Starting phenix.real_space_refine on Wed Apr 30 19:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c6q_45254/04_2025/9c6q_45254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c6q_45254/04_2025/9c6q_45254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c6q_45254/04_2025/9c6q_45254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c6q_45254/04_2025/9c6q_45254.map" model { file = "/net/cci-nas-00/data/ceres_data/9c6q_45254/04_2025/9c6q_45254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c6q_45254/04_2025/9c6q_45254.cif" } resolution = 3.18 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= 0.006 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 P 12 5.49 5 S 24 5.16 5 C 6189 2.51 5 N 1721 2.21 5 O 1895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9841 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 241 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "C" Number of atoms: 9600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9600 Classifications: {'peptide': 1190} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1155} Time building chain proxies: 7.83, per 1000 atoms: 0.80 Number of scatterers: 9841 At special positions: 0 Unit cell: (90.3495, 106.531, 133.951, 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) S 24 16.00 P 12 15.00 O 1895 8.00 N 1721 7.00 C 6189 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 49.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.564A pdb=" N PHE C 8 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 9 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 37 removed outlier: 3.558A pdb=" N THR C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 55 through 78 removed outlier: 3.565A pdb=" N ALA C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 75 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 111 Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.777A pdb=" N LEU C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 162 through 178 removed outlier: 3.827A pdb=" N GLN C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 208 removed outlier: 3.518A pdb=" N ASN C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 200 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 removed outlier: 3.691A pdb=" N ALA C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 removed outlier: 4.085A pdb=" N LYS C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 234' Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 276 through 287 removed outlier: 3.798A pdb=" N VAL C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.508A pdb=" N PHE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 321 Processing helix chain 'C' and resid 322 through 337 removed outlier: 3.799A pdb=" N ASN C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 433 removed outlier: 3.508A pdb=" N PHE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS C 422 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.840A pdb=" N GLU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 removed outlier: 3.863A pdb=" N GLY C 536 " --> pdb=" O MET C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 564 removed outlier: 3.640A pdb=" N GLU C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 605 through 616 Processing helix chain 'C' and resid 621 through 629 Processing helix chain 'C' and resid 637 through 657 removed outlier: 3.523A pdb=" N SER C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 674 No H-bonds generated for 'chain 'C' and resid 672 through 674' Processing helix chain 'C' and resid 675 through 693 Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.698A pdb=" N SER C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 723 " --> pdb=" O HIS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 738 removed outlier: 3.532A pdb=" N ALA C 738 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 808 removed outlier: 4.359A pdb=" N ASN C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN C 794 " --> pdb=" O HIS C 790 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 824 removed outlier: 3.554A pdb=" N MET C 824 " --> pdb=" O ARG C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 836 Processing helix chain 'C' and resid 839 through 855 removed outlier: 3.807A pdb=" N SER C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 879 Processing helix chain 'C' and resid 891 through 901 removed outlier: 3.619A pdb=" N SER C 901 " --> pdb=" O ASN C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.409A pdb=" N ARG C 913 " --> pdb=" O ASP C 909 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 938 " --> pdb=" O VAL C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 960 removed outlier: 3.531A pdb=" N ILE C 947 " --> pdb=" O SER C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1002 No H-bonds generated for 'chain 'C' and resid 1000 through 1002' Processing helix chain 'C' and resid 1009 through 1014 removed outlier: 3.972A pdb=" N CYS C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C1014 " --> pdb=" O GLU C1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1009 through 1014' Processing helix chain 'C' and resid 1014 through 1020 removed outlier: 3.900A pdb=" N LEU C1018 " --> pdb=" O SER C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1032 Processing helix chain 'C' and resid 1045 through 1052 removed outlier: 3.799A pdb=" N THR C1050 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C1051 " --> pdb=" O ILE C1047 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C1052 " --> pdb=" O MET C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1067 removed outlier: 3.584A pdb=" N ALA C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1127 removed outlier: 4.536A pdb=" N SER C1116 " --> pdb=" O SER C1112 " (cutoff:3.500A) Processing helix chain 'C' and resid 1176 through 1187 removed outlier: 3.649A pdb=" N VAL C1180 " --> pdb=" O ASN C1176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.723A pdb=" N ALA C 43 " --> pdb=" O ALA C 537 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 539 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 267 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU C 540 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 269 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE C 542 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 271 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU C 87 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE C 270 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.833A pdb=" N THR C 92 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 292 removed outlier: 3.720A pdb=" N LEU C 521 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 354 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 342 through 344 removed outlier: 3.844A pdb=" N LYS C 382 " --> pdb=" O ASP C 377 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 377 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 384 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 595 through 601 removed outlier: 6.811A pdb=" N VAL C 595 " --> pdb=" O ILE C 866 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU C 868 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 597 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL C 870 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS C 599 " --> pdb=" O VAL C 870 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 773 " --> pdb=" O TYR C 662 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 731 " --> pdb=" O SER C 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 744 through 745 removed outlier: 3.628A pdb=" N TYR C 744 " --> pdb=" O SER C 769 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 974 through 975 Processing sheet with id=AA9, first strand: chain 'C' and resid 997 through 998 Processing sheet with id=AB1, first strand: chain 'C' and resid 1072 through 1074 removed outlier: 3.797A pdb=" N THR C1072 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C1089 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN C1086 " --> pdb=" O LEU C1099 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C1099 " --> pdb=" O ASN C1086 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE C1131 " --> pdb=" O ILE C1162 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE C1164 " --> pdb=" O PHE C1131 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR C1133 " --> pdb=" O ILE C1164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C1163 " --> pdb=" O ARG C1145 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C1145 " --> pdb=" O GLU C1163 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1182 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: 3.71 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2047 1.33 - 1.45: 2395 1.45 - 1.57: 5558 1.57 - 1.69: 23 1.69 - 1.81: 39 Bond restraints: 10062 Sorted by residual: bond pdb=" C GLU C 465 " pdb=" N SER C 466 " ideal model delta sigma weight residual 1.335 1.697 -0.362 1.38e-02 5.25e+03 6.88e+02 bond pdb=" C LEU C 456 " pdb=" N THR C 457 " ideal model delta sigma weight residual 1.334 1.525 -0.191 1.41e-02 5.03e+03 1.84e+02 bond pdb=" N GLU C 463 " pdb=" CA GLU C 463 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.23e+00 bond pdb=" N PHE C 459 " pdb=" CA PHE C 459 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.26e-02 6.30e+03 6.10e+00 bond pdb=" N HIS C 458 " pdb=" CA HIS C 458 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.28e+00 ... (remaining 10057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 13621 4.41 - 8.82: 24 8.82 - 13.22: 1 13.22 - 17.63: 2 17.63 - 22.04: 1 Bond angle restraints: 13649 Sorted by residual: angle pdb=" CA LEU C 456 " pdb=" C LEU C 456 " pdb=" N THR C 457 " ideal model delta sigma weight residual 118.14 96.10 22.04 1.31e+00 5.83e-01 2.83e+02 angle pdb=" O LEU C 456 " pdb=" C LEU C 456 " pdb=" N THR C 457 " ideal model delta sigma weight residual 122.43 138.64 -16.21 1.34e+00 5.57e-01 1.46e+02 angle pdb=" C LEU C 456 " pdb=" N THR C 457 " pdb=" CA THR C 457 " ideal model delta sigma weight residual 120.71 103.17 17.54 1.67e+00 3.59e-01 1.10e+02 angle pdb=" C PHE C 999 " pdb=" CA PHE C 999 " pdb=" CB PHE C 999 " ideal model delta sigma weight residual 116.63 110.70 5.93 1.16e+00 7.43e-01 2.61e+01 angle pdb=" C LYS C 590 " pdb=" N ASP C 591 " pdb=" CA ASP C 591 " ideal model delta sigma weight residual 122.09 129.84 -7.75 1.86e+00 2.89e-01 1.73e+01 ... (remaining 13644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 5277 16.85 - 33.71: 577 33.71 - 50.56: 139 50.56 - 67.42: 38 67.42 - 84.27: 16 Dihedral angle restraints: 6047 sinusoidal: 2551 harmonic: 3496 Sorted by residual: dihedral pdb=" CA ILE C 294 " pdb=" C ILE C 294 " pdb=" N TRP C 295 " pdb=" CA TRP C 295 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA THR C 780 " pdb=" C THR C 780 " pdb=" N GLN C 781 " pdb=" CA GLN C 781 " ideal model delta harmonic sigma weight residual -180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE C 459 " pdb=" C PHE C 459 " pdb=" N ASN C 460 " pdb=" CA ASN C 460 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1164 0.044 - 0.089: 257 0.089 - 0.133: 74 0.133 - 0.178: 6 0.178 - 0.222: 1 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA VAL C 354 " pdb=" N VAL C 354 " pdb=" C VAL C 354 " pdb=" CB VAL C 354 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB THR C 80 " pdb=" CA THR C 80 " pdb=" OG1 THR C 80 " pdb=" CG2 THR C 80 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA LEU C 356 " pdb=" N LEU C 356 " pdb=" C LEU C 356 " pdb=" CB LEU C 356 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 1499 not shown) Planarity restraints: 1736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 456 " 0.029 2.00e-02 2.50e+03 7.35e-02 5.41e+01 pdb=" C LEU C 456 " -0.126 2.00e-02 2.50e+03 pdb=" O LEU C 456 " 0.057 2.00e-02 2.50e+03 pdb=" N THR C 457 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 473 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.82e+00 pdb=" CG ASP C 473 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 473 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 473 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 181 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 182 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 182 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 182 " 0.025 5.00e-02 4.00e+02 ... (remaining 1733 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 175 2.69 - 3.24: 9101 3.24 - 3.80: 13587 3.80 - 4.35: 17694 4.35 - 4.90: 30147 Nonbonded interactions: 70704 Sorted by model distance: nonbonded pdb=" OE2 GLU C 465 " pdb=" OH TYR C 469 " model vdw 2.139 3.040 nonbonded pdb=" OH TYR C 733 " pdb=" O GLU C 777 " model vdw 2.145 3.040 nonbonded pdb=" O CYS C1013 " pdb=" OH TYR C1103 " model vdw 2.168 3.040 nonbonded pdb=" N LEU C 456 " pdb=" N THR C 457 " model vdw 2.265 2.560 nonbonded pdb=" O TYR C 662 " pdb=" OG SER C 773 " model vdw 2.269 3.040 ... (remaining 70699 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=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: 10.140 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: 0.690 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.850 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 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 : 0.005 0.362 10062 Z= 0.325 Angle : 0.637 22.041 13649 Z= 0.369 Chirality : 0.040 0.222 1502 Planarity : 0.004 0.074 1736 Dihedral : 15.428 84.274 3783 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1188 helix: 1.92 (0.24), residues: 524 sheet: -0.03 (0.49), residues: 120 loop : -2.18 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 428 HIS 0.005 0.001 HIS C 307 PHE 0.019 0.001 PHE C 8 TYR 0.027 0.001 TYR C 469 ARG 0.004 0.000 ARG C1145 Details of bonding type rmsd hydrogen bonds : bond 0.18526 ( 410) hydrogen bonds : angle 5.83313 ( 1182) covalent geometry : bond 0.00477 (10062) covalent geometry : angle 0.63723 (13649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: C 119 ARG cc_start: 0.7367 (ttt180) cc_final: 0.6978 (ttt-90) REVERT: C 422 LYS cc_start: 0.5476 (mtmm) cc_final: 0.4753 (mmtt) REVERT: C 517 LYS cc_start: 0.7411 (mmmt) cc_final: 0.6812 (mmtm) REVERT: C 599 LYS cc_start: 0.7392 (ttmm) cc_final: 0.7076 (tptt) REVERT: C 948 GLN cc_start: 0.7513 (tp40) cc_final: 0.7221 (mm-40) REVERT: C 952 ASP cc_start: 0.7998 (m-30) cc_final: 0.7730 (m-30) REVERT: C 1022 GLN cc_start: 0.5712 (pt0) cc_final: 0.5332 (pm20) outliers start: 2 outliers final: 1 residues processed: 179 average time/residue: 0.2673 time to fit residues: 64.6930 Evaluate side-chains 94 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 94 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 70 GLN C 335 ASN C 364 HIS C 462 GLN C 575 GLN C 668 ASN C 836 HIS C 951 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.215002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170393 restraints weight = 10895.832| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.06 r_work: 0.3494 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10062 Z= 0.136 Angle : 0.578 8.316 13649 Z= 0.304 Chirality : 0.041 0.140 1502 Planarity : 0.005 0.067 1736 Dihedral : 9.481 77.255 1437 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.18 % Allowed : 5.79 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.13 (0.25), residues: 1188 helix: 1.81 (0.23), residues: 534 sheet: 0.24 (0.48), residues: 114 loop : -2.27 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 643 HIS 0.006 0.001 HIS C 364 PHE 0.021 0.002 PHE C 607 TYR 0.018 0.002 TYR C 127 ARG 0.007 0.001 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 410) hydrogen bonds : angle 3.99669 ( 1182) covalent geometry : bond 0.00287 (10062) covalent geometry : angle 0.57786 (13649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 51 THR cc_start: 0.7266 (p) cc_final: 0.6962 (p) REVERT: C 517 LYS cc_start: 0.7413 (mmmt) cc_final: 0.6650 (mmtm) REVERT: C 540 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 599 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7712 (tttp) REVERT: C 661 ARG cc_start: 0.7021 (mtp180) cc_final: 0.6611 (mmm-85) REVERT: C 863 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.7148 (ttm-80) REVERT: C 882 SER cc_start: 0.7551 (p) cc_final: 0.7067 (t) REVERT: C 931 LYS cc_start: 0.7471 (tppt) cc_final: 0.6840 (ttpt) REVERT: C 952 ASP cc_start: 0.8335 (m-30) cc_final: 0.8060 (m-30) REVERT: C 954 ARG cc_start: 0.7186 (mtm180) cc_final: 0.6913 (mtt180) REVERT: C 1022 GLN cc_start: 0.5970 (pt0) cc_final: 0.5342 (pm20) outliers start: 23 outliers final: 15 residues processed: 109 average time/residue: 0.2637 time to fit residues: 39.4741 Evaluate side-chains 104 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 774 ILE Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1180 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 HIS C 668 ASN C 951 GLN C1042 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.212929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175856 restraints weight = 11157.621| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.81 r_work: 0.3485 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10062 Z= 0.119 Angle : 0.507 7.994 13649 Z= 0.268 Chirality : 0.038 0.141 1502 Planarity : 0.003 0.037 1736 Dihedral : 9.020 77.106 1434 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.90 % Allowed : 8.26 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.09 (0.25), residues: 1188 helix: 2.03 (0.23), residues: 534 sheet: 0.39 (0.48), residues: 114 loop : -2.21 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 643 HIS 0.004 0.001 HIS C 496 PHE 0.017 0.001 PHE C 607 TYR 0.010 0.001 TYR C 892 ARG 0.003 0.000 ARG C 669 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 410) hydrogen bonds : angle 3.83455 ( 1182) covalent geometry : bond 0.00252 (10062) covalent geometry : angle 0.50693 (13649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.021 Fit side-chains REVERT: C 51 THR cc_start: 0.7467 (p) cc_final: 0.7159 (p) REVERT: C 119 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6800 (ttt-90) REVERT: C 230 GLU cc_start: 0.7764 (tp30) cc_final: 0.7332 (tm-30) REVERT: C 517 LYS cc_start: 0.7318 (mmmt) cc_final: 0.6363 (tmtt) REVERT: C 521 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7666 (mp) REVERT: C 540 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 599 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7838 (tttp) REVERT: C 931 LYS cc_start: 0.7675 (tppt) cc_final: 0.7128 (ttpt) REVERT: C 952 ASP cc_start: 0.8428 (m-30) cc_final: 0.8130 (m-30) REVERT: C 954 ARG cc_start: 0.7475 (mtm180) cc_final: 0.7241 (mtt90) REVERT: C 1022 GLN cc_start: 0.6448 (pt0) cc_final: 0.5571 (pm20) REVERT: C 1059 GLU cc_start: 0.7243 (mt-10) cc_final: 0.7039 (mt-10) outliers start: 20 outliers final: 6 residues processed: 109 average time/residue: 0.3103 time to fit residues: 45.5337 Evaluate side-chains 90 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 ARG Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 0.0980 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.212558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.173159 restraints weight = 11081.702| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.89 r_work: 0.3480 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10062 Z= 0.092 Angle : 0.459 8.766 13649 Z= 0.241 Chirality : 0.038 0.134 1502 Planarity : 0.003 0.037 1736 Dihedral : 8.853 75.803 1434 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.95 % Allowed : 10.16 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.34 (0.25), residues: 1188 helix: 2.28 (0.23), residues: 534 sheet: 0.63 (0.49), residues: 114 loop : -2.16 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 428 HIS 0.003 0.001 HIS C 178 PHE 0.012 0.001 PHE C 607 TYR 0.009 0.001 TYR C 662 ARG 0.003 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 410) hydrogen bonds : angle 3.56300 ( 1182) covalent geometry : bond 0.00185 (10062) covalent geometry : angle 0.45890 (13649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.151 Fit side-chains REVERT: C 51 THR cc_start: 0.7487 (p) cc_final: 0.7181 (p) REVERT: C 230 GLU cc_start: 0.7703 (tp30) cc_final: 0.7353 (tm-30) REVERT: C 599 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7852 (tttp) REVERT: C 708 MET cc_start: 0.8010 (mtt) cc_final: 0.7513 (mtt) REVERT: C 931 LYS cc_start: 0.7646 (tppt) cc_final: 0.7029 (ttpt) REVERT: C 952 ASP cc_start: 0.8412 (m-30) cc_final: 0.8090 (m-30) REVERT: C 954 ARG cc_start: 0.7465 (mtm180) cc_final: 0.7255 (mtt90) REVERT: C 1022 GLN cc_start: 0.6430 (pt0) cc_final: 0.5533 (pm20) outliers start: 10 outliers final: 5 residues processed: 86 average time/residue: 0.2553 time to fit residues: 31.7108 Evaluate side-chains 78 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1180 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 0.0770 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 836 HIS C 951 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.204124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154448 restraints weight = 11047.264| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 4.77 r_work: 0.3284 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10062 Z= 0.168 Angle : 0.573 8.481 13649 Z= 0.301 Chirality : 0.041 0.192 1502 Planarity : 0.004 0.043 1736 Dihedral : 9.339 72.231 1434 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.09 % Allowed : 10.83 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1188 helix: 1.95 (0.23), residues: 535 sheet: 0.28 (0.46), residues: 126 loop : -2.34 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 428 HIS 0.006 0.001 HIS C 496 PHE 0.026 0.002 PHE C 607 TYR 0.016 0.002 TYR C 258 ARG 0.005 0.001 ARG C1083 Details of bonding type rmsd hydrogen bonds : bond 0.06067 ( 410) hydrogen bonds : angle 3.97800 ( 1182) covalent geometry : bond 0.00379 (10062) covalent geometry : angle 0.57304 (13649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 1.151 Fit side-chains REVERT: C 51 THR cc_start: 0.7654 (p) cc_final: 0.7363 (p) REVERT: C 124 GLN cc_start: 0.5954 (mt0) cc_final: 0.5392 (mt0) REVERT: C 517 LYS cc_start: 0.7331 (mmmt) cc_final: 0.6281 (tmtt) REVERT: C 521 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7706 (mp) REVERT: C 540 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8070 (mp) REVERT: C 599 LYS cc_start: 0.8363 (ttmm) cc_final: 0.8052 (tttm) REVERT: C 697 THR cc_start: 0.8343 (p) cc_final: 0.7927 (m) REVERT: C 708 MET cc_start: 0.7968 (mtt) cc_final: 0.7665 (mtt) REVERT: C 931 LYS cc_start: 0.7838 (tppt) cc_final: 0.7169 (ttpt) REVERT: C 952 ASP cc_start: 0.8493 (m-30) cc_final: 0.8139 (m-30) REVERT: C 954 ARG cc_start: 0.7696 (mtm180) cc_final: 0.7379 (mtt90) REVERT: C 1022 GLN cc_start: 0.6877 (pt0) cc_final: 0.5737 (pm20) REVERT: C 1029 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7443 (mt-10) outliers start: 22 outliers final: 12 residues processed: 101 average time/residue: 0.2587 time to fit residues: 37.1578 Evaluate side-chains 90 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1062 VAL Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 THR Chi-restraints excluded: chain C residue 1180 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 15 optimal weight: 0.0670 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 8 optimal weight: 0.5980 overall best weight: 1.0920 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.207361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162009 restraints weight = 11092.101| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.33 r_work: 0.3415 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10062 Z= 0.117 Angle : 0.499 8.898 13649 Z= 0.262 Chirality : 0.039 0.171 1502 Planarity : 0.003 0.038 1736 Dihedral : 9.054 72.816 1434 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.52 % Allowed : 13.39 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1188 helix: 2.12 (0.23), residues: 533 sheet: 0.37 (0.48), residues: 121 loop : -2.25 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 428 HIS 0.004 0.001 HIS C 496 PHE 0.013 0.001 PHE C 607 TYR 0.010 0.001 TYR C 258 ARG 0.004 0.000 ARG C1083 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 410) hydrogen bonds : angle 3.72615 ( 1182) covalent geometry : bond 0.00259 (10062) covalent geometry : angle 0.49862 (13649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 1.036 Fit side-chains REVERT: C 1 MET cc_start: 0.1526 (ppp) cc_final: 0.1172 (ppp) REVERT: C 51 THR cc_start: 0.7639 (p) cc_final: 0.7340 (p) REVERT: C 123 GLU cc_start: 0.6741 (tp30) cc_final: 0.6158 (mp0) REVERT: C 599 LYS cc_start: 0.8337 (ttmm) cc_final: 0.8002 (tttm) REVERT: C 697 THR cc_start: 0.8339 (p) cc_final: 0.7960 (m) REVERT: C 931 LYS cc_start: 0.7827 (tppt) cc_final: 0.7202 (ttpt) REVERT: C 952 ASP cc_start: 0.8422 (m-30) cc_final: 0.8056 (m-30) REVERT: C 954 ARG cc_start: 0.7592 (mtm180) cc_final: 0.7378 (mtt90) REVERT: C 1022 GLN cc_start: 0.7048 (pt0) cc_final: 0.5918 (pm20) REVERT: C 1029 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7464 (mt-10) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 0.2451 time to fit residues: 33.3174 Evaluate side-chains 86 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 586 ARG Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 89 optimal weight: 0.0070 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN C 592 ASN C 951 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.204977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160055 restraints weight = 11369.097| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.45 r_work: 0.3376 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10062 Z= 0.138 Angle : 0.542 11.034 13649 Z= 0.285 Chirality : 0.040 0.190 1502 Planarity : 0.004 0.072 1736 Dihedral : 9.221 71.094 1434 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.90 % Allowed : 13.87 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.05 (0.25), residues: 1188 helix: 2.07 (0.23), residues: 534 sheet: 0.33 (0.49), residues: 116 loop : -2.32 (0.23), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 428 HIS 0.005 0.001 HIS C 496 PHE 0.014 0.001 PHE C 416 TYR 0.015 0.001 TYR C 744 ARG 0.002 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 410) hydrogen bonds : angle 3.89506 ( 1182) covalent geometry : bond 0.00309 (10062) covalent geometry : angle 0.54211 (13649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 1.083 Fit side-chains REVERT: C 1 MET cc_start: 0.1538 (ppp) cc_final: 0.0867 (ppp) REVERT: C 51 THR cc_start: 0.7648 (p) cc_final: 0.7331 (p) REVERT: C 123 GLU cc_start: 0.6692 (tp30) cc_final: 0.6114 (mp0) REVERT: C 124 GLN cc_start: 0.6058 (OUTLIER) cc_final: 0.5606 (mt0) REVERT: C 517 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6398 (tmtt) REVERT: C 521 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7597 (mp) REVERT: C 599 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8129 (tttm) REVERT: C 628 HIS cc_start: 0.7991 (t70) cc_final: 0.7284 (m170) REVERT: C 663 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.6534 (tpt) REVERT: C 697 THR cc_start: 0.8416 (p) cc_final: 0.8207 (m) REVERT: C 931 LYS cc_start: 0.7879 (tppt) cc_final: 0.7264 (ttpt) REVERT: C 952 ASP cc_start: 0.8465 (m-30) cc_final: 0.8085 (m-30) REVERT: C 954 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7364 (mtt90) REVERT: C 1029 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: C 1145 ARG cc_start: 0.6840 (mtm-85) cc_final: 0.6520 (mtt180) outliers start: 20 outliers final: 10 residues processed: 99 average time/residue: 0.2483 time to fit residues: 34.6243 Evaluate side-chains 86 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 THR Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 81 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 116 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN C 951 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.207073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162851 restraints weight = 11248.326| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.22 r_work: 0.3391 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10062 Z= 0.098 Angle : 0.488 11.586 13649 Z= 0.254 Chirality : 0.038 0.138 1502 Planarity : 0.003 0.058 1736 Dihedral : 8.961 70.410 1434 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.14 % Allowed : 15.29 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1188 helix: 2.27 (0.23), residues: 537 sheet: 0.82 (0.53), residues: 99 loop : -2.29 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 428 HIS 0.004 0.001 HIS C 178 PHE 0.011 0.001 PHE C 416 TYR 0.009 0.001 TYR C1133 ARG 0.002 0.000 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 410) hydrogen bonds : angle 3.61928 ( 1182) covalent geometry : bond 0.00200 (10062) covalent geometry : angle 0.48776 (13649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.118 Fit side-chains REVERT: C 1 MET cc_start: 0.1476 (ppp) cc_final: 0.0775 (ppp) REVERT: C 51 THR cc_start: 0.7673 (p) cc_final: 0.7360 (p) REVERT: C 123 GLU cc_start: 0.6638 (tp30) cc_final: 0.6211 (mp0) REVERT: C 124 GLN cc_start: 0.5752 (OUTLIER) cc_final: 0.5191 (mt0) REVERT: C 599 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8077 (tttm) REVERT: C 607 PHE cc_start: 0.6274 (t80) cc_final: 0.5866 (t80) REVERT: C 628 HIS cc_start: 0.7987 (t70) cc_final: 0.7264 (m170) REVERT: C 663 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6419 (tpt) REVERT: C 697 THR cc_start: 0.8353 (p) cc_final: 0.8078 (m) REVERT: C 931 LYS cc_start: 0.7830 (tppt) cc_final: 0.7244 (ttpt) REVERT: C 952 ASP cc_start: 0.8437 (m-30) cc_final: 0.8045 (m-30) REVERT: C 954 ARG cc_start: 0.7633 (mtm180) cc_final: 0.7375 (mtt90) REVERT: C 1029 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: C 1145 ARG cc_start: 0.6794 (mtm-85) cc_final: 0.6485 (mtt180) outliers start: 12 outliers final: 8 residues processed: 87 average time/residue: 0.2782 time to fit residues: 34.6419 Evaluate side-chains 83 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1134 VAL Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 623 HIS C 951 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.204948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.161709 restraints weight = 11213.475| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.40 r_work: 0.3386 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10062 Z= 0.118 Angle : 0.516 12.410 13649 Z= 0.267 Chirality : 0.039 0.139 1502 Planarity : 0.003 0.052 1736 Dihedral : 9.018 69.624 1434 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.52 % Allowed : 15.10 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.24 (0.25), residues: 1188 helix: 2.25 (0.23), residues: 536 sheet: 0.80 (0.53), residues: 99 loop : -2.27 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 428 HIS 0.004 0.001 HIS C 496 PHE 0.014 0.001 PHE C 8 TYR 0.011 0.001 TYR C 258 ARG 0.007 0.000 ARG C 421 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 410) hydrogen bonds : angle 3.69147 ( 1182) covalent geometry : bond 0.00259 (10062) covalent geometry : angle 0.51559 (13649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.071 Fit side-chains REVERT: C 1 MET cc_start: 0.1536 (ppp) cc_final: 0.0837 (ppp) REVERT: C 51 THR cc_start: 0.7687 (p) cc_final: 0.7376 (p) REVERT: C 123 GLU cc_start: 0.6762 (tp30) cc_final: 0.6120 (mp0) REVERT: C 521 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7534 (mp) REVERT: C 540 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8015 (mp) REVERT: C 599 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8167 (tttm) REVERT: C 607 PHE cc_start: 0.6436 (t80) cc_final: 0.6021 (t80) REVERT: C 628 HIS cc_start: 0.8039 (t70) cc_final: 0.7320 (m170) REVERT: C 663 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6537 (tpt) REVERT: C 697 THR cc_start: 0.8380 (p) cc_final: 0.8142 (m) REVERT: C 931 LYS cc_start: 0.7873 (tppt) cc_final: 0.7253 (ttpt) REVERT: C 952 ASP cc_start: 0.8524 (m-30) cc_final: 0.8147 (m-30) REVERT: C 954 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7420 (mtt90) REVERT: C 1029 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: C 1145 ARG cc_start: 0.6876 (mtm-85) cc_final: 0.6575 (mtt180) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.2510 time to fit residues: 30.9310 Evaluate side-chains 85 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 89 optimal weight: 0.0670 chunk 71 optimal weight: 0.1980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN C 951 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.208063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.164708 restraints weight = 11229.659| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.09 r_work: 0.3439 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10062 Z= 0.093 Angle : 0.477 12.306 13649 Z= 0.247 Chirality : 0.038 0.135 1502 Planarity : 0.003 0.050 1736 Dihedral : 8.848 69.176 1434 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.71 % Allowed : 15.00 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1188 helix: 2.42 (0.23), residues: 537 sheet: 0.82 (0.51), residues: 104 loop : -2.24 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 428 HIS 0.003 0.001 HIS C 178 PHE 0.010 0.001 PHE C 416 TYR 0.009 0.001 TYR C1133 ARG 0.006 0.000 ARG C 421 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 410) hydrogen bonds : angle 3.49321 ( 1182) covalent geometry : bond 0.00192 (10062) covalent geometry : angle 0.47726 (13649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.082 Fit side-chains REVERT: C 1 MET cc_start: 0.1527 (ppp) cc_final: 0.0804 (ppp) REVERT: C 51 THR cc_start: 0.7664 (p) cc_final: 0.7365 (p) REVERT: C 230 GLU cc_start: 0.7688 (tp30) cc_final: 0.7432 (tm-30) REVERT: C 521 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7349 (mp) REVERT: C 540 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7987 (mp) REVERT: C 599 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8072 (tttm) REVERT: C 607 PHE cc_start: 0.6231 (t80) cc_final: 0.5608 (t80) REVERT: C 628 HIS cc_start: 0.8013 (t70) cc_final: 0.7295 (m170) REVERT: C 663 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.6416 (tpt) REVERT: C 697 THR cc_start: 0.8336 (p) cc_final: 0.8072 (m) REVERT: C 931 LYS cc_start: 0.7808 (tppt) cc_final: 0.7193 (ttpt) REVERT: C 952 ASP cc_start: 0.8429 (m-30) cc_final: 0.8045 (m-30) REVERT: C 954 ARG cc_start: 0.7590 (mtm180) cc_final: 0.7355 (mtt90) REVERT: C 1022 GLN cc_start: 0.7289 (pt0) cc_final: 0.6174 (pm20) REVERT: C 1029 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: C 1145 ARG cc_start: 0.6819 (mtm-85) cc_final: 0.6524 (mtt180) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.2419 time to fit residues: 29.7527 Evaluate side-chains 87 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 586 ARG Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 THR Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.0470 chunk 54 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 30.0000 chunk 6 optimal weight: 0.0010 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN C 951 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.209791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.166785 restraints weight = 11265.611| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.99 r_work: 0.3468 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10062 Z= 0.086 Angle : 0.460 11.804 13649 Z= 0.239 Chirality : 0.037 0.149 1502 Planarity : 0.003 0.047 1736 Dihedral : 8.747 68.882 1434 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.04 % Allowed : 15.67 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.54 (0.25), residues: 1188 helix: 2.51 (0.23), residues: 542 sheet: 0.95 (0.51), residues: 104 loop : -2.20 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 428 HIS 0.004 0.000 HIS C 178 PHE 0.008 0.001 PHE C 416 TYR 0.010 0.001 TYR C1133 ARG 0.006 0.000 ARG C 421 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 410) hydrogen bonds : angle 3.37302 ( 1182) covalent geometry : bond 0.00172 (10062) covalent geometry : angle 0.45961 (13649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6180.47 seconds wall clock time: 108 minutes 45.04 seconds (6525.04 seconds total)