Starting phenix.real_space_refine on Sun Jul 27 22:10:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4b_35168/07_2025/8i4b_35168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4b_35168/07_2025/8i4b_35168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i4b_35168/07_2025/8i4b_35168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4b_35168/07_2025/8i4b_35168.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4b_35168/07_2025/8i4b_35168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4b_35168/07_2025/8i4b_35168.cif" } resolution = 3.13 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= 0.063 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 43 5.16 5 C 6316 2.51 5 N 1637 2.21 5 O 1731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9727 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 9727 Classifications: {'peptide': 1218} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1178} Chain breaks: 2 Time building chain proxies: 5.83, per 1000 atoms: 0.60 Number of scatterers: 9727 At special positions: 0 Unit cell: (77.04, 114.49, 149.8, 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 43 16.00 O 1731 8.00 N 1637 7.00 C 6316 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=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 5 sheets defined 66.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.797A pdb=" N PHE A 23 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.676A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 75 Processing helix chain 'A' and resid 79 through 93 removed outlier: 5.379A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 121 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 151 through 179 removed outlier: 3.640A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.676A pdb=" N LYS A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.476A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N HIS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.586A pdb=" N ALA A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.536A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 248 No H-bonds generated for 'chain 'A' and resid 247 through 248' Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 265 through 282 removed outlier: 4.415A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 342 removed outlier: 4.154A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.550A pdb=" N VAL A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 390 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.552A pdb=" N VAL A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 520 removed outlier: 4.493A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.734A pdb=" N ASP A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.567A pdb=" N SER A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.868A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.573A pdb=" N TYR A 596 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.759A pdb=" N ALA A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 709 " --> pdb=" O PHE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 744 removed outlier: 3.917A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 806 removed outlier: 3.500A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.839A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 816 " --> pdb=" O PHE A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.662A pdb=" N ASP A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.573A pdb=" N ILE A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 866 Processing helix chain 'A' and resid 869 through 884 removed outlier: 3.632A pdb=" N ILE A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 876 " --> pdb=" O GLY A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.880A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.630A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 932 Processing helix chain 'A' and resid 936 through 967 removed outlier: 3.855A pdb=" N LEU A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1017 removed outlier: 4.254A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 removed outlier: 4.054A pdb=" N SER A1086 " --> pdb=" O SER A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1108 Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1130 through 1136 removed outlier: 3.563A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.681A pdb=" N PHE A1223 " --> pdb=" O ILE A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 removed outlier: 3.727A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1277 removed outlier: 3.720A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A1277 " --> pdb=" O VAL A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 435 removed outlier: 3.905A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.447A pdb=" N THR A 587 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL A 443 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A 589 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 602 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 606 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.651A pdb=" N GLY A 487 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 6.921A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 6.490A pdb=" N VAL A1071 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1653 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: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1654 1.32 - 1.44: 2578 1.44 - 1.56: 5633 1.56 - 1.69: 1 1.69 - 1.81: 70 Bond restraints: 9936 Sorted by residual: bond pdb=" CB ARG A 782 " pdb=" CG ARG A 782 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.38e+01 bond pdb=" CB GLN A 845 " pdb=" CG GLN A 845 " ideal model delta sigma weight residual 1.520 1.422 0.098 3.00e-02 1.11e+03 1.06e+01 bond pdb=" CB VAL A 159 " pdb=" CG1 VAL A 159 " ideal model delta sigma weight residual 1.521 1.415 0.106 3.30e-02 9.18e+02 1.03e+01 bond pdb=" CB ILE A 331 " pdb=" CG2 ILE A 331 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.82e+00 bond pdb=" CB THR A 99 " pdb=" CG2 THR A 99 " ideal model delta sigma weight residual 1.521 1.420 0.101 3.30e-02 9.18e+02 9.33e+00 ... (remaining 9931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 13079 2.77 - 5.54: 336 5.54 - 8.31: 37 8.31 - 11.08: 8 11.08 - 13.85: 3 Bond angle restraints: 13463 Sorted by residual: angle pdb=" CB MET A 990 " pdb=" CG MET A 990 " pdb=" SD MET A 990 " ideal model delta sigma weight residual 112.70 126.55 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CG1 ILE A 147 " pdb=" CB ILE A 147 " pdb=" CG2 ILE A 147 " ideal model delta sigma weight residual 110.70 97.12 13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C ARG A1220 " pdb=" N GLU A1221 " pdb=" CA GLU A1221 " ideal model delta sigma weight residual 122.56 115.53 7.03 1.72e+00 3.38e-01 1.67e+01 angle pdb=" CG1 ILE A 805 " pdb=" CB ILE A 805 " pdb=" CG2 ILE A 805 " ideal model delta sigma weight residual 110.70 99.33 11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C ASP A 43 " pdb=" N MET A 44 " pdb=" CA MET A 44 " ideal model delta sigma weight residual 120.87 127.24 -6.37 1.69e+00 3.50e-01 1.42e+01 ... (remaining 13458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5346 17.76 - 35.53: 499 35.53 - 53.29: 79 53.29 - 71.06: 11 71.06 - 88.82: 6 Dihedral angle restraints: 5941 sinusoidal: 2382 harmonic: 3559 Sorted by residual: dihedral pdb=" CA ASP A 975 " pdb=" C ASP A 975 " pdb=" N ALA A 976 " pdb=" CA ALA A 976 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER A 252 " pdb=" C SER A 252 " pdb=" N CYS A 253 " pdb=" CA CYS A 253 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ILE A 194 " pdb=" C ILE A 194 " pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 5938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1316 0.086 - 0.171: 230 0.171 - 0.257: 12 0.257 - 0.343: 2 0.343 - 0.428: 1 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB VAL A 889 " pdb=" CA VAL A 889 " pdb=" CG1 VAL A 889 " pdb=" CG2 VAL A 889 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 346 " pdb=" CA ILE A 346 " pdb=" CG1 ILE A 346 " pdb=" CG2 ILE A 346 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1558 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 218 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO A 219 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 109 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO A 110 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 840 " -0.027 2.00e-02 2.50e+03 2.11e-02 7.77e+00 pdb=" CG PHE A 840 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 840 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 840 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 840 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 840 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 840 " -0.014 2.00e-02 2.50e+03 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 745 2.71 - 3.26: 9858 3.26 - 3.80: 15696 3.80 - 4.35: 19666 4.35 - 4.90: 33704 Nonbonded interactions: 79669 Sorted by model distance: nonbonded pdb=" OD1 ASP A 953 " pdb=" NE2 GLN A 994 " model vdw 2.161 3.120 nonbonded pdb=" O THR A 488 " pdb=" OG SER A 491 " model vdw 2.179 3.040 nonbonded pdb=" OG SER A 479 " pdb=" O GLN A 481 " model vdw 2.195 3.040 nonbonded pdb=" O ARG A 706 " pdb=" NH1 ARG A 706 " model vdw 2.213 3.120 nonbonded pdb=" OE2 GLU A1221 " pdb=" NZ LYS A1222 " model vdw 2.218 3.120 ... (remaining 79664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 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: 1.020 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.580 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 0.017 0.117 9936 Z= 0.677 Angle : 1.070 13.849 13463 Z= 0.581 Chirality : 0.063 0.428 1561 Planarity : 0.007 0.079 1673 Dihedral : 14.068 88.819 3635 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.17 (0.22), residues: 1212 helix: -1.25 (0.17), residues: 795 sheet: -0.48 (0.54), residues: 72 loop : -1.68 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 64 HIS 0.014 0.002 HIS A 153 PHE 0.046 0.004 PHE A 840 TYR 0.031 0.003 TYR A1016 ARG 0.012 0.001 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.14592 ( 571) hydrogen bonds : angle 6.64014 ( 1653) covalent geometry : bond 0.01669 ( 9936) covalent geometry : angle 1.06991 (13463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.050 Fit side-chains REVERT: A 206 ASP cc_start: 0.8006 (m-30) cc_final: 0.7619 (m-30) REVERT: A 319 MET cc_start: 0.8159 (tpp) cc_final: 0.7638 (mmt) REVERT: A 345 VAL cc_start: 0.8308 (p) cc_final: 0.8074 (m) REVERT: A 887 ARG cc_start: 0.6917 (mtm110) cc_final: 0.6534 (mtt180) REVERT: A 1135 LEU cc_start: 0.8577 (mp) cc_final: 0.7922 (tt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2410 time to fit residues: 40.6821 Evaluate side-chains 91 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.0370 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 0.0870 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN A 492 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.252373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.189696 restraints weight = 10093.362| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.89 r_work: 0.3608 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9936 Z= 0.117 Angle : 0.538 8.005 13463 Z= 0.286 Chirality : 0.039 0.141 1561 Planarity : 0.005 0.052 1673 Dihedral : 4.613 17.505 1314 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.56 % Allowed : 5.18 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.24), residues: 1212 helix: 0.41 (0.19), residues: 798 sheet: 0.34 (0.58), residues: 64 loop : -0.85 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.004 0.001 HIS A 35 PHE 0.022 0.002 PHE A 941 TYR 0.021 0.001 TYR A1016 ARG 0.004 0.001 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 571) hydrogen bonds : angle 4.32642 ( 1653) covalent geometry : bond 0.00239 ( 9936) covalent geometry : angle 0.53838 (13463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.942 Fit side-chains REVERT: A 121 GLU cc_start: 0.7616 (tt0) cc_final: 0.7279 (mt-10) REVERT: A 122 ASN cc_start: 0.8563 (m-40) cc_final: 0.8302 (m-40) REVERT: A 147 ILE cc_start: 0.7935 (tt) cc_final: 0.7723 (tt) REVERT: A 173 MET cc_start: 0.8140 (mtm) cc_final: 0.7860 (mtp) REVERT: A 268 PHE cc_start: 0.7231 (m-10) cc_final: 0.6975 (m-80) REVERT: A 345 VAL cc_start: 0.8434 (p) cc_final: 0.8166 (m) REVERT: A 391 LEU cc_start: 0.8215 (mt) cc_final: 0.7963 (mt) REVERT: A 717 LEU cc_start: 0.7702 (tp) cc_final: 0.7501 (tp) REVERT: A 744 MET cc_start: 0.7327 (ptp) cc_final: 0.7075 (tmm) REVERT: A 805 ILE cc_start: 0.8288 (tt) cc_final: 0.8026 (tt) REVERT: A 887 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6823 (mtt180) REVERT: A 922 ARG cc_start: 0.7398 (tpp80) cc_final: 0.6909 (tmm-80) REVERT: A 1015 GLU cc_start: 0.6992 (tp30) cc_final: 0.6440 (tt0) REVERT: A 1018 ASP cc_start: 0.6805 (t70) cc_final: 0.6586 (t70) outliers start: 6 outliers final: 2 residues processed: 108 average time/residue: 0.2373 time to fit residues: 36.1247 Evaluate side-chains 85 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 1038 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 47 optimal weight: 0.4980 chunk 79 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 102 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 602 GLN A 924 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.250770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.188943 restraints weight = 10293.359| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.92 r_work: 0.3600 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9936 Z= 0.123 Angle : 0.501 6.086 13463 Z= 0.265 Chirality : 0.039 0.149 1561 Planarity : 0.004 0.051 1673 Dihedral : 4.131 16.350 1314 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.66 % Allowed : 6.87 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.71 (0.25), residues: 1212 helix: 0.93 (0.19), residues: 805 sheet: 0.45 (0.53), residues: 75 loop : -0.47 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.004 0.001 HIS A 798 PHE 0.020 0.002 PHE A 336 TYR 0.012 0.001 TYR A 157 ARG 0.004 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 571) hydrogen bonds : angle 3.98942 ( 1653) covalent geometry : bond 0.00275 ( 9936) covalent geometry : angle 0.50056 (13463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.961 Fit side-chains REVERT: A 33 ILE cc_start: 0.7889 (mm) cc_final: 0.7553 (mt) REVERT: A 70 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7732 (tmm160) REVERT: A 89 TRP cc_start: 0.7975 (p-90) cc_final: 0.7630 (p-90) REVERT: A 121 GLU cc_start: 0.7658 (tt0) cc_final: 0.7359 (mt-10) REVERT: A 345 VAL cc_start: 0.8585 (p) cc_final: 0.8335 (m) REVERT: A 805 ILE cc_start: 0.8204 (tt) cc_final: 0.7891 (tt) REVERT: A 887 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7355 (mtt90) REVERT: A 922 ARG cc_start: 0.7260 (tpp80) cc_final: 0.6934 (tmm-80) REVERT: A 926 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7929 (tt) REVERT: A 1018 ASP cc_start: 0.6893 (t70) cc_final: 0.6590 (t0) REVERT: A 1107 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 1135 LEU cc_start: 0.7970 (mp) cc_final: 0.7691 (mp) outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 0.2354 time to fit residues: 32.1393 Evaluate side-chains 91 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 45 optimal weight: 30.0000 chunk 67 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4673 r_free = 0.4673 target = 0.250226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.189193 restraints weight = 10131.144| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.06 r_work: 0.3564 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9936 Z= 0.125 Angle : 0.481 5.611 13463 Z= 0.254 Chirality : 0.039 0.142 1561 Planarity : 0.004 0.050 1673 Dihedral : 3.963 16.301 1314 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.85 % Allowed : 8.85 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1212 helix: 1.11 (0.19), residues: 802 sheet: 0.39 (0.55), residues: 80 loop : -0.13 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.003 0.001 HIS A 798 PHE 0.019 0.001 PHE A 336 TYR 0.013 0.001 TYR A 157 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 571) hydrogen bonds : angle 3.87104 ( 1653) covalent geometry : bond 0.00288 ( 9936) covalent geometry : angle 0.48089 (13463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 1.259 Fit side-chains REVERT: A 33 ILE cc_start: 0.7874 (mm) cc_final: 0.7625 (mt) REVERT: A 89 TRP cc_start: 0.7880 (p-90) cc_final: 0.7667 (p-90) REVERT: A 121 GLU cc_start: 0.7736 (tt0) cc_final: 0.7531 (mt-10) REVERT: A 345 VAL cc_start: 0.8605 (p) cc_final: 0.8346 (m) REVERT: A 820 ARG cc_start: 0.7503 (ttp-110) cc_final: 0.7099 (ttm170) REVERT: A 887 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7419 (mtt90) REVERT: A 922 ARG cc_start: 0.7252 (tpp80) cc_final: 0.6920 (tmm-80) REVERT: A 926 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8106 (tp) REVERT: A 1018 ASP cc_start: 0.7131 (t70) cc_final: 0.6825 (t70) REVERT: A 1107 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 1135 LEU cc_start: 0.8090 (mp) cc_final: 0.7840 (mp) REVERT: A 1155 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6214 (tt) outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 0.3419 time to fit residues: 50.0372 Evaluate side-chains 92 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4666 r_free = 0.4666 target = 0.249242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.188451 restraints weight = 10065.232| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.93 r_work: 0.3563 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9936 Z= 0.135 Angle : 0.484 9.094 13463 Z= 0.254 Chirality : 0.040 0.151 1561 Planarity : 0.003 0.049 1673 Dihedral : 3.883 16.091 1314 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.94 % Allowed : 9.79 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1212 helix: 1.21 (0.19), residues: 799 sheet: 0.57 (0.55), residues: 80 loop : -0.02 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.004 0.001 HIS A 153 PHE 0.020 0.001 PHE A 336 TYR 0.012 0.001 TYR A 157 ARG 0.004 0.000 ARG A 782 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 571) hydrogen bonds : angle 3.83701 ( 1653) covalent geometry : bond 0.00314 ( 9936) covalent geometry : angle 0.48356 (13463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.951 Fit side-chains REVERT: A 33 ILE cc_start: 0.7845 (mm) cc_final: 0.7637 (mt) REVERT: A 41 GLU cc_start: 0.7963 (mp0) cc_final: 0.7475 (mt-10) REVERT: A 89 TRP cc_start: 0.7899 (p-90) cc_final: 0.7692 (p-90) REVERT: A 345 VAL cc_start: 0.8609 (p) cc_final: 0.8378 (m) REVERT: A 820 ARG cc_start: 0.7541 (ttp-110) cc_final: 0.7087 (ttm170) REVERT: A 887 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7429 (mtt180) REVERT: A 926 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7859 (tp) REVERT: A 1018 ASP cc_start: 0.7201 (t70) cc_final: 0.6988 (t0) REVERT: A 1107 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8131 (mt-10) REVERT: A 1135 LEU cc_start: 0.8197 (mp) cc_final: 0.7937 (mp) REVERT: A 1155 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6315 (tt) outliers start: 10 outliers final: 5 residues processed: 97 average time/residue: 0.2121 time to fit residues: 29.8679 Evaluate side-chains 94 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.251671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189487 restraints weight = 10088.995| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.95 r_work: 0.3604 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9936 Z= 0.104 Angle : 0.453 8.346 13463 Z= 0.236 Chirality : 0.038 0.138 1561 Planarity : 0.003 0.046 1673 Dihedral : 3.725 14.989 1314 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.04 % Allowed : 10.08 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1212 helix: 1.40 (0.19), residues: 802 sheet: 0.61 (0.55), residues: 80 loop : 0.09 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.003 0.000 HIS A 153 PHE 0.016 0.001 PHE A 336 TYR 0.011 0.001 TYR A 157 ARG 0.003 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 571) hydrogen bonds : angle 3.68426 ( 1653) covalent geometry : bond 0.00225 ( 9936) covalent geometry : angle 0.45282 (13463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.996 Fit side-chains REVERT: A 41 GLU cc_start: 0.7966 (mp0) cc_final: 0.7531 (mt-10) REVERT: A 74 ASP cc_start: 0.7845 (t0) cc_final: 0.7117 (t0) REVERT: A 126 MET cc_start: 0.7264 (mpp) cc_final: 0.6674 (ppp) REVERT: A 127 ASP cc_start: 0.6782 (t0) cc_final: 0.6529 (t0) REVERT: A 186 MET cc_start: 0.6593 (tpp) cc_final: 0.6352 (ttm) REVERT: A 345 VAL cc_start: 0.8536 (p) cc_final: 0.8301 (m) REVERT: A 887 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7540 (mtt90) REVERT: A 890 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7364 (mmtm) REVERT: A 926 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7840 (tp) REVERT: A 1018 ASP cc_start: 0.7280 (t70) cc_final: 0.7039 (t70) REVERT: A 1107 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8164 (mt-10) REVERT: A 1135 LEU cc_start: 0.8273 (mp) cc_final: 0.8015 (mp) REVERT: A 1155 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6277 (tt) REVERT: A 1220 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6933 (mtt90) outliers start: 11 outliers final: 6 residues processed: 99 average time/residue: 0.2328 time to fit residues: 33.0393 Evaluate side-chains 94 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 44 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4676 r_free = 0.4676 target = 0.250922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.189038 restraints weight = 10127.594| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.04 r_work: 0.3591 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9936 Z= 0.111 Angle : 0.456 7.789 13463 Z= 0.239 Chirality : 0.039 0.148 1561 Planarity : 0.003 0.046 1673 Dihedral : 3.685 15.305 1314 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.22 % Allowed : 10.92 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1212 helix: 1.48 (0.19), residues: 801 sheet: 0.61 (0.55), residues: 80 loop : 0.23 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.004 0.001 HIS A 153 PHE 0.017 0.001 PHE A 336 TYR 0.011 0.001 TYR A 157 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 571) hydrogen bonds : angle 3.68165 ( 1653) covalent geometry : bond 0.00246 ( 9936) covalent geometry : angle 0.45600 (13463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.032 Fit side-chains REVERT: A 41 GLU cc_start: 0.7949 (mp0) cc_final: 0.7537 (mt-10) REVERT: A 74 ASP cc_start: 0.7996 (t0) cc_final: 0.7720 (t0) REVERT: A 76 GLN cc_start: 0.8128 (pm20) cc_final: 0.7793 (tt0) REVERT: A 126 MET cc_start: 0.7344 (mpp) cc_final: 0.6751 (ppp) REVERT: A 127 ASP cc_start: 0.6902 (t0) cc_final: 0.6654 (t0) REVERT: A 345 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8374 (m) REVERT: A 820 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7057 (ttm170) REVERT: A 887 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7394 (mtt180) REVERT: A 890 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7404 (mmtm) REVERT: A 926 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7883 (tp) REVERT: A 1018 ASP cc_start: 0.7303 (t70) cc_final: 0.6998 (t0) REVERT: A 1107 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 1135 LEU cc_start: 0.8319 (mp) cc_final: 0.8053 (mp) REVERT: A 1155 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6441 (tt) REVERT: A 1220 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6962 (mtt90) outliers start: 13 outliers final: 7 residues processed: 93 average time/residue: 0.2304 time to fit residues: 30.9157 Evaluate side-chains 93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 48 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS A 725 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.246353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.183783 restraints weight = 10157.235| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.12 r_work: 0.3491 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9936 Z= 0.212 Angle : 0.538 7.031 13463 Z= 0.281 Chirality : 0.043 0.160 1561 Planarity : 0.004 0.048 1673 Dihedral : 3.972 17.634 1314 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.13 % Allowed : 11.49 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1212 helix: 1.15 (0.19), residues: 793 sheet: 0.55 (0.54), residues: 80 loop : 0.08 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 734 HIS 0.008 0.001 HIS A 153 PHE 0.025 0.002 PHE A 336 TYR 0.013 0.001 TYR A 737 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 571) hydrogen bonds : angle 3.96385 ( 1653) covalent geometry : bond 0.00521 ( 9936) covalent geometry : angle 0.53805 (13463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7964 (mp0) cc_final: 0.7690 (mt-10) REVERT: A 186 MET cc_start: 0.6666 (tpp) cc_final: 0.6363 (ttm) REVERT: A 345 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8495 (m) REVERT: A 887 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7663 (mtt90) REVERT: A 897 ARG cc_start: 0.6862 (ttm-80) cc_final: 0.6492 (ttt-90) REVERT: A 922 ARG cc_start: 0.7387 (tpp80) cc_final: 0.6842 (tmm-80) REVERT: A 926 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7702 (tp) REVERT: A 1007 MET cc_start: 0.8576 (tpt) cc_final: 0.8367 (mmm) REVERT: A 1107 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 1155 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6535 (tt) REVERT: A 1220 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6860 (mtt90) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.2417 time to fit residues: 31.0708 Evaluate side-chains 91 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 74 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4668 r_free = 0.4668 target = 0.249745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.187244 restraints weight = 10069.143| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.08 r_work: 0.3562 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9936 Z= 0.115 Angle : 0.469 6.963 13463 Z= 0.245 Chirality : 0.039 0.166 1561 Planarity : 0.003 0.047 1673 Dihedral : 3.746 15.507 1314 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.04 % Allowed : 11.86 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1212 helix: 1.45 (0.19), residues: 794 sheet: 0.60 (0.54), residues: 80 loop : 0.24 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.004 0.001 HIS A 153 PHE 0.018 0.001 PHE A 336 TYR 0.012 0.001 TYR A 157 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 571) hydrogen bonds : angle 3.74494 ( 1653) covalent geometry : bond 0.00258 ( 9936) covalent geometry : angle 0.46873 (13463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8005 (mp0) cc_final: 0.7721 (mt-10) REVERT: A 76 GLN cc_start: 0.8132 (pm20) cc_final: 0.7811 (pm20) REVERT: A 126 MET cc_start: 0.7459 (mpp) cc_final: 0.6853 (ppp) REVERT: A 345 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8424 (m) REVERT: A 763 TRP cc_start: 0.8614 (t60) cc_final: 0.8325 (t-100) REVERT: A 887 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7461 (mtt90) REVERT: A 897 ARG cc_start: 0.6778 (ttm-80) cc_final: 0.6430 (ttt-90) REVERT: A 926 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7681 (tp) REVERT: A 1107 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 1135 LEU cc_start: 0.8349 (mp) cc_final: 0.8107 (mp) REVERT: A 1155 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6622 (tt) REVERT: A 1220 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6881 (mtt90) outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 0.2287 time to fit residues: 31.2822 Evaluate side-chains 97 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4655 r_free = 0.4655 target = 0.248109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.181524 restraints weight = 10068.005| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.90 r_work: 0.3546 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9936 Z= 0.151 Angle : 0.498 6.707 13463 Z= 0.260 Chirality : 0.040 0.150 1561 Planarity : 0.004 0.060 1673 Dihedral : 3.818 16.695 1314 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.04 % Allowed : 11.96 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1212 helix: 1.40 (0.19), residues: 794 sheet: 0.61 (0.54), residues: 80 loop : 0.20 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.006 0.001 HIS A 153 PHE 0.020 0.002 PHE A 336 TYR 0.012 0.001 TYR A 157 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 571) hydrogen bonds : angle 3.81484 ( 1653) covalent geometry : bond 0.00359 ( 9936) covalent geometry : angle 0.49789 (13463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8203 (mp0) cc_final: 0.7852 (mt-10) REVERT: A 76 GLN cc_start: 0.8165 (pm20) cc_final: 0.7716 (pm20) REVERT: A 345 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8455 (m) REVERT: A 763 TRP cc_start: 0.8737 (t60) cc_final: 0.8385 (t-100) REVERT: A 887 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7767 (mtt90) REVERT: A 897 ARG cc_start: 0.6877 (ttm-80) cc_final: 0.6528 (ttt-90) REVERT: A 922 ARG cc_start: 0.7405 (tpp80) cc_final: 0.6685 (tmm-80) REVERT: A 926 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7643 (tp) REVERT: A 1107 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 1135 LEU cc_start: 0.8162 (mp) cc_final: 0.7913 (mp) REVERT: A 1155 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6265 (tt) REVERT: A 1183 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8157 (mm-40) REVERT: A 1220 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6824 (mtt90) outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 0.2307 time to fit residues: 31.3655 Evaluate side-chains 96 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1220 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 30.0000 chunk 84 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.249675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.186110 restraints weight = 9918.331| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.02 r_work: 0.3561 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9936 Z= 0.123 Angle : 0.469 6.564 13463 Z= 0.245 Chirality : 0.039 0.143 1561 Planarity : 0.003 0.054 1673 Dihedral : 3.715 15.550 1314 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.13 % Allowed : 11.86 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1212 helix: 1.53 (0.19), residues: 797 sheet: 0.70 (0.54), residues: 80 loop : 0.25 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.005 0.001 HIS A 153 PHE 0.020 0.001 PHE A 389 TYR 0.011 0.001 TYR A 157 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 571) hydrogen bonds : angle 3.71573 ( 1653) covalent geometry : bond 0.00283 ( 9936) covalent geometry : angle 0.46876 (13463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.37 seconds wall clock time: 99 minutes 5.88 seconds (5945.88 seconds total)