Starting phenix.real_space_refine on Wed Sep 17 23:54:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bdd_44449/09_2025/9bdd_44449.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bdd_44449/09_2025/9bdd_44449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bdd_44449/09_2025/9bdd_44449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bdd_44449/09_2025/9bdd_44449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bdd_44449/09_2025/9bdd_44449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bdd_44449/09_2025/9bdd_44449.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 59 5.16 5 C 7666 2.51 5 N 2189 2.21 5 O 2335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12313 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1723 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 206} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1552 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 4, 'PHE:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "E" Number of atoms: 7746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7746 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 67, 'TRANS': 917} Chain breaks: 2 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "N" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "T" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'APC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.23 Number of scatterers: 12313 At special positions: 0 Unit cell: (111.863, 130.229, 103.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 64 15.00 O 2335 8.00 N 2189 7.00 C 7666 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: 0.87 Conformation dependent library (CDL) restraints added in 461.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2674 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 58.9% alpha, 7.7% beta 25 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 208 through 223 removed outlier: 3.503A pdb=" N TYR A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.722A pdb=" N GLU A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.810A pdb=" N ASP A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.919A pdb=" N TYR A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 3.610A pdb=" N ALA B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 223 removed outlier: 3.847A pdb=" N LYS B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 removed outlier: 4.149A pdb=" N HIS B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 338 through 354 removed outlier: 3.757A pdb=" N LEU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 237 Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.847A pdb=" N GLN E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.536A pdb=" N TYR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 291 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.921A pdb=" N ILE E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.825A pdb=" N ALA E 409 " --> pdb=" O HIS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 462 removed outlier: 3.629A pdb=" N GLU E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 490 Processing helix chain 'E' and resid 497 through 520 removed outlier: 4.171A pdb=" N GLN E 517 " --> pdb=" O VAL E 513 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 519 " --> pdb=" O GLN E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 538 removed outlier: 3.680A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS E 535 " --> pdb=" O ARG E 531 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 586 Processing helix chain 'E' and resid 624 through 633 Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 692 through 705 removed outlier: 3.574A pdb=" N ALA E 698 " --> pdb=" O GLY E 694 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS E 705 " --> pdb=" O GLN E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 723 removed outlier: 3.655A pdb=" N LEU E 716 " --> pdb=" O ARG E 712 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 738 Processing helix chain 'E' and resid 747 through 750 Processing helix chain 'E' and resid 751 through 789 removed outlier: 3.508A pdb=" N LYS E 767 " --> pdb=" O ALA E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 836 through 850 removed outlier: 3.732A pdb=" N TRP E 840 " --> pdb=" O HIS E 836 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 883 through 888 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 937 through 944 removed outlier: 3.731A pdb=" N ALA E 942 " --> pdb=" O SER E 938 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER E 943 " --> pdb=" O VAL E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 970 Processing helix chain 'E' and resid 975 through 982 removed outlier: 3.569A pdb=" N LEU E 981 " --> pdb=" O VAL E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 997 removed outlier: 3.899A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1017 removed outlier: 4.157A pdb=" N LYS E1012 " --> pdb=" O LEU E1008 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG E1013 " --> pdb=" O GLN E1009 " (cutoff:3.500A) Processing helix chain 'E' and resid 1024 through 1044 removed outlier: 3.667A pdb=" N ALA E1028 " --> pdb=" O PHE E1024 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR E1031 " --> pdb=" O GLU E1027 " (cutoff:3.500A) Processing helix chain 'E' and resid 1045 through 1065 Processing helix chain 'E' and resid 1111 through 1141 removed outlier: 3.828A pdb=" N PHE E1119 " --> pdb=" O GLN E1115 " (cutoff:3.500A) Proline residue: E1120 - end of helix removed outlier: 3.685A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1156 through 1158 No H-bonds generated for 'chain 'E' and resid 1156 through 1158' Processing helix chain 'E' and resid 1159 through 1177 removed outlier: 3.549A pdb=" N GLN E1170 " --> pdb=" O VAL E1166 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE E1171 " --> pdb=" O CYS E1167 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU E1177 " --> pdb=" O ARG E1173 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1192 Processing helix chain 'E' and resid 1197 through 1209 removed outlier: 3.628A pdb=" N THR E1207 " --> pdb=" O GLN E1203 " (cutoff:3.500A) Processing helix chain 'E' and resid 1221 through 1225 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 197 removed outlier: 7.207A pdb=" N VAL A 191 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP A 186 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 193 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 228 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 232 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 175 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TYR A 229 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N MET A 276 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 231 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA3, first strand: chain 'B' and resid 191 through 197 removed outlier: 6.249A pdb=" N HIS B 184 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP B 194 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP B 182 " --> pdb=" O TRP B 194 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN B 196 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 180 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER B 169 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N VAL B 230 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 171 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU B 232 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE B 173 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR B 229 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N MET B 276 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 231 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AA5, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AA6, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.957A pdb=" N GLU E 495 " --> pdb=" O LEU E 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 588 through 590 Processing sheet with id=AA8, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AA9, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AB1, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AB2, first strand: chain 'E' and resid 919 through 922 Processing sheet with id=AB3, first strand: chain 'E' and resid 1069 through 1071 599 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3493 1.34 - 1.46: 2669 1.46 - 1.58: 6344 1.58 - 1.70: 120 1.70 - 1.82: 96 Bond restraints: 12722 Sorted by residual: bond pdb=" N ILE E 618 " pdb=" CA ILE E 618 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.08e-02 8.57e+03 1.00e+01 bond pdb=" N PHE E1217 " pdb=" CA PHE E1217 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.21e-02 6.83e+03 7.97e+00 bond pdb=" N VAL E 615 " pdb=" CA VAL E 615 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.70e+00 bond pdb=" N ARG E 613 " pdb=" CA ARG E 613 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.24e-02 6.50e+03 7.41e+00 bond pdb=" N GLN E 616 " pdb=" CA GLN E 616 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.27e-02 6.20e+03 6.62e+00 ... (remaining 12717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 17046 1.84 - 3.68: 385 3.68 - 5.52: 67 5.52 - 7.36: 30 7.36 - 9.20: 2 Bond angle restraints: 17530 Sorted by residual: angle pdb=" C LEU B 304 " pdb=" N PHE B 305 " pdb=" CA PHE B 305 " ideal model delta sigma weight residual 121.70 130.90 -9.20 1.80e+00 3.09e-01 2.61e+01 angle pdb=" CA ALA E1216 " pdb=" C ALA E1216 " pdb=" O ALA E1216 " ideal model delta sigma weight residual 121.20 115.95 5.25 1.04e+00 9.25e-01 2.55e+01 angle pdb=" CA ASP E1218 " pdb=" C ASP E1218 " pdb=" O ASP E1218 " ideal model delta sigma weight residual 121.56 116.30 5.26 1.09e+00 8.42e-01 2.32e+01 angle pdb=" CA ASP E1218 " pdb=" C ASP E1218 " pdb=" N LEU E1219 " ideal model delta sigma weight residual 115.51 121.33 -5.82 1.27e+00 6.20e-01 2.10e+01 angle pdb=" N GLN E1221 " pdb=" CA GLN E1221 " pdb=" C GLN E1221 " ideal model delta sigma weight residual 113.17 107.78 5.39 1.26e+00 6.30e-01 1.83e+01 ... (remaining 17525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.27: 7059 28.27 - 56.55: 429 56.55 - 84.82: 85 84.82 - 113.10: 0 113.10 - 141.37: 1 Dihedral angle restraints: 7574 sinusoidal: 3471 harmonic: 4103 Sorted by residual: dihedral pdb=" CA VAL E1149 " pdb=" C VAL E1149 " pdb=" N HIS E1150 " pdb=" CA HIS E1150 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLY E 661 " pdb=" C GLY E 661 " pdb=" N ALA E 662 " pdb=" CA ALA E 662 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP A 194 " pdb=" C TRP A 194 " pdb=" N GLN A 195 " pdb=" CA GLN A 195 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 7571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1952 0.127 - 0.254: 22 0.254 - 0.381: 0 0.381 - 0.509: 3 0.509 - 0.636: 10 Chirality restraints: 1987 Sorted by residual: chirality pdb=" P DA N -24 " pdb=" OP1 DA N -24 " pdb=" OP2 DA N -24 " pdb=" O5' DA N -24 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DC T 2 " pdb=" OP1 DC T 2 " pdb=" OP2 DC T 2 " pdb=" O5' DC T 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" P DG T -1 " pdb=" OP1 DG T -1 " pdb=" OP2 DG T -1 " pdb=" O5' DG T -1 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 1984 not shown) Planarity restraints: 2021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E1215 " 0.022 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C GLY E1215 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY E1215 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA E1216 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E1151 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ASP E1151 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP E1151 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS E1152 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 249 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C HIS B 249 " 0.037 2.00e-02 2.50e+03 pdb=" O HIS B 249 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE B 250 " -0.012 2.00e-02 2.50e+03 ... (remaining 2018 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2364 2.78 - 3.31: 11269 3.31 - 3.84: 20450 3.84 - 4.37: 23275 4.37 - 4.90: 39509 Nonbonded interactions: 96867 Sorted by model distance: nonbonded pdb=" NH1 ARG E 967 " pdb=" O LEU E 981 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.274 3.040 nonbonded pdb=" OD2 ASP E 970 " pdb=" OH TYR E1031 " model vdw 2.348 3.040 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 278 " model vdw 2.349 3.120 nonbonded pdb=" O VAL E1222 " pdb=" OG SER E1225 " model vdw 2.351 3.040 ... (remaining 96862 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 'A' and (resid 151 or (resid 152 and (name N or name CA or name C or name \ O or name CB )) or resid 153 through 160 or (resid 161 through 162 and (name N \ or name CA or name C or name O or name CB )) or resid 163 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throug \ h 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) or \ resid 189 through 198 or (resid 199 and (name N or name CA or name C or name O o \ r name CB )) or resid 200 through 266 or (resid 267 and (name N or name CA or na \ me C or name O or name CB )) or resid 268 through 282 or (resid 283 and (name N \ or name CA or name C or name O or name CB )) or resid 284 through 285 or (resid \ 286 and (name N or name CA or name C or name O or name CB )) or resid 287 or (re \ sid 288 and (name N or name CA or name C or name O or name CB )) or resid 289 th \ rough 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) \ or resid 298 or (resid 299 and (name N or name CA or name C or name O or name C \ B )) or resid 300 through 301 or (resid 302 and (name N or name CA or name C or \ name O or name CB )) or resid 303 through 306 or resid 313 through 316 or (resid \ 317 and (name N or name CA or name C or name O or name CB )) or resid 318 or re \ sid 320 through 326 or (resid 327 and (name N or name CA or name C or name O or \ name CB )) or resid 328 or (resid 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 332 or (resid 333 and (name N or name CA or \ name C or name O or name CB )) or resid 334 or (resid 335 through 336 and (name \ N or name CA or name C or name O or name CB )) or resid 337 through 351 or (resi \ d 352 and (name N or name CA or name C or name O or name CB )) or resid 353 thro \ ugh 355 or (resid 356 through 357 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'B' and (resid 151 through 238 or (resid 239 through 240 and (name N or n \ ame CA or name C or name O or name CB )) or resid 241 through 318 or (resid 320 \ and (name N or name CA or name C or name O or name CB )) or resid 321 through 35 \ 7)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 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 0.040 12722 Z= 0.195 Angle : 0.703 9.196 17530 Z= 0.382 Chirality : 0.060 0.636 1987 Planarity : 0.006 0.053 2021 Dihedral : 17.263 141.372 4900 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.26 % Allowed : 0.94 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.21), residues: 1383 helix: 0.88 (0.18), residues: 751 sheet: 0.09 (0.42), residues: 125 loop : -0.88 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 936 TYR 0.020 0.001 TYR B 258 PHE 0.016 0.001 PHE E1024 TRP 0.030 0.002 TRP A 194 HIS 0.014 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00367 (12722) covalent geometry : angle 0.70281 (17530) hydrogen bonds : bond 0.16475 ( 668) hydrogen bonds : angle 5.91204 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 316 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 172 SER cc_start: 0.7356 (t) cc_final: 0.6870 (p) REVERT: B 171 ILE cc_start: 0.7971 (mm) cc_final: 0.7735 (mp) REVERT: B 217 SER cc_start: 0.6539 (t) cc_final: 0.6173 (m) REVERT: B 223 MET cc_start: 0.7479 (mtt) cc_final: 0.7123 (mtm) REVERT: B 304 LEU cc_start: 0.7074 (mt) cc_final: 0.6834 (mt) REVERT: E 225 ARG cc_start: 0.5678 (mtt180) cc_final: 0.5433 (mtp-110) REVERT: E 279 GLU cc_start: 0.6898 (mp0) cc_final: 0.6349 (mp0) REVERT: E 385 SER cc_start: 0.7441 (t) cc_final: 0.6898 (p) REVERT: E 405 HIS cc_start: 0.6670 (t-90) cc_final: 0.6318 (m90) REVERT: E 466 SER cc_start: 0.6832 (t) cc_final: 0.6464 (p) REVERT: E 502 ARG cc_start: 0.6194 (mtm-85) cc_final: 0.5939 (mtm180) REVERT: E 543 VAL cc_start: 0.7138 (m) cc_final: 0.6912 (t) REVERT: E 544 PRO cc_start: 0.7789 (Cg_exo) cc_final: 0.7486 (Cg_endo) REVERT: E 613 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6295 (mtt90) REVERT: E 638 THR cc_start: 0.6965 (p) cc_final: 0.6755 (m) REVERT: E 682 GLU cc_start: 0.6544 (tt0) cc_final: 0.6105 (tp30) REVERT: E 826 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6727 (tt0) REVERT: E 858 ARG cc_start: 0.6372 (ttp-110) cc_final: 0.6110 (ptp90) REVERT: E 873 ASP cc_start: 0.6742 (t0) cc_final: 0.6467 (t0) REVERT: E 883 LYS cc_start: 0.7211 (mtmm) cc_final: 0.7000 (mtmm) REVERT: E 900 GLU cc_start: 0.6370 (tp30) cc_final: 0.6076 (tp30) REVERT: E 922 ASP cc_start: 0.6415 (p0) cc_final: 0.6106 (p0) REVERT: E 991 LYS cc_start: 0.5936 (ttpt) cc_final: 0.5500 (ttmm) REVERT: E 1064 MET cc_start: 0.6223 (ttp) cc_final: 0.5917 (mtm) outliers start: 3 outliers final: 2 residues processed: 317 average time/residue: 0.5703 time to fit residues: 195.7603 Evaluate side-chains 249 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 246 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 613 ARG Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 1220 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 251 HIS B 249 HIS B 262 ASN B 324 HIS B 346 GLN E 244 HIS E 250 HIS E 265 ASN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 440 GLN E 512 HIS E 515 GLN E 529 HIS E 608 HIS E 617 GLN E 629 GLN E 728 GLN E 812 HIS E 920 HIS E 921 GLN E 930 HIS E 945 ASN E 953 GLN E 969 GLN E 979 GLN E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1117 ASN E1150 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.165839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133452 restraints weight = 16260.311| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.87 r_work: 0.3556 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12722 Z= 0.137 Angle : 0.557 8.547 17530 Z= 0.294 Chirality : 0.039 0.162 1987 Planarity : 0.005 0.053 2021 Dihedral : 18.413 140.685 2262 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.06 % Allowed : 11.40 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1383 helix: 1.60 (0.19), residues: 782 sheet: 0.07 (0.41), residues: 125 loop : -0.50 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 411 TYR 0.017 0.001 TYR B 258 PHE 0.017 0.001 PHE E1024 TRP 0.028 0.002 TRP E1026 HIS 0.008 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00300 (12722) covalent geometry : angle 0.55652 (17530) hydrogen bonds : bond 0.04749 ( 668) hydrogen bonds : angle 3.86130 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 SER cc_start: 0.8238 (m) cc_final: 0.7938 (p) REVERT: A 301 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8067 (ttpp) REVERT: A 339 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: A 352 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: B 241 SER cc_start: 0.7939 (p) cc_final: 0.7722 (t) REVERT: B 305 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.6425 (m-10) REVERT: E 303 LEU cc_start: 0.7939 (mt) cc_final: 0.7688 (mm) REVERT: E 385 SER cc_start: 0.8336 (t) cc_final: 0.8102 (p) REVERT: E 502 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7448 (mtm180) REVERT: E 543 VAL cc_start: 0.8196 (m) cc_final: 0.7992 (t) REVERT: E 544 PRO cc_start: 0.8600 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: E 686 THR cc_start: 0.8703 (p) cc_final: 0.8437 (m) REVERT: E 787 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: E 1114 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8122 (mttp) outliers start: 36 outliers final: 10 residues processed: 264 average time/residue: 0.5660 time to fit residues: 162.4798 Evaluate side-chains 245 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN B 284 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 454 ASN E 515 GLN E 616 GLN E 728 GLN E 920 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1181 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130521 restraints weight = 16361.419| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.72 r_work: 0.3504 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12722 Z= 0.214 Angle : 0.599 7.777 17530 Z= 0.317 Chirality : 0.042 0.184 1987 Planarity : 0.005 0.059 2021 Dihedral : 18.272 139.975 2255 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.06 % Allowed : 14.98 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1383 helix: 1.70 (0.18), residues: 775 sheet: 0.15 (0.45), residues: 111 loop : -0.60 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 178 TYR 0.026 0.002 TYR B 258 PHE 0.015 0.002 PHE E 794 TRP 0.019 0.002 TRP E1026 HIS 0.006 0.001 HIS E1156 Details of bonding type rmsd covalent geometry : bond 0.00507 (12722) covalent geometry : angle 0.59919 (17530) hydrogen bonds : bond 0.05324 ( 668) hydrogen bonds : angle 3.90400 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8434 (mm) cc_final: 0.8096 (mp) REVERT: A 292 SER cc_start: 0.8241 (m) cc_final: 0.7888 (p) REVERT: A 301 LYS cc_start: 0.8342 (ttpp) cc_final: 0.8134 (ttpp) REVERT: A 339 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: A 352 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: B 241 SER cc_start: 0.8026 (p) cc_final: 0.7825 (t) REVERT: B 301 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7976 (tppp) REVERT: E 261 LEU cc_start: 0.7878 (tp) cc_final: 0.7546 (tm) REVERT: E 303 LEU cc_start: 0.7912 (mt) cc_final: 0.7659 (mm) REVERT: E 385 SER cc_start: 0.8324 (t) cc_final: 0.7989 (m) REVERT: E 500 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8221 (mp) REVERT: E 544 PRO cc_start: 0.8642 (Cg_exo) cc_final: 0.8330 (Cg_endo) REVERT: E 642 GLU cc_start: 0.7608 (mp0) cc_final: 0.7408 (mp0) REVERT: E 645 ASP cc_start: 0.7982 (m-30) cc_final: 0.7541 (m-30) REVERT: E 787 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: E 1016 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: E 1114 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8181 (mttp) outliers start: 36 outliers final: 12 residues processed: 255 average time/residue: 0.5745 time to fit residues: 158.7250 Evaluate side-chains 252 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 0.0470 chunk 32 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 614 ASN E 728 GLN E 920 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** 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 = 0.4047 r_free = 0.4047 target = 0.163116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130782 restraints weight = 16226.125| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.84 r_work: 0.3520 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12722 Z= 0.132 Angle : 0.537 7.243 17530 Z= 0.283 Chirality : 0.039 0.180 1987 Planarity : 0.005 0.050 2021 Dihedral : 18.108 139.603 2255 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.40 % Allowed : 15.91 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.22), residues: 1383 helix: 1.93 (0.19), residues: 778 sheet: 0.27 (0.44), residues: 115 loop : -0.55 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 178 TYR 0.013 0.001 TYR B 258 PHE 0.014 0.001 PHE B 305 TRP 0.017 0.002 TRP E1026 HIS 0.004 0.001 HIS E 815 Details of bonding type rmsd covalent geometry : bond 0.00290 (12722) covalent geometry : angle 0.53681 (17530) hydrogen bonds : bond 0.04219 ( 668) hydrogen bonds : angle 3.70241 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8459 (mm) cc_final: 0.8126 (mp) REVERT: A 292 SER cc_start: 0.8219 (m) cc_final: 0.7857 (p) REVERT: A 339 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7748 (mm-30) REVERT: A 352 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: B 241 SER cc_start: 0.7973 (p) cc_final: 0.7772 (t) REVERT: B 305 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.6424 (m-10) REVERT: E 261 LEU cc_start: 0.7770 (tp) cc_final: 0.7476 (tt) REVERT: E 303 LEU cc_start: 0.7918 (mt) cc_final: 0.7657 (mm) REVERT: E 385 SER cc_start: 0.8271 (t) cc_final: 0.8026 (p) REVERT: E 686 THR cc_start: 0.8682 (p) cc_final: 0.8464 (m) REVERT: E 1016 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: E 1114 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8124 (mttp) outliers start: 40 outliers final: 17 residues processed: 259 average time/residue: 0.5731 time to fit residues: 161.3738 Evaluate side-chains 253 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 482 MET Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1147 VAL Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 135 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN E 728 GLN E 920 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** 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 = 0.4023 r_free = 0.4023 target = 0.160496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127947 restraints weight = 16329.682| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.85 r_work: 0.3494 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12722 Z= 0.157 Angle : 0.557 10.674 17530 Z= 0.291 Chirality : 0.040 0.173 1987 Planarity : 0.005 0.050 2021 Dihedral : 18.068 139.316 2255 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.81 % Allowed : 17.79 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.22), residues: 1383 helix: 1.97 (0.18), residues: 777 sheet: 0.33 (0.45), residues: 115 loop : -0.51 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 178 TYR 0.017 0.001 TYR B 258 PHE 0.012 0.001 PHE E 794 TRP 0.015 0.002 TRP E1026 HIS 0.005 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00361 (12722) covalent geometry : angle 0.55706 (17530) hydrogen bonds : bond 0.04504 ( 668) hydrogen bonds : angle 3.71546 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8426 (mm) cc_final: 0.8093 (mp) REVERT: A 292 SER cc_start: 0.8266 (m) cc_final: 0.7906 (p) REVERT: A 352 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: B 241 SER cc_start: 0.7991 (p) cc_final: 0.7784 (t) REVERT: B 301 LYS cc_start: 0.8556 (tppp) cc_final: 0.8185 (tppt) REVERT: E 256 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7562 (ttp80) REVERT: E 260 THR cc_start: 0.7193 (m) cc_final: 0.6862 (p) REVERT: E 303 LEU cc_start: 0.7925 (mt) cc_final: 0.7667 (mm) REVERT: E 385 SER cc_start: 0.8285 (t) cc_final: 0.7966 (m) REVERT: E 500 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8210 (mp) REVERT: E 645 ASP cc_start: 0.8025 (m-30) cc_final: 0.7666 (m-30) REVERT: E 787 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7908 (tp40) REVERT: E 854 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7527 (mtp180) REVERT: E 1016 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: E 1114 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8119 (mttp) REVERT: E 1220 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7382 (mp0) outliers start: 33 outliers final: 15 residues processed: 251 average time/residue: 0.5771 time to fit residues: 157.1791 Evaluate side-chains 254 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1208 LEU Chi-restraints excluded: chain E residue 1220 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 0.0070 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS E 249 HIS E 304 GLN E 369 ASN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129126 restraints weight = 16250.823| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.86 r_work: 0.3508 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12722 Z= 0.129 Angle : 0.524 8.069 17530 Z= 0.275 Chirality : 0.038 0.172 1987 Planarity : 0.004 0.049 2021 Dihedral : 17.990 139.161 2255 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.89 % Allowed : 18.47 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.22), residues: 1383 helix: 2.03 (0.18), residues: 779 sheet: 0.38 (0.47), residues: 109 loop : -0.55 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 613 TYR 0.009 0.001 TYR B 258 PHE 0.016 0.001 PHE B 305 TRP 0.013 0.001 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00288 (12722) covalent geometry : angle 0.52384 (17530) hydrogen bonds : bond 0.04041 ( 668) hydrogen bonds : angle 3.59907 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8417 (mm) cc_final: 0.8075 (mp) REVERT: A 292 SER cc_start: 0.8239 (m) cc_final: 0.7865 (p) REVERT: B 241 SER cc_start: 0.7985 (p) cc_final: 0.7774 (t) REVERT: B 301 LYS cc_start: 0.8373 (tppp) cc_final: 0.8047 (tppt) REVERT: B 338 GLU cc_start: 0.6713 (mp0) cc_final: 0.6454 (mp0) REVERT: E 256 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7557 (ttp80) REVERT: E 303 LEU cc_start: 0.7921 (mt) cc_final: 0.7646 (mm) REVERT: E 385 SER cc_start: 0.8253 (t) cc_final: 0.7968 (m) REVERT: E 615 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7992 (t) REVERT: E 645 ASP cc_start: 0.7996 (m-30) cc_final: 0.7793 (m-30) REVERT: E 787 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7875 (tp40) REVERT: E 854 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7548 (mtp180) REVERT: E 886 MET cc_start: 0.8762 (mtt) cc_final: 0.8220 (mtt) REVERT: E 1016 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: E 1114 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8097 (mttp) outliers start: 34 outliers final: 14 residues processed: 252 average time/residue: 0.5798 time to fit residues: 158.9016 Evaluate side-chains 248 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 405 HIS Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN E 304 GLN E 369 ASN E 728 GLN E 903 ASN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.160811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128120 restraints weight = 16234.831| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.88 r_work: 0.3494 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12722 Z= 0.143 Angle : 0.535 10.360 17530 Z= 0.279 Chirality : 0.039 0.175 1987 Planarity : 0.005 0.058 2021 Dihedral : 17.919 138.936 2255 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.23 % Allowed : 18.38 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.22), residues: 1383 helix: 2.04 (0.18), residues: 779 sheet: 0.37 (0.47), residues: 109 loop : -0.60 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 613 TYR 0.011 0.001 TYR B 258 PHE 0.014 0.001 PHE B 305 TRP 0.014 0.002 TRP B 194 HIS 0.006 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00327 (12722) covalent geometry : angle 0.53506 (17530) hydrogen bonds : bond 0.04206 ( 668) hydrogen bonds : angle 3.60358 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8413 (mm) cc_final: 0.8079 (mp) REVERT: A 292 SER cc_start: 0.8235 (m) cc_final: 0.7876 (p) REVERT: B 241 SER cc_start: 0.8018 (p) cc_final: 0.7797 (t) REVERT: B 301 LYS cc_start: 0.8229 (tppp) cc_final: 0.7969 (tppt) REVERT: B 338 GLU cc_start: 0.6712 (mp0) cc_final: 0.6458 (mp0) REVERT: E 256 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7597 (ttp80) REVERT: E 303 LEU cc_start: 0.7936 (mt) cc_final: 0.7668 (mm) REVERT: E 385 SER cc_start: 0.8286 (t) cc_final: 0.7968 (m) REVERT: E 602 LEU cc_start: 0.8379 (mm) cc_final: 0.8118 (mt) REVERT: E 615 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7973 (t) REVERT: E 787 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7883 (tp40) REVERT: E 854 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7552 (mtp180) REVERT: E 886 MET cc_start: 0.8759 (mtt) cc_final: 0.8482 (mtt) REVERT: E 1016 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7110 (mt-10) outliers start: 38 outliers final: 21 residues processed: 250 average time/residue: 0.5635 time to fit residues: 152.9705 Evaluate side-chains 252 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN E 304 GLN E 369 ASN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128667 restraints weight = 16140.096| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.83 r_work: 0.3506 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12722 Z= 0.130 Angle : 0.523 8.597 17530 Z= 0.274 Chirality : 0.038 0.175 1987 Planarity : 0.004 0.048 2021 Dihedral : 17.838 138.762 2255 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.81 % Allowed : 18.98 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.22), residues: 1383 helix: 2.09 (0.18), residues: 779 sheet: 0.41 (0.48), residues: 107 loop : -0.58 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 613 TYR 0.008 0.001 TYR E 533 PHE 0.020 0.001 PHE B 305 TRP 0.014 0.001 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00290 (12722) covalent geometry : angle 0.52337 (17530) hydrogen bonds : bond 0.03952 ( 668) hydrogen bonds : angle 3.56724 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8402 (mm) cc_final: 0.8066 (mp) REVERT: A 292 SER cc_start: 0.8229 (m) cc_final: 0.7858 (p) REVERT: B 241 SER cc_start: 0.8002 (p) cc_final: 0.7782 (t) REVERT: B 338 GLU cc_start: 0.6675 (mp0) cc_final: 0.6425 (mp0) REVERT: E 279 GLU cc_start: 0.7959 (mp0) cc_final: 0.7452 (mp0) REVERT: E 303 LEU cc_start: 0.7930 (mt) cc_final: 0.7646 (mm) REVERT: E 385 SER cc_start: 0.8250 (t) cc_final: 0.7965 (m) REVERT: E 602 LEU cc_start: 0.8354 (mm) cc_final: 0.8092 (mt) REVERT: E 615 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7962 (t) REVERT: E 787 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7857 (tp40) REVERT: E 854 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7524 (mtp180) REVERT: E 886 MET cc_start: 0.8754 (mtt) cc_final: 0.8228 (mtt) REVERT: E 1016 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7082 (mt-10) outliers start: 33 outliers final: 21 residues processed: 246 average time/residue: 0.5817 time to fit residues: 155.5539 Evaluate side-chains 252 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 582 MET Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 250 HIS E 304 GLN E 369 ASN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.160398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127865 restraints weight = 16150.717| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.84 r_work: 0.3492 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12722 Z= 0.154 Angle : 0.548 8.815 17530 Z= 0.284 Chirality : 0.039 0.175 1987 Planarity : 0.005 0.050 2021 Dihedral : 17.801 138.542 2255 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.47 % Allowed : 20.17 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.22), residues: 1383 helix: 1.99 (0.18), residues: 781 sheet: 0.35 (0.47), residues: 107 loop : -0.61 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 613 TYR 0.010 0.001 TYR B 258 PHE 0.013 0.001 PHE B 305 TRP 0.013 0.002 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00356 (12722) covalent geometry : angle 0.54823 (17530) hydrogen bonds : bond 0.04264 ( 668) hydrogen bonds : angle 3.61980 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.448 Fit side-chains REVERT: A 289 ILE cc_start: 0.8403 (mm) cc_final: 0.8068 (mp) REVERT: A 292 SER cc_start: 0.8244 (m) cc_final: 0.7871 (p) REVERT: B 241 SER cc_start: 0.8020 (p) cc_final: 0.7804 (t) REVERT: B 301 LYS cc_start: 0.8271 (tppp) cc_final: 0.7883 (tppt) REVERT: B 304 LEU cc_start: 0.7328 (mt) cc_final: 0.7104 (tt) REVERT: B 338 GLU cc_start: 0.6680 (mp0) cc_final: 0.6441 (mp0) REVERT: E 260 THR cc_start: 0.7220 (m) cc_final: 0.6971 (p) REVERT: E 279 GLU cc_start: 0.7981 (mp0) cc_final: 0.7482 (mp0) REVERT: E 303 LEU cc_start: 0.7924 (mt) cc_final: 0.7656 (mm) REVERT: E 385 SER cc_start: 0.8255 (t) cc_final: 0.7948 (m) REVERT: E 602 LEU cc_start: 0.8367 (mm) cc_final: 0.8095 (mt) REVERT: E 615 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7970 (t) REVERT: E 787 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7868 (tp40) REVERT: E 854 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.7546 (mtp180) REVERT: E 886 MET cc_start: 0.8755 (mtt) cc_final: 0.8468 (mtt) REVERT: E 1016 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6980 (mt-10) outliers start: 29 outliers final: 24 residues processed: 241 average time/residue: 0.5905 time to fit residues: 154.3403 Evaluate side-chains 250 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 582 MET Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 616 GLN Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 250 HIS E 304 GLN E 369 ASN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.161235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128657 restraints weight = 16264.340| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.86 r_work: 0.3491 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12722 Z= 0.147 Angle : 0.556 12.679 17530 Z= 0.286 Chirality : 0.039 0.175 1987 Planarity : 0.005 0.051 2021 Dihedral : 17.758 138.376 2255 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.64 % Allowed : 19.91 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.22), residues: 1383 helix: 2.00 (0.18), residues: 781 sheet: 0.36 (0.48), residues: 107 loop : -0.63 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 613 TYR 0.009 0.001 TYR E 533 PHE 0.015 0.001 PHE B 305 TRP 0.016 0.002 TRP B 194 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00339 (12722) covalent geometry : angle 0.55627 (17530) hydrogen bonds : bond 0.04190 ( 668) hydrogen bonds : angle 3.62673 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2766 Ramachandran restraints generated. 1383 Oldfield, 0 Emsley, 1383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 289 ILE cc_start: 0.8405 (mm) cc_final: 0.8070 (mp) REVERT: A 292 SER cc_start: 0.8250 (m) cc_final: 0.7877 (p) REVERT: B 241 SER cc_start: 0.8012 (p) cc_final: 0.7800 (t) REVERT: B 301 LYS cc_start: 0.8175 (tppp) cc_final: 0.7784 (tppt) REVERT: E 260 THR cc_start: 0.7214 (m) cc_final: 0.6997 (p) REVERT: E 279 GLU cc_start: 0.7981 (mp0) cc_final: 0.7451 (mp0) REVERT: E 303 LEU cc_start: 0.7927 (mt) cc_final: 0.7650 (mm) REVERT: E 385 SER cc_start: 0.8249 (t) cc_final: 0.7970 (m) REVERT: E 602 LEU cc_start: 0.8360 (mm) cc_final: 0.8086 (mt) REVERT: E 615 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7967 (t) REVERT: E 787 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7863 (tp40) REVERT: E 854 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7542 (mtp180) REVERT: E 1016 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7078 (mt-10) outliers start: 31 outliers final: 24 residues processed: 242 average time/residue: 0.6110 time to fit residues: 160.2332 Evaluate side-chains 250 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain E residue 582 MET Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain E residue 615 VAL Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 778 GLU Chi-restraints excluded: chain E residue 787 GLN Chi-restraints excluded: chain E residue 917 LEU Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 951 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1016 GLU Chi-restraints excluded: chain E residue 1055 THR Chi-restraints excluded: chain E residue 1063 HIS Chi-restraints excluded: chain E residue 1079 ILE Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.0070 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 250 HIS E 304 GLN E 369 ASN E 728 GLN E 920 HIS E1030 HIS ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127655 restraints weight = 16362.035| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.89 r_work: 0.3487 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12722 Z= 0.134 Angle : 0.542 8.570 17530 Z= 0.280 Chirality : 0.038 0.174 1987 Planarity : 0.004 0.051 2021 Dihedral : 17.716 138.249 2255 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.55 % Allowed : 20.26 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.22), residues: 1383 helix: 2.06 (0.18), residues: 781 sheet: 0.36 (0.48), residues: 107 loop : -0.61 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 613 TYR 0.009 0.001 TYR A 325 PHE 0.011 0.001 PHE E1024 TRP 0.014 0.001 TRP E1026 HIS 0.004 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00302 (12722) covalent geometry : angle 0.54206 (17530) hydrogen bonds : bond 0.03988 ( 668) hydrogen bonds : angle 3.56983 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4973.85 seconds wall clock time: 85 minutes 12.78 seconds (5112.78 seconds total)