 52.256 1.00 55.81 S ATOM 6657 SG CYS B 103 42.977 32.717 50.994 1.00 59.48 S ATOM 7131 SG CYS B 177 41.272 30.475 48.590 1.00 54.63 S ATOM 7143 SG CYS B 179 39.096 33.155 50.131 1.00 56.71 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AASN A 16 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 16 " occ=0.50 residue: pdb=" N AHIS A 711 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 711 " occ=0.50 residue: pdb=" N ACYS A 725 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 725 " occ=0.50 residue: pdb=" N ACYS A1008 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A1008 " occ=0.50 residue: pdb=" N ATRP B 54 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 54 " occ=0.50 Time building chain proxies: 8.72, per 1000 atoms: 1.01 Number of scatterers: 8603 At special positions: 0 Unit cell: (86.7623, 91.189, 138.997, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 57 16.00 O 1697 8.00 N 1433 7.00 C 5415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 103 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 100 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 177 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 179 " Number of angles added : 6 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 17 sheets defined 23.5% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.073A pdb=" N GLN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1062 Processing helix chain 'A' and resid 1069 through 1075 Processing helix chain 'A' and resid 1091 through 1096 Processing helix chain 'A' and resid 1097 through 1100 Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1125 through 1138 removed outlier: 3.887A pdb=" N LEU A1129 " --> pdb=" O THR A1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 142 through 158 removed outlier: 4.215A pdb=" N ARG B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 200 through 216 Processing helix chain 'C' and resid 354 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 375 through 378 removed outlier: 4.311A pdb=" N LYS C 378 " --> pdb=" O PRO C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 375 through 378' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 414 through 433 Processing helix chain 'C' and resid 437 through 455 removed outlier: 3.628A pdb=" N VAL C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.775A pdb=" N LYS E 6 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 6.615A pdb=" N GLY A1031 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE A1007 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A1029 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N HIS A1009 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER A1027 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A1027 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A1040 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1029 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A1038 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 6.690A pdb=" N LEU A 39 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU A 54 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 41 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.183A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.201A pdb=" N LEU A 135 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.588A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.588A pdb=" N VAL A 181 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 167 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 169 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 177 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 218 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 4.257A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 280 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP A 299 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU A 288 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU A 297 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 313 through 318 removed outlier: 6.666A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER A 331 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 352 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 333 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.984A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.333A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 762 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN A 806 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 811 through 819 removed outlier: 5.549A pdb=" N ALA A 813 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA A 834 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 847 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY A 846 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU A 865 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 870 through 876 removed outlier: 3.863A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 911 through 917 removed outlier: 7.052A pdb=" N VAL A 930 " --> pdb=" O ARG A 947 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG A 947 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 932 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 941 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.869A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE A 959 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN A 964 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AB8, first strand: chain 'B' and resid 66 through 67 364 hydrogen bonds defined for protein. 991 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: 3.21 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1820 1.33 - 1.46: 2666 1.46 - 1.58: 4100 1.58 - 1.71: 1 1.71 - 1.84: 85 Bond restraints: 8672 Sorted by residual: bond pdb=" C PHE C 450 " pdb=" O PHE C 450 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.15e-02 7.56e+03 8.26e+00 bond pdb=" CA SER A 379 " pdb=" CB SER A 379 " ideal model delta sigma weight residual 1.533 1.488 0.045 1.60e-02 3.91e+03 7.95e+00 bond pdb=" C21 YK3 B1002 " pdb=" C4 YK3 B1002 " ideal model delta sigma weight residual 1.370 1.423 -0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" CA ALA B 148 " pdb=" CB ALA B 148 " ideal model delta sigma weight residual 1.528 1.487 0.041 1.56e-02 4.11e+03 7.03e+00 bond pdb=" CG HIS A 789 " pdb=" CD2 HIS A 789 " ideal model delta sigma weight residual 1.354 1.325 0.029 1.10e-02 8.26e+03 6.79e+00 ... (remaining 8667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 11542 2.40 - 4.81: 201 4.81 - 7.21: 5 7.21 - 9.61: 1 9.61 - 12.02: 2 Bond angle restraints: 11751 Sorted by residual: angle pdb=" N MET C 442 " pdb=" CA MET C 442 " pdb=" C MET C 442 " ideal model delta sigma weight residual 113.38 105.14 8.24 1.23e+00 6.61e-01 4.48e+01 angle pdb=" N ALA C 441 " pdb=" CA ALA C 441 " pdb=" C ALA C 441 " ideal model delta sigma weight residual 113.97 108.17 5.80 1.28e+00 6.10e-01 2.06e+01 angle pdb=" C9 YK3 B1002 " pdb=" N YK3 B1002 " pdb=" S YK3 B1002 " ideal model delta sigma weight residual 118.17 130.19 -12.02 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N ALA C 443 " pdb=" CA ALA C 443 " pdb=" C ALA C 443 " ideal model delta sigma weight residual 111.24 106.18 5.06 1.29e+00 6.01e-01 1.54e+01 angle pdb=" N PHE C 454 " pdb=" CA PHE C 454 " pdb=" C PHE C 454 " ideal model delta sigma weight residual 111.69 106.94 4.75 1.23e+00 6.61e-01 1.49e+01 ... (remaining 11746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4702 17.61 - 35.21: 383 35.21 - 52.81: 114 52.81 - 70.42: 30 70.42 - 88.02: 16 Dihedral angle restraints: 5245 sinusoidal: 2134 harmonic: 3111 Sorted by residual: dihedral pdb=" CA GLN A 332 " pdb=" C GLN A 332 " pdb=" N LEU A 333 " pdb=" CA LEU A 333 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PRO A 223 " pdb=" C PRO A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CG ARG C 444 " pdb=" CD ARG C 444 " pdb=" NE ARG C 444 " pdb=" CZ ARG C 444 " ideal model delta sinusoidal sigma weight residual 90.00 40.84 49.16 2 1.50e+01 4.44e-03 1.22e+01 ... (remaining 5242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 581 0.037 - 0.074: 416 0.074 - 0.111: 233 0.111 - 0.148: 81 0.148 - 0.185: 13 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA TRP C 374 " pdb=" N TRP C 374 " pdb=" C TRP C 374 " pdb=" CB TRP C 374 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA VAL A 874 " pdb=" N VAL A 874 " pdb=" C VAL A 874 " pdb=" CB VAL A 874 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CB VAL C 439 " pdb=" CA VAL C 439 " pdb=" CG1 VAL C 439 " pdb=" CG2 VAL C 439 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 1321 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 441 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ALA C 441 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA C 441 " -0.026 2.00e-02 2.50e+03 pdb=" N MET C 442 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 440 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C VAL C 440 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL C 440 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA C 441 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 442 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C MET C 442 " 0.049 2.00e-02 2.50e+03 pdb=" O MET C 442 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 443 " -0.016 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 723 2.75 - 3.28: 8308 3.28 - 3.82: 15182 3.82 - 4.36: 18809 4.36 - 4.90: 31145 Nonbonded interactions: 74167 Sorted by model distance: nonbonded pdb=" OH TYR B 62 " pdb=" OE2 GLU C 438 " model vdw 2.207 3.040 nonbonded pdb=" ND1 HIS C 369 " pdb=" OH TYR C 372 " model vdw 2.210 3.120 nonbonded pdb=" OG1 THR A 118 " pdb=" NH2 ARG A 134 " model vdw 2.302 3.120 nonbonded pdb=" OE2 GLU B 193 " pdb=" OH TYR B 199 " model vdw 2.303 3.040 nonbonded pdb=" ND2 ASN A 950 " pdb=" OE1 GLU A 994 " model vdw 2.306 3.120 ... (remaining 74162 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.008 0.053 8672 Z= 0.499 Angle : 0.883 12.016 11751 Z= 0.556 Chirality : 0.061 0.185 1324 Planarity : 0.006 0.057 1500 Dihedral : 15.573 88.024 3235 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.70 % Allowed : 12.42 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1057 helix: 0.23 (0.37), residues: 217 sheet: 0.00 (0.26), residues: 384 loop : -0.34 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.007 TRP A 953 HIS 0.011 0.004 HIS B 138 PHE 0.030 0.006 PHE A 942 TYR 0.023 0.006 TYR B 76 ARG 0.019 0.002 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.004 Fit side-chains REVERT: A 150 LYS cc_start: 0.5626 (tptt) cc_final: 0.4650 (tptp) REVERT: A 224 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6971 (mm-30) REVERT: A 254 LYS cc_start: 0.6884 (mttt) cc_final: 0.6222 (ptpp) REVERT: A 267 ASN cc_start: 0.8138 (p0) cc_final: 0.7689 (p0) REVERT: A 847 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7938 (mtm180) outliers start: 14 outliers final: 8 residues processed: 121 average time/residue: 1.7361 time to fit residues: 220.4596 Evaluate side-chains 112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 HIS C 428 ASN C 447 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8672 Z= 0.161 Angle : 0.550 6.466 11751 Z= 0.292 Chirality : 0.044 0.163 1324 Planarity : 0.004 0.037 1500 Dihedral : 5.823 48.892 1186 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.44 % Allowed : 12.21 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1057 helix: 0.95 (0.36), residues: 219 sheet: 0.18 (0.26), residues: 368 loop : -0.38 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 207 HIS 0.004 0.001 HIS C 369 PHE 0.016 0.002 PHE C 450 TYR 0.011 0.001 TYR C 372 ARG 0.006 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.006 Fit side-chains REVERT: A 70 LYS cc_start: 0.7185 (mtpm) cc_final: 0.6225 (mppt) REVERT: A 150 LYS cc_start: 0.5829 (tptt) cc_final: 0.4621 (tptp) REVERT: A 158 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7209 (ttp-170) REVERT: A 210 GLU cc_start: 0.5421 (tm-30) cc_final: 0.4984 (tm-30) REVERT: A 224 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7021 (mm-30) REVERT: A 254 LYS cc_start: 0.6677 (mttt) cc_final: 0.6012 (ptpp) REVERT: A 267 ASN cc_start: 0.8174 (p0) cc_final: 0.7680 (p0) REVERT: A 847 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7718 (mtm180) REVERT: A 859 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6428 (pt0) outliers start: 21 outliers final: 7 residues processed: 120 average time/residue: 1.7504 time to fit residues: 220.7369 Evaluate side-chains 112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 950 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8672 Z= 0.323 Angle : 0.652 6.947 11751 Z= 0.345 Chirality : 0.047 0.171 1324 Planarity : 0.004 0.045 1500 Dihedral : 6.187 52.333 1180 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.02 % Allowed : 13.16 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1057 helix: 1.07 (0.36), residues: 220 sheet: 0.18 (0.26), residues: 373 loop : -0.44 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 207 HIS 0.006 0.001 HIS A1077 PHE 0.020 0.003 PHE A 169 TYR 0.017 0.002 TYR A 718 ARG 0.005 0.001 ARG C 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.034 Fit side-chains REVERT: A 70 LYS cc_start: 0.7192 (mtpm) cc_final: 0.6253 (mppt) REVERT: A 99 ASP cc_start: 0.6786 (m-30) cc_final: 0.6284 (t70) REVERT: A 150 LYS cc_start: 0.5608 (tttt) cc_final: 0.4518 (tptp) REVERT: A 210 GLU cc_start: 0.5547 (tm-30) cc_final: 0.5147 (tm-30) REVERT: A 224 GLU cc_start: 0.7617 (mt-10) cc_final: 0.6941 (mm-30) REVERT: A 254 LYS cc_start: 0.6750 (mttt) cc_final: 0.6086 (ptpp) REVERT: A 267 ASN cc_start: 0.8216 (p0) cc_final: 0.7716 (p0) REVERT: A 859 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6469 (pt0) REVERT: A 1106 GLN cc_start: 0.4744 (tp40) cc_final: 0.4507 (tp-100) REVERT: C 407 LEU cc_start: 0.4338 (OUTLIER) cc_final: 0.4057 (mp) outliers start: 17 outliers final: 7 residues processed: 123 average time/residue: 1.6902 time to fit residues: 218.5399 Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 0.0010 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8672 Z= 0.164 Angle : 0.533 5.947 11751 Z= 0.282 Chirality : 0.043 0.159 1324 Planarity : 0.003 0.036 1500 Dihedral : 5.639 55.808 1180 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.12 % Allowed : 13.48 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1057 helix: 1.45 (0.37), residues: 220 sheet: 0.20 (0.26), residues: 368 loop : -0.44 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 207 HIS 0.003 0.001 HIS A1077 PHE 0.015 0.002 PHE C 450 TYR 0.012 0.001 TYR A 891 ARG 0.005 0.000 ARG C 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.030 Fit side-chains REVERT: A 70 LYS cc_start: 0.7214 (mtpm) cc_final: 0.6236 (mppt) REVERT: A 150 LYS cc_start: 0.5577 (tttt) cc_final: 0.4504 (tptp) REVERT: A 210 GLU cc_start: 0.5528 (tm-30) cc_final: 0.5132 (tm-30) REVERT: A 224 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6884 (mm-30) REVERT: A 254 LYS cc_start: 0.6645 (mttt) cc_final: 0.5956 (ptpp) REVERT: A 267 ASN cc_start: 0.8228 (p0) cc_final: 0.7706 (p0) REVERT: A 847 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7454 (mtm180) REVERT: A 859 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6402 (pt0) REVERT: A 961 ASP cc_start: 0.7387 (p0) cc_final: 0.7125 (p0) REVERT: A 969 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7524 (pp20) REVERT: C 360 ILE cc_start: 0.4928 (OUTLIER) cc_final: 0.4720 (mp) REVERT: C 364 MET cc_start: 0.5852 (mtp) cc_final: 0.4620 (mmm) REVERT: C 377 TYR cc_start: 0.7399 (m-10) cc_final: 0.7108 (m-10) REVERT: C 378 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7174 (mmtm) REVERT: C 407 LEU cc_start: 0.4355 (OUTLIER) cc_final: 0.4042 (mp) REVERT: C 424 LEU cc_start: 0.5114 (OUTLIER) cc_final: 0.4830 (tm) REVERT: C 425 MET cc_start: 0.5186 (ttp) cc_final: 0.4948 (ttp) outliers start: 18 outliers final: 5 residues processed: 120 average time/residue: 1.7287 time to fit residues: 218.1831 Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8672 Z= 0.311 Angle : 0.642 7.475 11751 Z= 0.340 Chirality : 0.047 0.173 1324 Planarity : 0.004 0.044 1500 Dihedral : 5.946 51.592 1177 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.80 % Allowed : 14.33 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1057 helix: 1.21 (0.36), residues: 220 sheet: 0.14 (0.26), residues: 373 loop : -0.52 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 207 HIS 0.006 0.001 HIS A 789 PHE 0.017 0.003 PHE C 450 TYR 0.016 0.002 TYR A 718 ARG 0.005 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.911 Fit side-chains REVERT: A 27 GLU cc_start: 0.6493 (mp0) cc_final: 0.6061 (mp0) REVERT: A 70 LYS cc_start: 0.7199 (mtpm) cc_final: 0.6253 (mppt) REVERT: A 99 ASP cc_start: 0.6701 (m-30) cc_final: 0.6179 (t70) REVERT: A 150 LYS cc_start: 0.5592 (tttt) cc_final: 0.4489 (tptp) REVERT: A 210 GLU cc_start: 0.5552 (tm-30) cc_final: 0.5109 (tm-30) REVERT: A 224 GLU cc_start: 0.7624 (mt-10) cc_final: 0.6965 (mm-30) REVERT: A 254 LYS cc_start: 0.6687 (mttt) cc_final: 0.6000 (ptpp) REVERT: A 267 ASN cc_start: 0.8249 (p0) cc_final: 0.7715 (p0) REVERT: A 859 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6419 (pt0) REVERT: A 1106 GLN cc_start: 0.4752 (tp40) cc_final: 0.4535 (tp-100) REVERT: C 378 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7169 (mmtm) REVERT: C 383 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: C 407 LEU cc_start: 0.4259 (OUTLIER) cc_final: 0.3951 (mp) REVERT: C 424 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4774 (tm) outliers start: 15 outliers final: 4 residues processed: 124 average time/residue: 1.6785 time to fit residues: 218.5151 Evaluate side-chains 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8672 Z= 0.316 Angle : 0.645 7.933 11751 Z= 0.342 Chirality : 0.047 0.161 1324 Planarity : 0.004 0.041 1500 Dihedral : 5.826 54.259 1175 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.23 % Allowed : 14.12 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1057 helix: 1.07 (0.35), residues: 221 sheet: 0.10 (0.26), residues: 373 loop : -0.54 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 207 HIS 0.006 0.001 HIS A 789 PHE 0.018 0.003 PHE A 169 TYR 0.014 0.002 TYR A 718 ARG 0.006 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.047 Fit side-chains REVERT: A 27 GLU cc_start: 0.6455 (mp0) cc_final: 0.6009 (mp0) REVERT: A 70 LYS cc_start: 0.7190 (mtpm) cc_final: 0.6245 (mppt) REVERT: A 99 ASP cc_start: 0.6742 (m-30) cc_final: 0.6399 (m-30) REVERT: A 150 LYS cc_start: 0.5571 (tttt) cc_final: 0.4483 (tptp) REVERT: A 210 GLU cc_start: 0.5505 (tm-30) cc_final: 0.5031 (tm-30) REVERT: A 224 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6950 (mm-30) REVERT: A 254 LYS cc_start: 0.6690 (mttt) cc_final: 0.6002 (ptpp) REVERT: A 267 ASN cc_start: 0.8220 (p0) cc_final: 0.7725 (p0) REVERT: A 859 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6398 (pt0) REVERT: A 863 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: A 994 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: A 1106 GLN cc_start: 0.4717 (tp40) cc_final: 0.4506 (tp-100) REVERT: C 378 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7197 (mmtm) REVERT: C 383 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: C 407 LEU cc_start: 0.4272 (OUTLIER) cc_final: 0.3964 (mp) REVERT: C 421 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6120 (t0) REVERT: C 424 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4680 (tm) outliers start: 19 outliers final: 4 residues processed: 125 average time/residue: 1.7025 time to fit residues: 223.6389 Evaluate side-chains 125 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8672 Z= 0.167 Angle : 0.536 7.097 11751 Z= 0.284 Chirality : 0.044 0.147 1324 Planarity : 0.004 0.036 1500 Dihedral : 5.293 52.995 1175 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.70 % Allowed : 14.76 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1057 helix: 1.42 (0.36), residues: 221 sheet: 0.18 (0.26), residues: 371 loop : -0.53 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 207 HIS 0.003 0.001 HIS A 789 PHE 0.014 0.002 PHE C 450 TYR 0.012 0.001 TYR A 891 ARG 0.007 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.031 Fit side-chains REVERT: A 27 GLU cc_start: 0.6409 (mp0) cc_final: 0.5917 (mp0) REVERT: A 70 LYS cc_start: 0.7222 (mtpm) cc_final: 0.6246 (mppt) REVERT: A 150 LYS cc_start: 0.5600 (tttt) cc_final: 0.4465 (tptp) REVERT: A 210 GLU cc_start: 0.5559 (tm-30) cc_final: 0.5115 (tm-30) REVERT: A 224 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6986 (mm-30) REVERT: A 254 LYS cc_start: 0.6662 (mttt) cc_final: 0.5977 (ptpp) REVERT: A 267 ASN cc_start: 0.8229 (p0) cc_final: 0.7680 (p0) REVERT: A 859 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6381 (pt0) REVERT: A 961 ASP cc_start: 0.7369 (p0) cc_final: 0.7107 (p0) REVERT: A 969 GLU cc_start: 0.7806 (pp20) cc_final: 0.7604 (pm20) REVERT: A 994 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 1056 ASN cc_start: 0.6453 (m-40) cc_final: 0.6028 (m-40) REVERT: A 1106 GLN cc_start: 0.4757 (tp40) cc_final: 0.4541 (tp-100) REVERT: C 364 MET cc_start: 0.5928 (mtp) cc_final: 0.4634 (mmm) REVERT: C 378 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7258 (mmtm) REVERT: C 407 LEU cc_start: 0.4312 (OUTLIER) cc_final: 0.4002 (mp) REVERT: C 421 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.5996 (t0) REVERT: C 424 LEU cc_start: 0.5068 (OUTLIER) cc_final: 0.4859 (tm) REVERT: C 425 MET cc_start: 0.5270 (ttp) cc_final: 0.4937 (ttp) outliers start: 14 outliers final: 3 residues processed: 118 average time/residue: 1.8712 time to fit residues: 231.7565 Evaluate side-chains 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8672 Z= 0.201 Angle : 0.558 7.389 11751 Z= 0.295 Chirality : 0.044 0.149 1324 Planarity : 0.004 0.036 1500 Dihedral : 5.387 53.783 1175 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 14.97 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1057 helix: 1.39 (0.36), residues: 221 sheet: 0.12 (0.26), residues: 359 loop : -0.50 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 207 HIS 0.004 0.001 HIS A 789 PHE 0.015 0.002 PHE C 450 TYR 0.013 0.002 TYR A 891 ARG 0.006 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.964 Fit side-chains REVERT: A 27 GLU cc_start: 0.6353 (mp0) cc_final: 0.5884 (mp0) REVERT: A 70 LYS cc_start: 0.7217 (mtpm) cc_final: 0.6262 (mppt) REVERT: A 99 ASP cc_start: 0.6694 (m-30) cc_final: 0.6197 (t70) REVERT: A 150 LYS cc_start: 0.5607 (tttt) cc_final: 0.4455 (tptp) REVERT: A 210 GLU cc_start: 0.5543 (tm-30) cc_final: 0.5108 (tm-30) REVERT: A 224 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6941 (mm-30) REVERT: A 254 LYS cc_start: 0.6682 (mttt) cc_final: 0.5998 (ptpp) REVERT: A 267 ASN cc_start: 0.8237 (p0) cc_final: 0.7688 (p0) REVERT: A 859 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6393 (pt0) REVERT: A 961 ASP cc_start: 0.7356 (p0) cc_final: 0.7099 (p0) REVERT: A 994 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: A 1106 GLN cc_start: 0.4720 (tp40) cc_final: 0.4511 (tp-100) REVERT: C 364 MET cc_start: 0.5848 (mtp) cc_final: 0.4677 (mmm) REVERT: C 378 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7217 (mmtm) REVERT: C 383 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: C 407 LEU cc_start: 0.4258 (OUTLIER) cc_final: 0.3946 (mp) REVERT: C 421 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.5961 (t0) REVERT: C 425 MET cc_start: 0.5225 (ttp) cc_final: 0.4910 (ttp) outliers start: 15 outliers final: 3 residues processed: 122 average time/residue: 1.7736 time to fit residues: 226.7826 Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8672 Z= 0.181 Angle : 0.552 8.558 11751 Z= 0.290 Chirality : 0.044 0.152 1324 Planarity : 0.004 0.036 1500 Dihedral : 5.278 53.661 1175 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.49 % Allowed : 15.39 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1057 helix: 1.39 (0.36), residues: 221 sheet: 0.16 (0.26), residues: 371 loop : -0.50 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 207 HIS 0.004 0.001 HIS A 789 PHE 0.014 0.002 PHE C 450 TYR 0.012 0.002 TYR A 193 ARG 0.007 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.946 Fit side-chains REVERT: A 27 GLU cc_start: 0.6322 (mp0) cc_final: 0.5900 (mp0) REVERT: A 70 LYS cc_start: 0.7223 (mtpm) cc_final: 0.6266 (mppt) REVERT: A 150 LYS cc_start: 0.5560 (tttt) cc_final: 0.4402 (tptp) REVERT: A 210 GLU cc_start: 0.5512 (tm-30) cc_final: 0.5089 (tm-30) REVERT: A 224 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6923 (mm-30) REVERT: A 254 LYS cc_start: 0.6682 (mttt) cc_final: 0.5993 (ptpp) REVERT: A 267 ASN cc_start: 0.8235 (p0) cc_final: 0.7708 (p0) REVERT: A 859 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6373 (pt0) REVERT: A 887 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8060 (m) REVERT: A 961 ASP cc_start: 0.7341 (p0) cc_final: 0.7082 (p0) REVERT: A 994 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: A 1106 GLN cc_start: 0.4712 (tp40) cc_final: 0.4506 (tp-100) REVERT: C 364 MET cc_start: 0.5801 (mtp) cc_final: 0.4602 (mmm) REVERT: C 378 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7198 (mmtm) REVERT: C 383 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: C 407 LEU cc_start: 0.4275 (OUTLIER) cc_final: 0.3938 (mp) REVERT: C 421 ASP cc_start: 0.6455 (OUTLIER) cc_final: 0.5964 (t0) outliers start: 12 outliers final: 4 residues processed: 116 average time/residue: 1.6058 time to fit residues: 195.5015 Evaluate side-chains 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 0.0050 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8672 Z= 0.171 Angle : 0.540 7.929 11751 Z= 0.284 Chirality : 0.043 0.147 1324 Planarity : 0.004 0.036 1500 Dihedral : 5.184 53.300 1175 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.38 % Allowed : 15.61 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1057 helix: 1.42 (0.36), residues: 221 sheet: 0.15 (0.26), residues: 368 loop : -0.47 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 207 HIS 0.004 0.001 HIS C 437 PHE 0.013 0.002 PHE A1030 TYR 0.013 0.002 TYR A 193 ARG 0.007 0.000 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.990 Fit side-chains REVERT: A 27 GLU cc_start: 0.6243 (mp0) cc_final: 0.5849 (mp0) REVERT: A 70 LYS cc_start: 0.7223 (mtpm) cc_final: 0.6240 (mppt) REVERT: A 150 LYS cc_start: 0.5674 (tttt) cc_final: 0.4548 (tptp) REVERT: A 210 GLU cc_start: 0.5476 (tm-30) cc_final: 0.5053 (tm-30) REVERT: A 224 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6903 (mm-30) REVERT: A 254 LYS cc_start: 0.6675 (mttt) cc_final: 0.5986 (ptpp) REVERT: A 267 ASN cc_start: 0.8233 (p0) cc_final: 0.7704 (p0) REVERT: A 859 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6357 (pt0) REVERT: A 887 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8049 (m) REVERT: A 961 ASP cc_start: 0.7326 (p0) cc_final: 0.7077 (p0) REVERT: A 994 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: A 1106 GLN cc_start: 0.4712 (tp40) cc_final: 0.4509 (tp-100) REVERT: B 126 LYS cc_start: 0.7174 (mmtt) cc_final: 0.6920 (mptt) REVERT: C 364 MET cc_start: 0.5826 (mtp) cc_final: 0.4613 (mmm) REVERT: C 378 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7217 (mmtm) REVERT: C 383 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7299 (tp30) REVERT: C 407 LEU cc_start: 0.4231 (OUTLIER) cc_final: 0.3875 (mp) REVERT: C 421 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6191 (t0) outliers start: 11 outliers final: 4 residues processed: 116 average time/residue: 1.7352 time to fit residues: 211.3971 Evaluate side-chains 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 859 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 994 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.0070 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 84 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.188713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144895 restraints weight = 28410.420| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.85 r_work: 0.3575 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8672 Z= 0.130 Angle : 0.497 8.279 11751 Z= 0.261 Chirality : 0.043 0.140 1324 Planarity : 0.003 0.036 1500 Dihedral : 4.744 50.335 1175 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.38 % Allowed : 15.71 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1057 helix: 1.83 (0.37), residues: 214 sheet: 0.30 (0.26), residues: 365 loop : -0.40 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 893 HIS 0.003 0.001 HIS A 789 PHE 0.010 0.001 PHE A1030 TYR 0.013 0.001 TYR E 11 ARG 0.007 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4128.70 seconds wall clock time: 80 minutes 8.03 seconds (4808.03 seconds total)