Starting phenix.real_space_refine on Sun Dec 29 23:45:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zek_60037/12_2024/8zek_60037.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zek_60037/12_2024/8zek_60037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zek_60037/12_2024/8zek_60037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zek_60037/12_2024/8zek_60037.map" model { file = "/net/cci-nas-00/data/ceres_data/8zek_60037/12_2024/8zek_60037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zek_60037/12_2024/8zek_60037.cif" } resolution = 3.15 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= 0.009 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 52 5.16 5 C 7342 2.51 5 N 1935 2.21 5 O 2231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11560 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9642 Classifications: {'peptide': 1194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1153} Chain breaks: 1 Chain: "B" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 959 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "C" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 959 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Time building chain proxies: 8.51, per 1000 atoms: 0.74 Number of scatterers: 11560 At special positions: 0 Unit cell: (86, 112.66, 141.04, 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 52 16.00 O 2231 8.00 N 1935 7.00 C 7342 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 6 sheets defined 59.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 removed outlier: 4.110A pdb=" N ILE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 76 through 101 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.734A pdb=" N ASP A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.769A pdb=" N LEU A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.724A pdb=" N ILE A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.511A pdb=" N GLU A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 248 through 268 removed outlier: 3.511A pdb=" N VAL A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.747A pdb=" N LYS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 277' Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 317 through 335 Processing helix chain 'A' and resid 339 through 348 removed outlier: 4.191A pdb=" N GLN A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.687A pdb=" N ARG A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.604A pdb=" N VAL A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.661A pdb=" N HIS A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 410' Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 456 through 476 removed outlier: 3.600A pdb=" N GLU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 500 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 536 through 547 Processing helix chain 'A' and resid 561 through 564 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 626 through 636 removed outlier: 4.773A pdb=" N ASN A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 662 through 670 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 736 through 746 removed outlier: 5.906A pdb=" N GLU A 742 " --> pdb=" O ASN A 738 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 808 through 819 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 839 through 857 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.515A pdb=" N GLU A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS A 872 " --> pdb=" O LYS A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 867 through 872' Processing helix chain 'A' and resid 875 through 910 Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'A' and resid 939 through 962 removed outlier: 3.576A pdb=" N MET A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 989 Processing helix chain 'A' and resid 1013 through 1026 Processing helix chain 'A' and resid 1030 through 1045 removed outlier: 3.912A pdb=" N TYR A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1065 Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1099 through 1101 No H-bonds generated for 'chain 'A' and resid 1099 through 1101' Processing helix chain 'A' and resid 1104 through 1114 removed outlier: 3.730A pdb=" N VAL A1114 " --> pdb=" O ARG A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1131 Processing helix chain 'A' and resid 1137 through 1169 removed outlier: 3.641A pdb=" N ASP A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1178 Processing helix chain 'A' and resid 1179 through 1188 removed outlier: 4.177A pdb=" N GLY A1188 " --> pdb=" O TYR A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1199 removed outlier: 3.909A pdb=" N ILE A1197 " --> pdb=" O ASP A1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 27 removed outlier: 3.862A pdb=" N VAL B 11 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 77 through 111 removed outlier: 4.122A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU B 99 " --> pdb=" O TRP B 95 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASP B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 26 removed outlier: 3.844A pdb=" N VAL C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 45 removed outlier: 4.388A pdb=" N ASP C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 59 Processing helix chain 'C' and resid 77 through 97 removed outlier: 3.680A pdb=" N ILE C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 309 through 310 removed outlier: 7.151A pdb=" N TYR A 502 " --> pdb=" O LYS A 549 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN A 551 " --> pdb=" O TYR A 502 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA A 504 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 553 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL A 506 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 555 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 606 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 680 removed outlier: 3.633A pdb=" N ALA A 788 " --> pdb=" O VAL A 680 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 693 through 695 removed outlier: 4.513A pdb=" N TYR A 732 " --> pdb=" O ILE A 717 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1001 through 1003 583 hydrogen bonds defined for protein. 1719 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: 4.06 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3850 1.34 - 1.46: 2715 1.46 - 1.58: 5152 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 11809 Sorted by residual: bond pdb=" CA ILE A 489 " pdb=" CB ILE A 489 " ideal model delta sigma weight residual 1.534 1.545 -0.010 6.80e-03 2.16e+04 2.35e+00 bond pdb=" CA VAL A1115 " pdb=" C VAL A1115 " ideal model delta sigma weight residual 1.520 1.531 -0.012 8.80e-03 1.29e+04 1.77e+00 bond pdb=" CA ILE A 489 " pdb=" C ILE A 489 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.67e+00 bond pdb=" CA VAL A1115 " pdb=" CB VAL A1115 " ideal model delta sigma weight residual 1.534 1.543 -0.009 6.80e-03 2.16e+04 1.58e+00 bond pdb=" CB ILE A 848 " pdb=" CG2 ILE A 848 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 ... (remaining 11804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 15807 2.58 - 5.16: 142 5.16 - 7.74: 22 7.74 - 10.33: 8 10.33 - 12.91: 2 Bond angle restraints: 15981 Sorted by residual: angle pdb=" N TYR C 8 " pdb=" CA TYR C 8 " pdb=" C TYR C 8 " ideal model delta sigma weight residual 111.36 116.56 -5.20 1.09e+00 8.42e-01 2.28e+01 angle pdb=" CB MET A 98 " pdb=" CG MET A 98 " pdb=" SD MET A 98 " ideal model delta sigma weight residual 112.70 125.61 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C LEU A 488 " pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 120.24 122.54 -2.30 6.30e-01 2.52e+00 1.34e+01 angle pdb=" C ASP A 340 " pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta sigma weight residual 120.33 123.24 -2.91 8.00e-01 1.56e+00 1.32e+01 angle pdb=" CB MET A 170 " pdb=" CG MET A 170 " pdb=" SD MET A 170 " ideal model delta sigma weight residual 112.70 123.11 -10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 15976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 5964 15.05 - 30.10: 735 30.10 - 45.15: 240 45.15 - 60.20: 87 60.20 - 75.25: 65 Dihedral angle restraints: 7091 sinusoidal: 2895 harmonic: 4196 Sorted by residual: dihedral pdb=" CA GLN A 961 " pdb=" C GLN A 961 " pdb=" N MET A 962 " pdb=" CA MET A 962 " ideal model delta harmonic sigma weight residual -180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CB LYS A 276 " pdb=" CG LYS A 276 " pdb=" CD LYS A 276 " pdb=" CE LYS A 276 " ideal model delta sinusoidal sigma weight residual 60.00 117.71 -57.71 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA MET A 776 " pdb=" C MET A 776 " pdb=" N PRO A 777 " pdb=" CA PRO A 777 " ideal model delta harmonic sigma weight residual -180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 ... (remaining 7088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1157 0.032 - 0.064: 396 0.064 - 0.097: 121 0.097 - 0.129: 41 0.129 - 0.161: 5 Chirality restraints: 1720 Sorted by residual: chirality pdb=" CA ILE A 652 " pdb=" N ILE A 652 " pdb=" C ILE A 652 " pdb=" CB ILE A 652 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA TYR C 8 " pdb=" N TYR C 8 " pdb=" C TYR C 8 " pdb=" CB TYR C 8 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CG LEU A 707 " pdb=" CB LEU A 707 " pdb=" CD1 LEU A 707 " pdb=" CD2 LEU A 707 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1717 not shown) Planarity restraints: 2089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 616 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 617 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 109 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C VAL C 109 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL C 109 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU C 110 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 776 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 777 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 777 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 777 " 0.022 5.00e-02 4.00e+02 ... (remaining 2086 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2850 2.79 - 3.32: 12440 3.32 - 3.85: 21222 3.85 - 4.37: 23571 4.37 - 4.90: 37727 Nonbonded interactions: 97810 Sorted by model distance: nonbonded pdb=" OH TYR C 8 " pdb=" OD2 ASP C 93 " model vdw 2.266 3.040 nonbonded pdb=" O ALA A 664 " pdb=" OG SER A 668 " model vdw 2.281 3.040 nonbonded pdb=" O PHE A 757 " pdb=" NZ LYS A 778 " model vdw 2.282 3.120 nonbonded pdb=" O LYS A 681 " pdb=" ND2 ASN A 752 " model vdw 2.291 3.120 nonbonded pdb=" O TRP A 264 " pdb=" OG1 THR A 267 " model vdw 2.304 3.040 ... (remaining 97805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 0.010 Normalize map: mean=0, sd=1: 6.740 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.810 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5315 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11809 Z= 0.174 Angle : 0.675 12.907 15981 Z= 0.366 Chirality : 0.038 0.161 1720 Planarity : 0.003 0.056 2089 Dihedral : 17.294 75.250 4385 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.29 % Allowed : 19.94 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.22), residues: 1418 helix: 1.49 (0.19), residues: 764 sheet: -1.53 (0.56), residues: 72 loop : -1.17 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 696 HIS 0.005 0.001 HIS B 14 PHE 0.024 0.001 PHE A 832 TYR 0.021 0.001 TYR B 25 ARG 0.005 0.001 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.0278 (pmm) cc_final: -0.0518 (ptt) REVERT: A 318 HIS cc_start: 0.5016 (m90) cc_final: 0.4768 (t70) REVERT: A 356 ASP cc_start: 0.7124 (t70) cc_final: 0.6132 (m-30) REVERT: A 363 SER cc_start: 0.8321 (t) cc_final: 0.7691 (p) REVERT: A 517 MET cc_start: 0.5788 (pmm) cc_final: 0.4528 (mpp) REVERT: A 541 MET cc_start: 0.6569 (ppp) cc_final: 0.6056 (ptm) REVERT: A 562 TRP cc_start: 0.7046 (p-90) cc_final: 0.6670 (p-90) REVERT: A 638 MET cc_start: 0.7856 (pmm) cc_final: 0.7581 (pmm) REVERT: A 657 ILE cc_start: 0.5983 (mp) cc_final: 0.5422 (mm) REVERT: A 796 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8987 (tp30) REVERT: A 1132 LEU cc_start: 0.7829 (mt) cc_final: 0.7590 (tp) REVERT: A 1143 LEU cc_start: 0.8451 (mm) cc_final: 0.8250 (mt) REVERT: B 112 TYR cc_start: 0.8969 (m-80) cc_final: 0.8752 (m-80) REVERT: C 24 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7670 (tpp80) REVERT: C 25 TYR cc_start: 0.8048 (t80) cc_final: 0.7726 (t80) REVERT: C 29 ARG cc_start: 0.6403 (pmm-80) cc_final: 0.5958 (tpt90) REVERT: C 77 ASP cc_start: 0.7553 (m-30) cc_final: 0.6830 (t0) REVERT: C 92 ILE cc_start: 0.7864 (mm) cc_final: 0.7616 (mt) outliers start: 16 outliers final: 6 residues processed: 288 average time/residue: 0.2963 time to fit residues: 116.4248 Evaluate side-chains 144 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1187 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 258 ASN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN A 647 ASN A 702 ASN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11809 Z= 0.314 Angle : 0.706 10.620 15981 Z= 0.367 Chirality : 0.044 0.276 1720 Planarity : 0.005 0.059 2089 Dihedral : 4.827 50.633 1569 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.04 % Allowed : 19.45 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.22), residues: 1418 helix: 1.49 (0.19), residues: 764 sheet: -1.69 (0.54), residues: 78 loop : -1.24 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 696 HIS 0.009 0.002 HIS A 730 PHE 0.024 0.002 PHE A 832 TYR 0.021 0.002 TYR A1121 ARG 0.005 0.001 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.5953 (pp20) cc_final: 0.5752 (pp20) REVERT: A 318 HIS cc_start: 0.5619 (m90) cc_final: 0.5267 (t70) REVERT: A 363 SER cc_start: 0.8303 (t) cc_final: 0.8057 (p) REVERT: A 476 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.4601 (pm20) REVERT: A 512 MET cc_start: 0.7736 (pmm) cc_final: 0.7252 (pmm) REVERT: A 517 MET cc_start: 0.5995 (pmm) cc_final: 0.4795 (mpp) REVERT: A 541 MET cc_start: 0.6756 (ppp) cc_final: 0.6311 (ptp) REVERT: A 638 MET cc_start: 0.7924 (pmm) cc_final: 0.7469 (pmm) REVERT: A 652 ILE cc_start: 0.4727 (tp) cc_final: 0.4117 (tt) REVERT: A 668 SER cc_start: 0.8855 (m) cc_final: 0.8634 (p) REVERT: A 796 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8946 (tp30) REVERT: A 915 THR cc_start: -0.0581 (t) cc_final: -0.1029 (t) REVERT: B 103 ASN cc_start: 0.9228 (t0) cc_final: 0.8855 (m110) REVERT: C 28 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.5634 (mm) outliers start: 50 outliers final: 20 residues processed: 189 average time/residue: 0.2240 time to fit residues: 61.8573 Evaluate side-chains 141 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 889 LYS Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1187 PHE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 95 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN A 801 ASN B 5 ASN B 14 HIS B 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5615 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11809 Z= 0.212 Angle : 0.614 8.894 15981 Z= 0.310 Chirality : 0.041 0.255 1720 Planarity : 0.004 0.052 2089 Dihedral : 4.543 53.952 1566 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.55 % Allowed : 20.74 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.22), residues: 1418 helix: 1.54 (0.19), residues: 765 sheet: -1.34 (0.64), residues: 58 loop : -1.38 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 696 HIS 0.005 0.001 HIS B 35 PHE 0.018 0.002 PHE A 832 TYR 0.023 0.001 TYR A 57 ARG 0.005 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7632 (tmm) cc_final: 0.7335 (tmm) REVERT: A 221 TYR cc_start: 0.7071 (t80) cc_final: 0.6832 (t80) REVERT: A 318 HIS cc_start: 0.5657 (m90) cc_final: 0.5448 (t70) REVERT: A 363 SER cc_start: 0.8349 (t) cc_final: 0.8124 (p) REVERT: A 512 MET cc_start: 0.7715 (pmm) cc_final: 0.7260 (pmm) REVERT: A 517 MET cc_start: 0.6156 (pmm) cc_final: 0.5039 (mpp) REVERT: A 541 MET cc_start: 0.6666 (ppp) cc_final: 0.6374 (ptp) REVERT: A 638 MET cc_start: 0.7920 (pmm) cc_final: 0.7514 (pmm) REVERT: A 796 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8950 (tp30) outliers start: 44 outliers final: 22 residues processed: 152 average time/residue: 0.2460 time to fit residues: 55.0088 Evaluate side-chains 136 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 889 LYS Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 66 optimal weight: 0.0030 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 GLN A 896 ASN B 35 HIS C 48 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5629 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11809 Z= 0.177 Angle : 0.589 8.949 15981 Z= 0.297 Chirality : 0.040 0.191 1720 Planarity : 0.003 0.052 2089 Dihedral : 4.235 48.992 1563 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.66 % Allowed : 20.66 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.22), residues: 1418 helix: 1.52 (0.19), residues: 765 sheet: -1.34 (0.64), residues: 59 loop : -1.38 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 862 HIS 0.018 0.001 HIS B 35 PHE 0.014 0.002 PHE A 614 TYR 0.038 0.001 TYR B 50 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8295 (ptp-170) REVERT: A 208 TRP cc_start: 0.3111 (OUTLIER) cc_final: 0.2892 (m100) REVERT: A 221 TYR cc_start: 0.6949 (t80) cc_final: 0.6594 (t80) REVERT: A 318 HIS cc_start: 0.5851 (m90) cc_final: 0.5567 (t70) REVERT: A 363 SER cc_start: 0.8303 (t) cc_final: 0.8079 (p) REVERT: A 512 MET cc_start: 0.7691 (pmm) cc_final: 0.7253 (pmm) REVERT: A 517 MET cc_start: 0.6416 (pmm) cc_final: 0.5132 (mpp) REVERT: A 541 MET cc_start: 0.6759 (ppp) cc_final: 0.6463 (ptp) REVERT: A 638 MET cc_start: 0.7869 (pmm) cc_final: 0.7519 (pmm) REVERT: A 796 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8945 (tp30) REVERT: B 106 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8990 (mt) outliers start: 33 outliers final: 21 residues processed: 144 average time/residue: 0.2431 time to fit residues: 51.9332 Evaluate side-chains 138 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1109 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 34 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 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 48 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11809 Z= 0.172 Angle : 0.575 9.990 15981 Z= 0.292 Chirality : 0.040 0.173 1720 Planarity : 0.003 0.052 2089 Dihedral : 4.150 48.291 1562 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.66 % Allowed : 20.74 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.22), residues: 1418 helix: 1.59 (0.19), residues: 764 sheet: -1.22 (0.63), residues: 59 loop : -1.39 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 862 HIS 0.004 0.001 HIS A 730 PHE 0.014 0.002 PHE A1187 TYR 0.034 0.001 TYR B 49 ARG 0.008 0.001 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.6963 (t80) cc_final: 0.6499 (t80) REVERT: A 318 HIS cc_start: 0.5927 (m90) cc_final: 0.5624 (t70) REVERT: A 363 SER cc_start: 0.8315 (t) cc_final: 0.8095 (p) REVERT: A 512 MET cc_start: 0.7709 (pmm) cc_final: 0.7152 (pmm) REVERT: A 517 MET cc_start: 0.6423 (pmm) cc_final: 0.5139 (mpp) REVERT: A 558 ASN cc_start: 0.6478 (m-40) cc_final: 0.5819 (m110) REVERT: A 638 MET cc_start: 0.7888 (pmm) cc_final: 0.7576 (pmm) REVERT: A 796 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8895 (tp30) REVERT: B 57 MET cc_start: 0.7816 (tpp) cc_final: 0.7487 (tpp) REVERT: B 106 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8968 (mt) outliers start: 33 outliers final: 20 residues processed: 147 average time/residue: 0.2439 time to fit residues: 52.8167 Evaluate side-chains 135 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 889 LYS Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 79 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 646 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 HIS C 48 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11809 Z= 0.195 Angle : 0.594 10.655 15981 Z= 0.302 Chirality : 0.040 0.171 1720 Planarity : 0.003 0.047 2089 Dihedral : 4.176 48.009 1562 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.82 % Allowed : 21.23 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.22), residues: 1418 helix: 1.62 (0.19), residues: 764 sheet: -1.15 (0.64), residues: 58 loop : -1.34 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 208 HIS 0.005 0.001 HIS A 730 PHE 0.018 0.002 PHE A1187 TYR 0.026 0.001 TYR B 50 ARG 0.006 0.001 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.5802 (pp20) cc_final: 0.5534 (pt0) REVERT: A 221 TYR cc_start: 0.6933 (t80) cc_final: 0.6577 (t80) REVERT: A 318 HIS cc_start: 0.5952 (m90) cc_final: 0.5633 (t70) REVERT: A 356 ASP cc_start: 0.7574 (t0) cc_final: 0.7349 (t70) REVERT: A 363 SER cc_start: 0.8300 (t) cc_final: 0.8079 (p) REVERT: A 512 MET cc_start: 0.7677 (pmm) cc_final: 0.7102 (pmm) REVERT: A 517 MET cc_start: 0.6422 (pmm) cc_final: 0.5150 (mpp) REVERT: A 558 ASN cc_start: 0.6303 (m-40) cc_final: 0.5846 (m110) REVERT: A 584 MET cc_start: 0.6156 (tpp) cc_final: 0.5907 (tpp) REVERT: A 638 MET cc_start: 0.7813 (pmm) cc_final: 0.7491 (pmm) REVERT: B 106 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8950 (mt) outliers start: 35 outliers final: 25 residues processed: 139 average time/residue: 0.2260 time to fit residues: 46.6322 Evaluate side-chains 135 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 889 LYS Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 0.0060 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 48 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11809 Z= 0.177 Angle : 0.581 9.879 15981 Z= 0.295 Chirality : 0.040 0.187 1720 Planarity : 0.003 0.049 2089 Dihedral : 4.164 47.075 1562 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 21.31 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.22), residues: 1418 helix: 1.67 (0.19), residues: 764 sheet: -1.27 (0.64), residues: 58 loop : -1.35 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 862 HIS 0.004 0.001 HIS A 730 PHE 0.013 0.001 PHE A1187 TYR 0.023 0.001 TYR C 50 ARG 0.007 0.000 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7030 (t80) cc_final: 0.6633 (t80) REVERT: A 318 HIS cc_start: 0.6000 (m90) cc_final: 0.5682 (t70) REVERT: A 356 ASP cc_start: 0.7499 (t0) cc_final: 0.7277 (t70) REVERT: A 363 SER cc_start: 0.8242 (t) cc_final: 0.7905 (p) REVERT: A 512 MET cc_start: 0.7751 (pmm) cc_final: 0.7267 (pmm) REVERT: A 517 MET cc_start: 0.6382 (pmm) cc_final: 0.5130 (mpp) REVERT: A 558 ASN cc_start: 0.6310 (m-40) cc_final: 0.5744 (m110) REVERT: A 559 MET cc_start: 0.6557 (mmm) cc_final: 0.6242 (mmm) REVERT: A 638 MET cc_start: 0.7752 (pmm) cc_final: 0.7225 (pmm) REVERT: B 57 MET cc_start: 0.7766 (tpp) cc_final: 0.7274 (tpp) REVERT: B 106 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8941 (mt) outliers start: 32 outliers final: 25 residues processed: 133 average time/residue: 0.2423 time to fit residues: 47.1531 Evaluate side-chains 131 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 889 LYS Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS C 48 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11809 Z= 0.189 Angle : 0.593 9.939 15981 Z= 0.302 Chirality : 0.041 0.221 1720 Planarity : 0.003 0.047 2089 Dihedral : 4.188 46.287 1562 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.42 % Allowed : 21.23 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.22), residues: 1418 helix: 1.66 (0.19), residues: 764 sheet: -1.27 (0.65), residues: 58 loop : -1.37 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 862 HIS 0.005 0.001 HIS B 14 PHE 0.014 0.001 PHE A1187 TYR 0.021 0.001 TYR B 50 ARG 0.007 0.000 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7055 (t80) cc_final: 0.6657 (t80) REVERT: A 318 HIS cc_start: 0.6069 (m90) cc_final: 0.5738 (t70) REVERT: A 363 SER cc_start: 0.8245 (t) cc_final: 0.7919 (p) REVERT: A 517 MET cc_start: 0.6386 (pmm) cc_final: 0.5092 (mpp) REVERT: A 558 ASN cc_start: 0.6033 (m-40) cc_final: 0.5601 (m110) REVERT: A 638 MET cc_start: 0.7776 (pmm) cc_final: 0.7456 (pmm) REVERT: B 28 ILE cc_start: 0.7269 (mm) cc_final: 0.7046 (mt) REVERT: B 57 MET cc_start: 0.7702 (tpp) cc_final: 0.7168 (tpp) REVERT: B 106 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8926 (mt) outliers start: 30 outliers final: 25 residues processed: 128 average time/residue: 0.2443 time to fit residues: 47.0887 Evaluate side-chains 128 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 889 LYS Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 133 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 633 ASN A 918 ASN C 5 ASN C 48 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11809 Z= 0.178 Angle : 0.591 10.460 15981 Z= 0.300 Chirality : 0.040 0.225 1720 Planarity : 0.004 0.055 2089 Dihedral : 4.199 44.059 1562 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.02 % Allowed : 21.87 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.22), residues: 1418 helix: 1.70 (0.19), residues: 765 sheet: -1.38 (0.64), residues: 58 loop : -1.39 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 862 HIS 0.004 0.001 HIS A 730 PHE 0.012 0.001 PHE A 864 TYR 0.020 0.001 TYR B 50 ARG 0.009 0.000 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7085 (t80) cc_final: 0.6669 (t80) REVERT: A 286 GLN cc_start: 0.6734 (pt0) cc_final: 0.5717 (tt0) REVERT: A 318 HIS cc_start: 0.6297 (m90) cc_final: 0.6000 (t70) REVERT: A 363 SER cc_start: 0.8233 (t) cc_final: 0.7899 (p) REVERT: A 410 MET cc_start: 0.7594 (mpp) cc_final: 0.7357 (pmm) REVERT: A 517 MET cc_start: 0.6428 (pmm) cc_final: 0.5156 (mpp) REVERT: A 558 ASN cc_start: 0.6000 (m-40) cc_final: 0.5402 (m110) REVERT: A 559 MET cc_start: 0.6490 (mmm) cc_final: 0.6181 (mmm) REVERT: A 638 MET cc_start: 0.7573 (pmm) cc_final: 0.7202 (pmm) REVERT: B 28 ILE cc_start: 0.7307 (mm) cc_final: 0.7105 (mt) REVERT: B 57 MET cc_start: 0.7695 (tpp) cc_final: 0.7188 (tpp) REVERT: B 106 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8926 (mt) outliers start: 25 outliers final: 23 residues processed: 125 average time/residue: 0.2318 time to fit residues: 43.2843 Evaluate side-chains 126 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 889 LYS Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN C 48 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11809 Z= 0.191 Angle : 0.597 10.702 15981 Z= 0.303 Chirality : 0.041 0.206 1720 Planarity : 0.003 0.046 2089 Dihedral : 4.184 41.873 1562 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.10 % Allowed : 21.95 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.22), residues: 1418 helix: 1.70 (0.19), residues: 759 sheet: -1.19 (0.66), residues: 56 loop : -1.39 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 862 HIS 0.005 0.001 HIS A 730 PHE 0.014 0.001 PHE A1187 TYR 0.021 0.001 TYR B 50 ARG 0.006 0.000 ARG A1127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7203 (t80) cc_final: 0.6730 (t80) REVERT: A 286 GLN cc_start: 0.6834 (pt0) cc_final: 0.5821 (tt0) REVERT: A 318 HIS cc_start: 0.6320 (m90) cc_final: 0.6103 (t70) REVERT: A 363 SER cc_start: 0.8249 (t) cc_final: 0.7917 (p) REVERT: A 512 MET cc_start: 0.7629 (pmm) cc_final: 0.6058 (pmm) REVERT: A 517 MET cc_start: 0.6458 (pmm) cc_final: 0.5170 (mpp) REVERT: A 535 ASP cc_start: 0.8336 (m-30) cc_final: 0.8052 (m-30) REVERT: A 558 ASN cc_start: 0.6065 (m-40) cc_final: 0.5474 (m110) REVERT: A 559 MET cc_start: 0.6360 (mmm) cc_final: 0.6039 (mmm) REVERT: A 584 MET cc_start: 0.5874 (tpp) cc_final: 0.5581 (tpp) REVERT: A 638 MET cc_start: 0.7582 (pmm) cc_final: 0.7043 (pmm) REVERT: B 57 MET cc_start: 0.7687 (tpp) cc_final: 0.7158 (tpp) outliers start: 26 outliers final: 24 residues processed: 121 average time/residue: 0.2488 time to fit residues: 45.2442 Evaluate side-chains 119 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 857 GLN Chi-restraints excluded: chain A residue 889 LYS Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 112 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 98 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN C 48 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.101349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068404 restraints weight = 36430.858| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.08 r_work: 0.3134 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11809 Z= 0.166 Angle : 0.606 11.043 15981 Z= 0.302 Chirality : 0.041 0.386 1720 Planarity : 0.003 0.048 2089 Dihedral : 4.116 40.246 1562 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.86 % Allowed : 22.36 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.22), residues: 1418 helix: 1.72 (0.19), residues: 765 sheet: -1.03 (0.67), residues: 56 loop : -1.39 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 862 HIS 0.004 0.001 HIS C 48 PHE 0.011 0.001 PHE A 941 TYR 0.020 0.001 TYR B 50 ARG 0.009 0.000 ARG A 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2766.42 seconds wall clock time: 51 minutes 48.65 seconds (3108.65 seconds total)