Starting phenix.real_space_refine on Thu Jul 31 12:00:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g8q_51136/07_2025/9g8q_51136.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g8q_51136/07_2025/9g8q_51136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g8q_51136/07_2025/9g8q_51136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g8q_51136/07_2025/9g8q_51136.map" model { file = "/net/cci-nas-00/data/ceres_data/9g8q_51136/07_2025/9g8q_51136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g8q_51136/07_2025/9g8q_51136.cif" } resolution = 4.1 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= 0.000 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 60 5.16 5 C 8460 2.51 5 N 2267 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13313 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1268 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 20, 'TRANS': 142} Chain breaks: 1 Chain: "B" Number of atoms: 7299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7299 Classifications: {'peptide': 934} Link IDs: {'PTRANS': 22, 'TRANS': 911} Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "D" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Time building chain proxies: 18.62, per 1000 atoms: 1.40 Number of scatterers: 13313 At special positions: 0 Unit cell: (92.7808, 157.472, 114.061, 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 60 16.00 O 2526 8.00 N 2267 7.00 C 8460 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: 3.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 16 sheets defined 47.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.927A pdb=" N SER A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.402A pdb=" N TRP A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.511A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.649A pdb=" N SER A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 91 " --> pdb=" O TRP A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.788A pdb=" N LYS B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.660A pdb=" N LEU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 4.011A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 727 removed outlier: 4.360A pdb=" N LEU B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 754 through 773 Processing helix chain 'B' and resid 775 through 796 removed outlier: 3.584A pdb=" N THR B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 Processing helix chain 'B' and resid 842 through 857 Processing helix chain 'B' and resid 860 through 874 Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 909 removed outlier: 3.921A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 925 removed outlier: 3.641A pdb=" N ASN B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 943 Processing helix chain 'B' and resid 950 through 958 removed outlier: 3.815A pdb=" N TYR B 954 " --> pdb=" O GLU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.907A pdb=" N ALA B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 993 Processing helix chain 'B' and resid 995 through 1011 Processing helix chain 'B' and resid 1017 through 1033 Processing helix chain 'B' and resid 1035 through 1045 Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1066 through 1081 removed outlier: 3.645A pdb=" N SER B1070 " --> pdb=" O LEU B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1101 removed outlier: 3.667A pdb=" N LYS B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1117 removed outlier: 3.915A pdb=" N ALA B1107 " --> pdb=" O LYS B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1135 removed outlier: 3.504A pdb=" N MET B1135 " --> pdb=" O LEU B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1152 removed outlier: 3.855A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1172 removed outlier: 3.869A pdb=" N ARG B1161 " --> pdb=" O SER B1157 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 removed outlier: 3.733A pdb=" N LYS B1180 " --> pdb=" O VAL B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1206 removed outlier: 3.761A pdb=" N TRP B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1225 removed outlier: 3.893A pdb=" N ASP B1225 " --> pdb=" O ALA B1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 1228 through 1244 Processing helix chain 'B' and resid 1254 through 1266 Processing helix chain 'B' and resid 1269 through 1291 removed outlier: 4.181A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1312 Processing helix chain 'B' and resid 1317 through 1340 Processing helix chain 'B' and resid 1341 through 1356 removed outlier: 3.681A pdb=" N ASN B1356 " --> pdb=" O ASN B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1371 Processing helix chain 'B' and resid 1382 through 1396 removed outlier: 3.612A pdb=" N ASN B1396 " --> pdb=" O THR B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.618A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1433 Processing helix chain 'B' and resid 1436 through 1456 Processing helix chain 'B' and resid 1462 through 1478 Processing helix chain 'B' and resid 1480 through 1495 Processing helix chain 'B' and resid 1498 through 1511 removed outlier: 4.172A pdb=" N ARG B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1534 Processing helix chain 'B' and resid 1535 through 1549 removed outlier: 3.513A pdb=" N HIS B1549 " --> pdb=" O ASN B1545 " (cutoff:3.500A) Processing helix chain 'B' and resid 1552 through 1563 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.558A pdb=" N ARG A 20 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 737 through 740 removed outlier: 3.759A pdb=" N VAL B 737 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 10 removed outlier: 6.044A pdb=" N ILE C 7 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP C 302 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE C 9 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 300 " --> pdb=" O PHE C 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 21 through 25 removed outlier: 6.927A pdb=" N VAL C 46 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 72 removed outlier: 7.244A pdb=" N SER C 82 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL C 70 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA C 80 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 81 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG C 89 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER C 83 " --> pdb=" O HIS C 87 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 130 through 134 removed outlier: 3.547A pdb=" N LEU C 144 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS C 140 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.482A pdb=" N GLY C 166 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE C 154 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA C 164 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 196 through 197 removed outlier: 3.909A pdb=" N THR C 197 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 206 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 216 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 235 through 240 removed outlier: 3.783A pdb=" N VAL C 256 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 258 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 6 through 10 removed outlier: 6.108A pdb=" N ILE D 7 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP D 302 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE D 9 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 300 " --> pdb=" O PHE D 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 289 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.947A pdb=" N VAL D 46 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 67 through 72 removed outlier: 7.190A pdb=" N SER D 82 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL D 70 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA D 80 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 81 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER D 83 " --> pdb=" O HIS D 87 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.953A pdb=" N TYR D 142 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLY D 134 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS D 140 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.399A pdb=" N GLY D 166 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE D 154 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA D 164 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 174 " --> pdb=" O HIS D 184 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N HIS D 184 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 196 through 197 removed outlier: 3.630A pdb=" N THR D 197 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY D 226 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 235 through 240 removed outlier: 3.824A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1995 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: 5.25 Time building geometry restraints manager: 4.28 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: 2584 1.33 - 1.45: 3240 1.45 - 1.57: 7683 1.57 - 1.69: 1 1.69 - 1.81: 89 Bond restraints: 13597 Sorted by residual: bond pdb=" CG PRO B1120 " pdb=" CD PRO B1120 " ideal model delta sigma weight residual 1.503 1.396 0.107 3.40e-02 8.65e+02 9.93e+00 bond pdb=" CG GLU B1388 " pdb=" CD GLU B1388 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.19e+00 bond pdb=" CB PRO B1120 " pdb=" CG PRO B1120 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.20e+00 bond pdb=" CA LEU B1375 " pdb=" C LEU B1375 " ideal model delta sigma weight residual 1.524 1.554 -0.030 1.50e-02 4.44e+03 3.91e+00 bond pdb=" CG1 ILE B 696 " pdb=" CD1 ILE B 696 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 ... (remaining 13592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 17948 2.36 - 4.73: 407 4.73 - 7.09: 81 7.09 - 9.46: 17 9.46 - 11.82: 9 Bond angle restraints: 18462 Sorted by residual: angle pdb=" CA PRO B1120 " pdb=" N PRO B1120 " pdb=" CD PRO B1120 " ideal model delta sigma weight residual 112.00 102.49 9.51 1.40e+00 5.10e-01 4.61e+01 angle pdb=" N PRO B1120 " pdb=" CD PRO B1120 " pdb=" CG PRO B1120 " ideal model delta sigma weight residual 103.20 93.75 9.45 1.50e+00 4.44e-01 3.97e+01 angle pdb=" N GLU B1075 " pdb=" CA GLU B1075 " pdb=" CB GLU B1075 " ideal model delta sigma weight residual 110.16 118.42 -8.26 1.48e+00 4.57e-01 3.11e+01 angle pdb=" C ILE D 168 " pdb=" N ASP D 169 " pdb=" CA ASP D 169 " ideal model delta sigma weight residual 125.66 135.34 -9.68 1.85e+00 2.92e-01 2.74e+01 angle pdb=" C GLU B1014 " pdb=" N ASP B1015 " pdb=" CA ASP B1015 " ideal model delta sigma weight residual 124.31 132.63 -8.32 1.67e+00 3.59e-01 2.48e+01 ... (remaining 18457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7243 17.48 - 34.97: 735 34.97 - 52.45: 112 52.45 - 69.94: 18 69.94 - 87.42: 16 Dihedral angle restraints: 8124 sinusoidal: 3159 harmonic: 4965 Sorted by residual: dihedral pdb=" CA ASN A 34 " pdb=" C ASN A 34 " pdb=" N LEU A 35 " pdb=" CA LEU A 35 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual -180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLU A 174 " pdb=" C GLU A 174 " pdb=" N GLU A 175 " pdb=" CA GLU A 175 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 8121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1588 0.051 - 0.101: 387 0.101 - 0.152: 100 0.152 - 0.203: 12 0.203 - 0.253: 6 Chirality restraints: 2093 Sorted by residual: chirality pdb=" CA GLU B1388 " pdb=" N GLU B1388 " pdb=" C GLU B1388 " pdb=" CB GLU B1388 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ASP B1015 " pdb=" N ASP B1015 " pdb=" C ASP B1015 " pdb=" CB ASP B1015 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA GLU B1075 " pdb=" N GLU B1075 " pdb=" C GLU B1075 " pdb=" CB GLU B1075 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2090 not shown) Planarity restraints: 2349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 69 " -0.073 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A 70 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B1119 " -0.070 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B1120 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO B1120 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B1120 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1014 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C GLU B1014 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU B1014 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP B1015 " -0.021 2.00e-02 2.50e+03 ... (remaining 2346 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 323 2.69 - 3.24: 13302 3.24 - 3.79: 20551 3.79 - 4.35: 25869 4.35 - 4.90: 43909 Nonbonded interactions: 103954 Sorted by model distance: nonbonded pdb=" O VAL C 107 " pdb=" OG1 THR C 125 " model vdw 2.132 3.040 nonbonded pdb=" O VAL D 107 " pdb=" OG1 THR D 125 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP B 722 " pdb=" OH TYR B 766 " model vdw 2.190 3.040 nonbonded pdb=" OG SER D 115 " pdb=" OD1 ASP D 117 " model vdw 2.208 3.040 nonbonded pdb=" O ALA A 51 " pdb=" NE2 GLN B1205 " model vdw 2.210 3.120 ... (remaining 103949 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 606.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 45.910 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 656.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.004 0.107 13597 Z= 0.167 Angle : 0.898 11.824 18462 Z= 0.474 Chirality : 0.049 0.253 2093 Planarity : 0.006 0.112 2349 Dihedral : 14.467 87.422 4924 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -0.03 (0.21), residues: 1697 helix: 2.74 (0.18), residues: 779 sheet: -1.14 (0.37), residues: 186 loop : -3.05 (0.18), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 30 HIS 0.009 0.001 HIS B 812 PHE 0.027 0.002 PHE A 196 TYR 0.030 0.002 TYR B 648 ARG 0.009 0.001 ARG B1005 Details of bonding type rmsd hydrogen bonds : bond 0.15352 ( 685) hydrogen bonds : angle 5.23678 ( 1995) covalent geometry : bond 0.00363 (13597) covalent geometry : angle 0.89822 (18462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7149 (tmm) cc_final: 0.6299 (tmm) REVERT: B 781 ASP cc_start: 0.8415 (m-30) cc_final: 0.8089 (m-30) REVERT: B 896 MET cc_start: 0.8675 (mpp) cc_final: 0.8204 (mpp) REVERT: B 985 MET cc_start: 0.8256 (mpp) cc_final: 0.7851 (mpp) REVERT: B 1316 PHE cc_start: 0.6849 (p90) cc_final: 0.6264 (p90) REVERT: B 1415 MET cc_start: 0.7181 (mpp) cc_final: 0.6213 (mpp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2479 time to fit residues: 62.3918 Evaluate side-chains 117 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 132 optimal weight: 0.0770 chunk 51 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 0.0370 chunk 153 optimal weight: 2.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 643 GLN ** B 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1564 GLN D 131 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.078110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065029 restraints weight = 71417.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066806 restraints weight = 43845.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068051 restraints weight = 31261.549| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13597 Z= 0.137 Angle : 0.652 10.728 18462 Z= 0.341 Chirality : 0.043 0.195 2093 Planarity : 0.005 0.053 2349 Dihedral : 4.671 23.788 1815 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.78 % Favored : 91.04 % Rotamer: Outliers : 0.35 % Allowed : 4.38 % Favored : 95.28 % 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: 0.00 (0.21), residues: 1697 helix: 2.52 (0.18), residues: 784 sheet: -0.87 (0.35), residues: 222 loop : -2.91 (0.20), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.006 0.001 HIS B 812 PHE 0.010 0.001 PHE D 247 TYR 0.014 0.001 TYR B1320 ARG 0.006 0.001 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 685) hydrogen bonds : angle 4.04778 ( 1995) covalent geometry : bond 0.00296 (13597) covalent geometry : angle 0.65232 (18462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 1.629 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 195 ASP cc_start: 0.8532 (p0) cc_final: 0.8215 (t0) REVERT: B 781 ASP cc_start: 0.8532 (m-30) cc_final: 0.8106 (m-30) REVERT: B 896 MET cc_start: 0.8780 (mpp) cc_final: 0.8167 (mpp) REVERT: B 914 MET cc_start: 0.8606 (pmm) cc_final: 0.8331 (pmm) REVERT: B 1316 PHE cc_start: 0.7374 (p90) cc_final: 0.6673 (p90) REVERT: B 1394 MET cc_start: 0.8802 (mmm) cc_final: 0.8599 (mmm) REVERT: B 1415 MET cc_start: 0.7651 (mpp) cc_final: 0.7151 (mpp) REVERT: C 195 SER cc_start: 0.7246 (t) cc_final: 0.6475 (m) outliers start: 5 outliers final: 0 residues processed: 156 average time/residue: 0.2605 time to fit residues: 64.4804 Evaluate side-chains 105 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 105 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 643 GLN ** B 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS C 223 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.074431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.061592 restraints weight = 73574.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063266 restraints weight = 45111.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064456 restraints weight = 32350.901| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13597 Z= 0.164 Angle : 0.658 11.733 18462 Z= 0.346 Chirality : 0.043 0.190 2093 Planarity : 0.005 0.047 2349 Dihedral : 4.854 27.444 1815 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.78 % Favored : 91.10 % Rotamer: Outliers : 0.21 % Allowed : 4.72 % Favored : 95.07 % 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: -0.17 (0.20), residues: 1697 helix: 2.24 (0.18), residues: 785 sheet: -0.90 (0.33), residues: 228 loop : -2.84 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.009 0.001 HIS D 126 PHE 0.013 0.002 PHE D 247 TYR 0.018 0.001 TYR B1320 ARG 0.004 0.001 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 685) hydrogen bonds : angle 3.95550 ( 1995) covalent geometry : bond 0.00359 (13597) covalent geometry : angle 0.65819 (18462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7340 (tmm) cc_final: 0.6523 (tmm) REVERT: A 195 ASP cc_start: 0.8530 (p0) cc_final: 0.8256 (t0) REVERT: B 657 MET cc_start: 0.9174 (tmm) cc_final: 0.8964 (tmm) REVERT: B 914 MET cc_start: 0.8607 (pmm) cc_final: 0.8304 (pmm) REVERT: B 1243 MET cc_start: 0.8613 (ptp) cc_final: 0.8284 (ptp) REVERT: B 1415 MET cc_start: 0.8059 (mpp) cc_final: 0.7573 (mpp) REVERT: C 195 SER cc_start: 0.7445 (t) cc_final: 0.6624 (m) outliers start: 3 outliers final: 0 residues processed: 138 average time/residue: 0.2318 time to fit residues: 50.1470 Evaluate side-chains 98 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 131 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS ** B1321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.072355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059498 restraints weight = 73742.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061176 restraints weight = 45449.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.062321 restraints weight = 32737.812| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13597 Z= 0.170 Angle : 0.671 11.715 18462 Z= 0.349 Chirality : 0.043 0.181 2093 Planarity : 0.005 0.047 2349 Dihedral : 4.939 26.239 1815 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.78 % Favored : 90.10 % Rotamer: Outliers : 0.21 % Allowed : 4.86 % Favored : 94.93 % 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: -0.26 (0.20), residues: 1697 helix: 2.12 (0.18), residues: 785 sheet: -0.84 (0.33), residues: 226 loop : -2.88 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1436 HIS 0.011 0.001 HIS D 126 PHE 0.014 0.001 PHE D 247 TYR 0.017 0.002 TYR B1320 ARG 0.006 0.001 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 685) hydrogen bonds : angle 3.89492 ( 1995) covalent geometry : bond 0.00373 (13597) covalent geometry : angle 0.67073 (18462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7555 (tmm) cc_final: 0.6683 (tmm) REVERT: A 195 ASP cc_start: 0.8570 (p0) cc_final: 0.8235 (t0) REVERT: B 657 MET cc_start: 0.9175 (tmm) cc_final: 0.8970 (tmm) REVERT: B 781 ASP cc_start: 0.8516 (m-30) cc_final: 0.8116 (m-30) REVERT: B 914 MET cc_start: 0.8582 (pmm) cc_final: 0.8287 (pmm) REVERT: B 1394 MET cc_start: 0.8973 (mmm) cc_final: 0.8745 (mmm) REVERT: B 1415 MET cc_start: 0.8064 (mpp) cc_final: 0.7492 (mpp) outliers start: 3 outliers final: 0 residues processed: 144 average time/residue: 0.2422 time to fit residues: 53.4541 Evaluate side-chains 103 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 164 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 GLN ** B1321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.072362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059540 restraints weight = 75954.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061208 restraints weight = 46948.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.062377 restraints weight = 33883.145| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13597 Z= 0.151 Angle : 0.649 10.107 18462 Z= 0.340 Chirality : 0.043 0.183 2093 Planarity : 0.004 0.042 2349 Dihedral : 4.894 28.412 1815 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.13 % Favored : 90.75 % Rotamer: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.15 % 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: -0.23 (0.20), residues: 1697 helix: 2.14 (0.18), residues: 787 sheet: -0.70 (0.33), residues: 228 loop : -2.91 (0.20), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1436 HIS 0.008 0.001 HIS D 126 PHE 0.009 0.001 PHE C 150 TYR 0.016 0.001 TYR B1423 ARG 0.003 0.001 ARG B1560 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 685) hydrogen bonds : angle 3.83669 ( 1995) covalent geometry : bond 0.00330 (13597) covalent geometry : angle 0.64872 (18462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7506 (tmm) cc_final: 0.6717 (tmm) REVERT: A 194 MET cc_start: 0.5556 (tmm) cc_final: 0.5231 (tmm) REVERT: A 195 ASP cc_start: 0.8553 (p0) cc_final: 0.8265 (t0) REVERT: B 781 ASP cc_start: 0.8502 (m-30) cc_final: 0.8099 (m-30) REVERT: B 914 MET cc_start: 0.8663 (pmm) cc_final: 0.8344 (pmm) REVERT: B 1243 MET cc_start: 0.8598 (ptp) cc_final: 0.8321 (ptm) REVERT: B 1316 PHE cc_start: 0.7777 (p90) cc_final: 0.7337 (p90) REVERT: B 1394 MET cc_start: 0.8968 (mmm) cc_final: 0.8704 (mmm) REVERT: B 1415 MET cc_start: 0.8185 (mpp) cc_final: 0.7770 (mpp) REVERT: C 195 SER cc_start: 0.7393 (t) cc_final: 0.6530 (m) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2606 time to fit residues: 56.7942 Evaluate side-chains 98 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 164 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 84 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 0.0870 chunk 68 optimal weight: 0.2980 chunk 79 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 GLN B1151 HIS ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.073094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060038 restraints weight = 75880.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061791 restraints weight = 46976.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.062980 restraints weight = 33809.928| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13597 Z= 0.129 Angle : 0.640 12.994 18462 Z= 0.329 Chirality : 0.042 0.183 2093 Planarity : 0.004 0.043 2349 Dihedral : 4.770 25.031 1815 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.02 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -0.09 (0.21), residues: 1697 helix: 2.26 (0.19), residues: 787 sheet: -0.63 (0.33), residues: 228 loop : -2.87 (0.20), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1524 HIS 0.006 0.001 HIS B 812 PHE 0.008 0.001 PHE C 150 TYR 0.013 0.001 TYR B1320 ARG 0.003 0.000 ARG B1560 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 685) hydrogen bonds : angle 3.66940 ( 1995) covalent geometry : bond 0.00275 (13597) covalent geometry : angle 0.64034 (18462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7406 (tmm) cc_final: 0.6589 (tmm) REVERT: A 195 ASP cc_start: 0.8517 (p0) cc_final: 0.8195 (t0) REVERT: B 781 ASP cc_start: 0.8474 (m-30) cc_final: 0.8065 (m-30) REVERT: B 914 MET cc_start: 0.8591 (pmm) cc_final: 0.8310 (pmm) REVERT: B 1316 PHE cc_start: 0.7612 (p90) cc_final: 0.6942 (p90) REVERT: B 1394 MET cc_start: 0.8934 (mmm) cc_final: 0.8705 (mmm) REVERT: B 1415 MET cc_start: 0.8161 (mpp) cc_final: 0.7519 (mpp) REVERT: C 195 SER cc_start: 0.7359 (t) cc_final: 0.6602 (m) REVERT: D 123 THR cc_start: 0.8823 (p) cc_final: 0.8564 (t) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2302 time to fit residues: 51.4000 Evaluate side-chains 105 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 122 optimal weight: 0.3980 chunk 165 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1368 GLN ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.069697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056820 restraints weight = 76685.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058393 restraints weight = 48163.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.059380 restraints weight = 35306.584| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13597 Z= 0.205 Angle : 0.716 11.227 18462 Z= 0.373 Chirality : 0.045 0.179 2093 Planarity : 0.004 0.043 2349 Dihedral : 5.104 27.318 1815 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.96 % Favored : 89.92 % Rotamer: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.71 % 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: -0.44 (0.21), residues: 1697 helix: 1.91 (0.18), residues: 787 sheet: -0.91 (0.34), residues: 226 loop : -2.90 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1436 HIS 0.006 0.001 HIS D 126 PHE 0.016 0.002 PHE C 150 TYR 0.017 0.002 TYR B1320 ARG 0.006 0.001 ARG B 918 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 685) hydrogen bonds : angle 4.03050 ( 1995) covalent geometry : bond 0.00449 (13597) covalent geometry : angle 0.71561 (18462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7788 (tmm) cc_final: 0.7095 (tmm) REVERT: A 159 MET cc_start: 0.7145 (tmm) cc_final: 0.6906 (mmt) REVERT: A 195 ASP cc_start: 0.8651 (p0) cc_final: 0.8297 (t0) REVERT: B 781 ASP cc_start: 0.8535 (m-30) cc_final: 0.8149 (m-30) REVERT: B 914 MET cc_start: 0.8603 (pmm) cc_final: 0.8282 (pmm) REVERT: B 1103 LYS cc_start: 0.8968 (pttt) cc_final: 0.8725 (pttm) REVERT: B 1243 MET cc_start: 0.8558 (ptp) cc_final: 0.8276 (ptm) REVERT: B 1394 MET cc_start: 0.9075 (mmm) cc_final: 0.8778 (mmm) REVERT: B 1415 MET cc_start: 0.8162 (mpp) cc_final: 0.7232 (mpp) REVERT: C 297 GLU cc_start: 0.6315 (mp0) cc_final: 0.6049 (mp0) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2286 time to fit residues: 44.8194 Evaluate side-chains 93 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1413 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.070847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057889 restraints weight = 76406.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059464 restraints weight = 47745.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.060481 restraints weight = 34835.317| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13597 Z= 0.159 Angle : 0.677 11.526 18462 Z= 0.352 Chirality : 0.044 0.184 2093 Planarity : 0.004 0.043 2349 Dihedral : 5.017 28.539 1815 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.78 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -0.37 (0.21), residues: 1697 helix: 2.02 (0.18), residues: 786 sheet: -1.01 (0.32), residues: 248 loop : -2.91 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1463 HIS 0.005 0.001 HIS B 926 PHE 0.011 0.002 PHE C 150 TYR 0.026 0.001 TYR B1423 ARG 0.007 0.001 ARG B 819 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 685) hydrogen bonds : angle 3.88135 ( 1995) covalent geometry : bond 0.00346 (13597) covalent geometry : angle 0.67739 (18462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7729 (tmm) cc_final: 0.7008 (tmm) REVERT: A 16 ASP cc_start: 0.8822 (m-30) cc_final: 0.7664 (t0) REVERT: B 679 MET cc_start: 0.8866 (ptt) cc_final: 0.8181 (ptp) REVERT: B 781 ASP cc_start: 0.8520 (m-30) cc_final: 0.8134 (m-30) REVERT: B 914 MET cc_start: 0.8562 (pmm) cc_final: 0.8245 (pmm) REVERT: B 1063 MET cc_start: 0.7999 (tpp) cc_final: 0.7780 (tpp) REVERT: B 1103 LYS cc_start: 0.8949 (pttt) cc_final: 0.8646 (pttm) REVERT: B 1243 MET cc_start: 0.8539 (ptp) cc_final: 0.8267 (ptm) REVERT: B 1316 PHE cc_start: 0.7894 (p90) cc_final: 0.7447 (p90) REVERT: B 1415 MET cc_start: 0.8078 (mpp) cc_final: 0.7303 (mpp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2410 time to fit residues: 50.0095 Evaluate side-chains 97 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 42 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 168 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 44 optimal weight: 0.0770 chunk 46 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS B1179 GLN B1205 GLN ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1368 GLN ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.071736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058904 restraints weight = 74979.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060526 restraints weight = 46139.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061689 restraints weight = 33352.230| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13597 Z= 0.135 Angle : 0.671 13.749 18462 Z= 0.346 Chirality : 0.043 0.181 2093 Planarity : 0.004 0.043 2349 Dihedral : 4.871 27.131 1815 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.19 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -0.18 (0.21), residues: 1697 helix: 2.17 (0.18), residues: 786 sheet: -0.35 (0.36), residues: 200 loop : -2.91 (0.20), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1463 HIS 0.009 0.001 HIS D 126 PHE 0.010 0.001 PHE C 150 TYR 0.017 0.001 TYR B1525 ARG 0.004 0.000 ARG B 819 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 685) hydrogen bonds : angle 3.76674 ( 1995) covalent geometry : bond 0.00290 (13597) covalent geometry : angle 0.67093 (18462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7618 (tmm) cc_final: 0.6883 (tmm) REVERT: A 16 ASP cc_start: 0.8819 (m-30) cc_final: 0.7882 (t0) REVERT: A 195 ASP cc_start: 0.8810 (p0) cc_final: 0.8218 (t0) REVERT: B 781 ASP cc_start: 0.8513 (m-30) cc_final: 0.8089 (m-30) REVERT: B 914 MET cc_start: 0.8517 (pmm) cc_final: 0.8207 (pmm) REVERT: B 1103 LYS cc_start: 0.8909 (pttt) cc_final: 0.8576 (pttm) REVERT: B 1243 MET cc_start: 0.8503 (ptp) cc_final: 0.8216 (ptm) REVERT: B 1316 PHE cc_start: 0.7893 (p90) cc_final: 0.7461 (p90) REVERT: B 1415 MET cc_start: 0.8084 (mpp) cc_final: 0.7201 (mpp) REVERT: C 195 SER cc_start: 0.7353 (t) cc_final: 0.6511 (m) REVERT: D 213 TYR cc_start: 0.8997 (m-80) cc_final: 0.8777 (m-80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2349 time to fit residues: 49.4904 Evaluate side-chains 95 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 152 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1368 GLN ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.070276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057259 restraints weight = 75390.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.058895 restraints weight = 46486.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060048 restraints weight = 33680.123| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13597 Z= 0.160 Angle : 0.693 13.066 18462 Z= 0.357 Chirality : 0.044 0.179 2093 Planarity : 0.004 0.044 2349 Dihedral : 4.938 26.593 1815 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.90 % Favored : 89.98 % Rotamer: Outliers : 0.07 % Allowed : 0.62 % Favored : 99.31 % 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: -0.23 (0.21), residues: 1697 helix: 2.14 (0.18), residues: 784 sheet: -0.62 (0.35), residues: 210 loop : -2.87 (0.20), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 91 HIS 0.008 0.001 HIS D 126 PHE 0.013 0.001 PHE C 150 TYR 0.015 0.001 TYR B1320 ARG 0.004 0.001 ARG B 819 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 685) hydrogen bonds : angle 3.89521 ( 1995) covalent geometry : bond 0.00349 (13597) covalent geometry : angle 0.69311 (18462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7913 (tmm) cc_final: 0.7235 (tmm) REVERT: A 16 ASP cc_start: 0.8859 (m-30) cc_final: 0.8037 (t0) REVERT: B 781 ASP cc_start: 0.8536 (m-30) cc_final: 0.8135 (m-30) REVERT: B 914 MET cc_start: 0.8517 (pmm) cc_final: 0.8196 (pmm) REVERT: B 985 MET cc_start: 0.8520 (mpp) cc_final: 0.7407 (mpp) REVERT: B 1063 MET cc_start: 0.8001 (tpp) cc_final: 0.7793 (tpp) REVERT: B 1103 LYS cc_start: 0.8949 (pttt) cc_final: 0.8622 (pttm) REVERT: B 1243 MET cc_start: 0.8487 (ptp) cc_final: 0.8179 (ptm) REVERT: B 1316 PHE cc_start: 0.8005 (p90) cc_final: 0.7556 (p90) REVERT: B 1415 MET cc_start: 0.8167 (mpp) cc_final: 0.7526 (mpp) REVERT: C 195 SER cc_start: 0.7422 (t) cc_final: 0.6517 (m) REVERT: D 1 MET cc_start: 0.1326 (ptt) cc_final: 0.1025 (ptt) REVERT: D 213 TYR cc_start: 0.9029 (m-80) cc_final: 0.8799 (m-80) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2376 time to fit residues: 47.0956 Evaluate side-chains 93 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 79 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 139 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 GLN B1151 HIS ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.070317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.057390 restraints weight = 76798.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.059034 restraints weight = 46997.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.060164 restraints weight = 33847.499| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13597 Z= 0.165 Angle : 0.699 13.000 18462 Z= 0.363 Chirality : 0.044 0.177 2093 Planarity : 0.004 0.048 2349 Dihedral : 5.019 27.048 1815 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.08 % Favored : 89.81 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.58 % 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 (0.21), residues: 1697 helix: 2.05 (0.18), residues: 784 sheet: -0.99 (0.34), residues: 228 loop : -2.88 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1524 HIS 0.008 0.001 HIS D 126 PHE 0.013 0.002 PHE C 150 TYR 0.015 0.001 TYR B1320 ARG 0.006 0.001 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 685) hydrogen bonds : angle 3.93151 ( 1995) covalent geometry : bond 0.00361 (13597) covalent geometry : angle 0.69922 (18462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10326.39 seconds wall clock time: 186 minutes 56.02 seconds (11216.02 seconds total)