Starting phenix.real_space_refine on Sat Oct 24 20:23:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r96_53854/10_2026/9r96_53854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r96_53854/10_2026/9r96_53854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r96_53854/10_2026/9r96_53854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r96_53854/10_2026/9r96_53854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r96_53854/10_2026/9r96_53854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r96_53854/10_2026/9r96_53854.map" } resolution = 3.1 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 108 5.49 5 Mg 1 5.21 5 S 75 5.16 5 C 8952 2.51 5 N 2627 2.21 5 O 2843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14606 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1068, 8472 Classifications: {'peptide': 1068} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 68, 'TRANS': 999} Chain breaks: 3 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Conformer: "B" Number of residues, atoms: 1068, 8472 Classifications: {'peptide': 1068} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 68, 'TRANS': 999} Chain breaks: 3 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 bond proxies already assigned to first conformer: 8656 Chain: "N" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1039 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "T" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1012 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2590 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 304} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'3DA': 1, 'GTP': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p_pur': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1373 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain breaks: 2 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 563 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 563 " occ=0.50 Time building chain proxies: 4.67, per 1000 atoms: 0.32 Number of scatterers: 14606 At special positions: 0 Unit cell: (101.7, 131.4, 144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 108 15.00 Mg 1 11.99 O 2843 8.00 N 2627 7.00 C 8952 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 753.6 milliseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 10 sheets defined 62.7% alpha, 5.7% beta 44 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 122 through 146 Processing helix chain 'A' and resid 168 through 182 removed outlier: 4.596A pdb=" N ALA A 182 " --> pdb=" O CYS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.662A pdb=" N LEU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 237 removed outlier: 3.608A pdb=" N LEU A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.885A pdb=" N ALA A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.014A pdb=" N LYS A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 3.735A pdb=" N TYR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.337A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.505A pdb=" N LEU A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 340 through 355 removed outlier: 3.764A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 424 through 462 removed outlier: 3.550A pdb=" N GLU A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.615A pdb=" N ALA A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 521 removed outlier: 3.678A pdb=" N SER A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 4.152A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 532 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 Processing helix chain 'A' and resid 568 through 587 removed outlier: 3.657A pdb=" N THR A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 688 through 691 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 756 through 789 removed outlier: 3.794A pdb=" N SER A 774 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 837 through 850 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 890 through 907 Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 954 through 973 removed outlier: 3.884A pdb=" N GLY A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 973 " --> pdb=" O GLN A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 981 Processing helix chain 'A' and resid 990 through 997 removed outlier: 3.818A pdb=" N VAL A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1016 removed outlier: 3.666A pdb=" N LEU A1008 " --> pdb=" O TYR A1004 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 3.676A pdb=" N HIS A1030 " --> pdb=" O TRP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1064 Processing helix chain 'A' and resid 1111 through 1141 Proline residue: A1120 - end of helix removed outlier: 3.675A pdb=" N ILE A1124 " --> pdb=" O PRO A1120 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A1141 " --> pdb=" O LEU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1176 removed outlier: 3.639A pdb=" N VAL A1172 " --> pdb=" O ARG A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1192 Processing helix chain 'A' and resid 1197 through 1209 Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 3.533A pdb=" N GLN A1221 " --> pdb=" O ASP A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.289A pdb=" N HIS B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.537A pdb=" N LEU B 154 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.749A pdb=" N GLY B 221 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.523A pdb=" N GLN B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.565A pdb=" N PHE B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.730A pdb=" N HIS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 366 through 380 removed outlier: 3.512A pdb=" N SER B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 55 through 72 Proline residue: C 66 - end of helix Processing helix chain 'C' and resid 76 through 91 Processing helix chain 'C' and resid 92 through 121 removed outlier: 3.814A pdb=" N LYS C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C 121 " --> pdb=" O PHE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 152 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 180 through 190 Processing helix chain 'C' and resid 199 through 225 removed outlier: 4.449A pdb=" N ASN C 213 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA4, first strand: chain 'A' and resid 707 through 709 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA6, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AA7, first strand: chain 'A' and resid 919 through 922 Processing sheet with id=AA8, first strand: chain 'A' and resid 1069 through 1071 Processing sheet with id=AA9, first strand: chain 'A' and resid 1089 through 1091 Processing sheet with id=AB1, first strand: chain 'B' and resid 144 through 147 removed outlier: 7.222A pdb=" N VAL B 120 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE B 147 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA B 122 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU B 98 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 192 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 100 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N MET B 194 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS B 102 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 191 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE B 228 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY B 193 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 299 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 296 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N MET B 265 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 298 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 302 " --> pdb=" O GLU B 259 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2170 1.32 - 1.44: 4441 1.44 - 1.57: 8212 1.57 - 1.69: 209 1.69 - 1.81: 118 Bond restraints: 15150 Sorted by residual: bond pdb=" C3' DC T 42 " pdb=" C2' DC T 42 " ideal model delta sigma weight residual 1.516 1.640 -0.124 8.00e-03 1.56e+04 2.40e+02 bond pdb=" C3' DT T 47 " pdb=" C2' DT T 47 " ideal model delta sigma weight residual 1.516 1.623 -0.107 8.00e-03 1.56e+04 1.79e+02 bond pdb=" C3' DC T 9 " pdb=" C2' DC T 9 " ideal model delta sigma weight residual 1.516 1.621 -0.105 8.00e-03 1.56e+04 1.71e+02 bond pdb=" C4' DT T 47 " pdb=" O4' DT T 47 " ideal model delta sigma weight residual 1.446 1.321 0.125 1.00e-02 1.00e+04 1.57e+02 bond pdb=" O3' DT N 4 " pdb=" P DA N 5 " ideal model delta sigma weight residual 1.607 1.478 0.129 1.20e-02 6.94e+03 1.16e+02 ... (remaining 15145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 20529 2.84 - 5.67: 380 5.67 - 8.51: 45 8.51 - 11.34: 10 11.34 - 14.18: 7 Bond angle restraints: 20971 Sorted by residual: angle pdb=" C3' DT N 15 " pdb=" O3' DT N 15 " pdb=" P DG N 16 " ideal model delta sigma weight residual 119.70 108.25 11.45 1.20e+00 6.94e-01 9.11e+01 angle pdb=" C3' DC T 42 " pdb=" O3' DC T 42 " pdb=" P DC T 43 " ideal model delta sigma weight residual 119.70 108.26 11.44 1.20e+00 6.94e-01 9.09e+01 angle pdb=" C3' DG N 9 " pdb=" O3' DG N 9 " pdb=" P DG N 10 " ideal model delta sigma weight residual 119.70 108.51 11.19 1.20e+00 6.94e-01 8.69e+01 angle pdb=" C4' DC T 9 " pdb=" C3' DC T 9 " pdb=" C2' DC T 9 " ideal model delta sigma weight residual 103.10 96.43 6.67 9.00e-01 1.23e+00 5.49e+01 angle pdb=" C3' DA T 37 " pdb=" O3' DA T 37 " pdb=" P DC T 38 " ideal model delta sigma weight residual 119.70 110.90 8.80 1.20e+00 6.94e-01 5.38e+01 ... (remaining 20966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.16: 8275 30.16 - 60.33: 695 60.33 - 90.49: 22 90.49 - 120.65: 4 120.65 - 150.81: 4 Dihedral angle restraints: 9000 sinusoidal: 4400 harmonic: 4600 Sorted by residual: dihedral pdb=" C5' GTP R 101 " pdb=" O5' GTP R 101 " pdb=" PA GTP R 101 " pdb=" O3A GTP R 101 " ideal model delta sinusoidal sigma weight residual 69.27 -81.55 150.81 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O3B GTP A1301 " pdb=" O3A GTP A1301 " pdb=" PB GTP A1301 " pdb=" PA GTP A1301 " ideal model delta sinusoidal sigma weight residual 291.08 149.98 141.10 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O5' GTP A1301 " pdb=" O3A GTP A1301 " pdb=" PA GTP A1301 " pdb=" PB GTP A1301 " ideal model delta sinusoidal sigma weight residual -85.88 52.49 -138.36 1 2.00e+01 2.50e-03 4.19e+01 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2250 0.140 - 0.280: 56 0.280 - 0.420: 6 0.420 - 0.561: 15 0.561 - 0.701: 2 Chirality restraints: 2329 Sorted by residual: chirality pdb=" C4' DT T 47 " pdb=" C5' DT T 47 " pdb=" O4' DT T 47 " pdb=" C3' DT T 47 " both_signs ideal model delta sigma weight residual False -2.53 -1.83 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" P DC T 9 " pdb=" OP1 DC T 9 " pdb=" OP2 DC T 9 " pdb=" O5' DC T 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.21e+00 chirality pdb=" P DT T 47 " pdb=" OP1 DT T 47 " pdb=" OP2 DT T 47 " pdb=" O5' DT T 47 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.55e+00 ... (remaining 2326 not shown) Planarity restraints: 2324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 666 " -0.012 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C SER A 666 " 0.039 2.00e-02 2.50e+03 pdb=" O SER A 666 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO A 667 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 140 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C LEU A 140 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 140 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 141 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 237 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASP A 237 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP A 237 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 238 " -0.012 2.00e-02 2.50e+03 ... (remaining 2321 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 60 2.58 - 3.16: 10994 3.16 - 3.74: 22594 3.74 - 4.32: 30532 4.32 - 4.90: 49614 Nonbonded interactions: 113794 Sorted by model distance: nonbonded pdb=" OD2 ASP A1151 " pdb="MG MG A1302 " model vdw 1.998 2.170 nonbonded pdb=" OD1 ASP A 922 " pdb="MG MG A1302 " model vdw 2.102 2.170 nonbonded pdb=" N GLU A 189 " pdb=" OE1 GLU A 189 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASP A 310 " pdb=" NZ LYS A 353 " model vdw 2.235 3.120 nonbonded pdb=" O GLY A 923 " pdb="MG MG A1302 " model vdw 2.279 2.170 ... (remaining 113789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.450 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.660 Find NCS groups from input model: 0.040 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.007 0.129 15152 Z= 0.518 Angle : 0.933 14.180 20971 Z= 0.618 Chirality : 0.071 0.701 2329 Planarity : 0.005 0.040 2324 Dihedral : 18.898 150.815 6004 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.13 % Allowed : 10.83 % Favored : 88.05 % 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 are not related in a simple way. whole: 1.16 (0.21), residues: 1555 helix: 1.75 (0.17), residues: 907 sheet: -0.11 (0.55), residues: 84 loop : -0.70 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 82 TYR 0.027 0.002 TYR B 74 PHE 0.016 0.001 PHE A 802 TRP 0.016 0.001 TRP A 655 HIS 0.007 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.52 (15150) covalent geometry : angle 0.93328 / 0.62 (20971) hydrogen bonds : bond 0.17216 / 11.63 ( 803) hydrogen bonds : angle 6.12345 / 4.48 ( 2229) Misc. bond : bond 0.05033 / 2.41 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8122 (mtm) REVERT: A 946 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8731 (mp) REVERT: B 126 ASP cc_start: 0.6947 (t0) cc_final: 0.6533 (t0) REVERT: B 243 ASN cc_start: 0.6935 (t0) cc_final: 0.6682 (m-40) REVERT: C 52 LYS cc_start: 0.7876 (mtmt) cc_final: 0.7143 (mtmm) REVERT: C 57 TYR cc_start: 0.7091 (t80) cc_final: 0.6802 (t80) REVERT: C 60 PHE cc_start: 0.7483 (t80) cc_final: 0.7243 (t80) REVERT: C 218 TRP cc_start: 0.7716 (t60) cc_final: 0.6530 (t60) outliers start: 14 outliers final: 8 residues processed: 178 average time/residue: 0.1403 time to fit residues: 35.0117 Evaluate side-chains 159 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1132 MET Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.149030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094670 restraints weight = 21608.083| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.77 r_work: 0.3046 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15152 Z= 0.203 Angle : 0.652 8.466 20971 Z= 0.366 Chirality : 0.044 0.207 2329 Planarity : 0.005 0.048 2324 Dihedral : 20.667 151.095 2918 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.65 % Allowed : 12.33 % Favored : 86.02 % 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 are not related in a simple way. whole: 1.28 (0.21), residues: 1555 helix: 1.79 (0.17), residues: 922 sheet: -0.24 (0.52), residues: 82 loop : -0.57 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 285 TYR 0.012 0.002 TYR A1082 PHE 0.018 0.002 PHE A 802 TRP 0.014 0.002 TRP A 553 HIS 0.007 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (15150) covalent geometry : angle 0.65230 / 0.37 (20971) hydrogen bonds : bond 0.06715 / 4.47 ( 803) hydrogen bonds : angle 3.94553 / 2.91 ( 2229) Misc. bond : bond 0.00555 / 0.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 946 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8232 (mp) REVERT: A 988 LYS cc_start: 0.8306 (tppt) cc_final: 0.7736 (ttpp) REVERT: A 1206 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: B 86 GLN cc_start: 0.8618 (tt0) cc_final: 0.8313 (tp-100) REVERT: B 101 GLU cc_start: 0.8593 (tt0) cc_final: 0.8243 (tt0) REVERT: B 126 ASP cc_start: 0.6981 (t0) cc_final: 0.6503 (t0) REVERT: B 243 ASN cc_start: 0.6857 (t0) cc_final: 0.6471 (m-40) REVERT: B 272 ASP cc_start: 0.6719 (p0) cc_final: 0.6095 (p0) REVERT: B 396 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5899 (ttp-170) REVERT: C 52 LYS cc_start: 0.7697 (mtmt) cc_final: 0.7024 (mtmm) REVERT: C 57 TYR cc_start: 0.6525 (t80) cc_final: 0.5983 (t80) REVERT: C 60 PHE cc_start: 0.7498 (t80) cc_final: 0.7197 (t80) REVERT: C 108 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8290 (mm-40) REVERT: C 218 TRP cc_start: 0.7430 (t60) cc_final: 0.6625 (t60) REVERT: C 221 GLN cc_start: 0.8663 (mp10) cc_final: 0.8258 (pm20) outliers start: 21 outliers final: 7 residues processed: 167 average time/residue: 0.1450 time to fit residues: 33.8192 Evaluate side-chains 159 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [105, 100, 39, 101, 77, 35, 48, 38, 153, 49, 102] chunk 105 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1009 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094984 restraints weight = 33247.351| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.09 r_work: 0.3068 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15152 Z= 0.130 Angle : 0.568 7.933 20971 Z= 0.318 Chirality : 0.039 0.296 2329 Planarity : 0.005 0.043 2324 Dihedral : 20.733 148.081 2905 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.93 % Favored : 98.00 % Rotamer: Outliers : 1.50 % Allowed : 12.41 % Favored : 86.09 % 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 are not related in a simple way. whole: 1.69 (0.21), residues: 1555 helix: 2.18 (0.17), residues: 918 sheet: -0.12 (0.46), residues: 104 loop : -0.50 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 83 TYR 0.021 0.001 TYR C 211 PHE 0.018 0.001 PHE A 802 TRP 0.015 0.001 TRP C 218 HIS 0.003 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (15150) covalent geometry : angle 0.56753 / 0.32 (20971) hydrogen bonds : bond 0.05192 / 3.53 ( 803) hydrogen bonds : angle 3.57729 / 2.67 ( 2229) Misc. bond : bond 0.00088 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.7050 (tmm-80) cc_final: 0.6609 (mtm-85) REVERT: A 317 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: A 503 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7423 (mt-10) REVERT: A 946 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 988 LYS cc_start: 0.8301 (tppt) cc_final: 0.7705 (ttpp) REVERT: A 1206 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: B 86 GLN cc_start: 0.8594 (tt0) cc_final: 0.8251 (tp-100) REVERT: B 101 GLU cc_start: 0.8521 (tt0) cc_final: 0.8200 (tt0) REVERT: B 126 ASP cc_start: 0.7025 (t0) cc_final: 0.6516 (t0) REVERT: B 243 ASN cc_start: 0.6774 (t0) cc_final: 0.6391 (m-40) REVERT: B 272 ASP cc_start: 0.6855 (p0) cc_final: 0.6292 (p0) REVERT: B 293 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6499 (mm-40) REVERT: B 396 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5876 (ttp-170) REVERT: C 52 LYS cc_start: 0.7629 (mtmt) cc_final: 0.6975 (mtmm) REVERT: C 57 TYR cc_start: 0.6506 (t80) cc_final: 0.5967 (t80) REVERT: C 60 PHE cc_start: 0.7419 (t80) cc_final: 0.7184 (t80) REVERT: C 112 GLU cc_start: 0.8663 (tp30) cc_final: 0.8353 (mm-30) REVERT: C 218 TRP cc_start: 0.7434 (t60) cc_final: 0.6422 (t60) REVERT: C 221 GLN cc_start: 0.8638 (mp10) cc_final: 0.8300 (mp10) outliers start: 19 outliers final: 6 residues processed: 174 average time/residue: 0.1460 time to fit residues: 35.4421 Evaluate side-chains 166 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [7, 102, 60, 32, 45, 24, 128, 35, 160, 10, 88] chunk 7 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 920 HIS B 175 ASN B 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092438 restraints weight = 26622.878| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.74 r_work: 0.3040 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15152 Z= 0.178 Angle : 0.595 9.060 20971 Z= 0.329 Chirality : 0.040 0.260 2329 Planarity : 0.005 0.060 2324 Dihedral : 20.696 144.929 2904 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % Rotamer: Outliers : 2.03 % Allowed : 13.01 % Favored : 84.96 % 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 are not related in a simple way. whole: 1.60 (0.21), residues: 1555 helix: 2.08 (0.17), residues: 924 sheet: -0.06 (0.48), residues: 94 loop : -0.52 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG C 104 TYR 0.018 0.002 TYR B 74 PHE 0.019 0.002 PHE C 117 TRP 0.013 0.001 TRP A 553 HIS 0.005 0.001 HIS A1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (15150) covalent geometry : angle 0.59522 / 0.33 (20971) hydrogen bonds : bond 0.05735 / 3.87 ( 803) hydrogen bonds : angle 3.64248 / 2.71 ( 2229) Misc. bond : bond 0.00325 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.6982 (tmm-80) cc_final: 0.6715 (tmm-80) REVERT: A 503 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7401 (mt-10) REVERT: A 771 GLU cc_start: 0.7756 (mm-30) cc_final: 0.6612 (pt0) REVERT: A 946 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 988 LYS cc_start: 0.8400 (tppt) cc_final: 0.8156 (tppt) REVERT: A 1206 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: B 86 GLN cc_start: 0.8592 (tt0) cc_final: 0.8274 (tp-100) REVERT: B 101 GLU cc_start: 0.8505 (tt0) cc_final: 0.8174 (tt0) REVERT: B 126 ASP cc_start: 0.7089 (t0) cc_final: 0.6568 (t0) REVERT: B 243 ASN cc_start: 0.6964 (t0) cc_final: 0.6534 (m-40) REVERT: B 272 ASP cc_start: 0.6910 (p0) cc_final: 0.6398 (p0) REVERT: B 293 GLN cc_start: 0.6916 (mm110) cc_final: 0.6697 (mm-40) REVERT: B 301 MET cc_start: 0.9060 (mtt) cc_final: 0.8812 (mtt) REVERT: B 396 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.5963 (ttp-170) REVERT: C 52 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7140 (mtmm) REVERT: C 57 TYR cc_start: 0.6629 (t80) cc_final: 0.6088 (t80) REVERT: C 60 PHE cc_start: 0.7423 (t80) cc_final: 0.7132 (t80) REVERT: C 218 TRP cc_start: 0.7734 (t60) cc_final: 0.7163 (t60) outliers start: 26 outliers final: 16 residues processed: 172 average time/residue: 0.1436 time to fit residues: 34.7835 Evaluate side-chains 172 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [54, 126, 150, 161, 60, 23, 139, 21, 35, 27, 156] chunk 54 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 920 HIS B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.093182 restraints weight = 26909.309| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.76 r_work: 0.3049 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15152 Z= 0.155 Angle : 0.567 8.209 20971 Z= 0.314 Chirality : 0.039 0.270 2329 Planarity : 0.004 0.043 2324 Dihedral : 20.641 142.122 2904 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.55 % Rotamer: Outliers : 1.80 % Allowed : 13.53 % Favored : 84.66 % 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 are not related in a simple way. whole: 1.64 (0.21), residues: 1555 helix: 2.14 (0.17), residues: 924 sheet: -0.10 (0.48), residues: 94 loop : -0.56 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.022 0.001 TYR B 74 PHE 0.020 0.001 PHE C 117 TRP 0.012 0.001 TRP A 553 HIS 0.004 0.001 HIS A1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (15150) covalent geometry : angle 0.56653 / 0.31 (20971) hydrogen bonds : bond 0.05321 / 3.60 ( 803) hydrogen bonds : angle 3.54797 / 2.63 ( 2229) Misc. bond : bond 0.00183 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.6893 (tmm-80) cc_final: 0.6624 (tmm-80) REVERT: A 503 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7417 (mt-10) REVERT: A 988 LYS cc_start: 0.8436 (tppt) cc_final: 0.8207 (tppt) REVERT: A 1206 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: B 86 GLN cc_start: 0.8565 (tt0) cc_final: 0.8291 (tp-100) REVERT: B 101 GLU cc_start: 0.8529 (tt0) cc_final: 0.8193 (tt0) REVERT: B 126 ASP cc_start: 0.7098 (t0) cc_final: 0.6554 (t0) REVERT: B 243 ASN cc_start: 0.6996 (t0) cc_final: 0.6646 (m-40) REVERT: B 272 ASP cc_start: 0.7058 (p0) cc_final: 0.6497 (p0) REVERT: B 301 MET cc_start: 0.9090 (mtt) cc_final: 0.8836 (mtt) REVERT: B 396 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5987 (ttp-170) REVERT: C 52 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7170 (mtmm) REVERT: C 57 TYR cc_start: 0.6713 (t80) cc_final: 0.6109 (t80) REVERT: C 112 GLU cc_start: 0.8596 (tp30) cc_final: 0.8350 (mm-30) REVERT: C 218 TRP cc_start: 0.7767 (t60) cc_final: 0.6747 (t60) REVERT: C 221 GLN cc_start: 0.8573 (mp10) cc_final: 0.8295 (mp10) outliers start: 23 outliers final: 12 residues processed: 173 average time/residue: 0.1428 time to fit residues: 35.0304 Evaluate side-chains 163 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [122, 32, 103, 110, 10, 29, 41, 53, 56, 102, 76] chunk 122 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1196 GLN B 175 ASN C 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.148645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090667 restraints weight = 34010.555| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.10 r_work: 0.3001 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15152 Z= 0.187 Angle : 0.593 8.437 20971 Z= 0.326 Chirality : 0.040 0.231 2329 Planarity : 0.005 0.045 2324 Dihedral : 20.610 140.383 2901 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 2.03 % Allowed : 13.23 % Favored : 84.74 % 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 are not related in a simple way. whole: 1.52 (0.21), residues: 1555 helix: 2.05 (0.17), residues: 925 sheet: -0.19 (0.49), residues: 94 loop : -0.62 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 83 TYR 0.023 0.002 TYR B 74 PHE 0.033 0.002 PHE C 60 TRP 0.012 0.001 TRP A 553 HIS 0.005 0.001 HIS A1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (15150) covalent geometry : angle 0.59279 / 0.33 (20971) hydrogen bonds : bond 0.05753 / 3.86 ( 803) hydrogen bonds : angle 3.62603 / 2.69 ( 2229) Misc. bond : bond 0.00098 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.6888 (tmm-80) cc_final: 0.6610 (tmm-80) REVERT: A 503 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7397 (mt-10) REVERT: A 771 GLU cc_start: 0.7761 (mm-30) cc_final: 0.6619 (pt0) REVERT: A 946 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8264 (mp) REVERT: A 1041 GLN cc_start: 0.7946 (pm20) cc_final: 0.7677 (pm20) REVERT: A 1206 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: B 86 GLN cc_start: 0.8557 (tt0) cc_final: 0.8287 (tp-100) REVERT: B 101 GLU cc_start: 0.8517 (tt0) cc_final: 0.8211 (tt0) REVERT: B 126 ASP cc_start: 0.7136 (t0) cc_final: 0.6566 (t0) REVERT: B 243 ASN cc_start: 0.7036 (t0) cc_final: 0.6648 (m-40) REVERT: B 272 ASP cc_start: 0.7023 (p0) cc_final: 0.6452 (p0) REVERT: B 301 MET cc_start: 0.9071 (mtt) cc_final: 0.8829 (mtt) REVERT: B 396 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6026 (ttp-170) REVERT: C 52 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7201 (mtmm) REVERT: C 57 TYR cc_start: 0.6556 (t80) cc_final: 0.6076 (t80) REVERT: C 104 ARG cc_start: 0.7886 (mmt180) cc_final: 0.7504 (mmt90) REVERT: C 218 TRP cc_start: 0.7750 (t60) cc_final: 0.7215 (t60) outliers start: 26 outliers final: 17 residues processed: 169 average time/residue: 0.1418 time to fit residues: 33.4621 Evaluate side-chains 168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [22, 0, 63, 9, 118, 49, 119, 160, 99, 156, 13] chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.094079 restraints weight = 27660.345| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.82 r_work: 0.3066 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15152 Z= 0.128 Angle : 0.549 7.938 20971 Z= 0.303 Chirality : 0.038 0.192 2329 Planarity : 0.004 0.041 2324 Dihedral : 20.472 138.168 2901 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.19 % Favored : 97.74 % Rotamer: Outliers : 1.50 % Allowed : 13.83 % Favored : 84.66 % 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 are not related in a simple way. whole: 1.74 (0.21), residues: 1555 helix: 2.25 (0.17), residues: 924 sheet: -0.09 (0.49), residues: 94 loop : -0.56 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.022 0.001 TYR B 74 PHE 0.026 0.001 PHE C 60 TRP 0.009 0.001 TRP A1070 HIS 0.003 0.001 HIS A1125 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (15150) covalent geometry : angle 0.54853 / 0.30 (20971) hydrogen bonds : bond 0.04888 / 3.30 ( 803) hydrogen bonds : angle 3.45472 / 2.56 ( 2229) Misc. bond : bond 0.00076 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.6912 (tmm-80) cc_final: 0.6653 (tmm-80) REVERT: A 317 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: A 503 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7402 (mt-10) REVERT: A 946 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8169 (mp) REVERT: A 1206 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 1229 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7026 (t80) REVERT: B 86 GLN cc_start: 0.8539 (tt0) cc_final: 0.8251 (tp-100) REVERT: B 101 GLU cc_start: 0.8433 (tt0) cc_final: 0.8137 (tt0) REVERT: B 126 ASP cc_start: 0.7124 (t0) cc_final: 0.6545 (t0) REVERT: B 243 ASN cc_start: 0.6883 (t0) cc_final: 0.6443 (m-40) REVERT: B 272 ASP cc_start: 0.7137 (p0) cc_final: 0.6564 (p0) REVERT: B 301 MET cc_start: 0.9036 (mtt) cc_final: 0.8801 (mtt) REVERT: B 396 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.6039 (ttp-170) REVERT: C 52 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7241 (mtmm) REVERT: C 57 TYR cc_start: 0.6557 (t80) cc_final: 0.6097 (t80) REVERT: C 104 ARG cc_start: 0.7896 (mmt180) cc_final: 0.7512 (mmt90) REVERT: C 112 GLU cc_start: 0.8561 (tp30) cc_final: 0.8321 (mm-30) REVERT: C 218 TRP cc_start: 0.7585 (t60) cc_final: 0.6965 (t60) REVERT: C 221 GLN cc_start: 0.8880 (mp10) cc_final: 0.8654 (pm20) outliers start: 19 outliers final: 11 residues processed: 171 average time/residue: 0.1413 time to fit residues: 33.9714 Evaluate side-chains 168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [157, 94, 37, 74, 111, 26, 50, 24, 130, 77, 102] chunk 157 optimal weight: 6.9990 chunk 94 optimal weight: 0.0270 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 50.0000 chunk 26 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094736 restraints weight = 34762.917| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.16 r_work: 0.3065 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 15152 Z= 0.122 Angle : 0.534 8.023 20971 Z= 0.295 Chirality : 0.037 0.150 2329 Planarity : 0.004 0.039 2324 Dihedral : 20.231 133.013 2901 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.62 % Rotamer: Outliers : 1.43 % Allowed : 14.21 % Favored : 84.36 % 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 are not related in a simple way. whole: 1.91 (0.21), residues: 1555 helix: 2.42 (0.17), residues: 918 sheet: -0.18 (0.47), residues: 99 loop : -0.51 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 82 TYR 0.020 0.001 TYR B 74 PHE 0.023 0.001 PHE C 117 TRP 0.016 0.001 TRP C 218 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (15150) covalent geometry : angle 0.53417 / 0.29 (20971) hydrogen bonds : bond 0.04471 / 3.02 ( 803) hydrogen bonds : angle 3.32397 / 2.46 ( 2229) Misc. bond : bond 0.00048 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.2237 (tpt) cc_final: 0.1966 (tmm) REVERT: A 317 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: A 503 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7432 (mt-10) REVERT: A 731 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7925 (m) REVERT: A 771 GLU cc_start: 0.7726 (mm-30) cc_final: 0.6589 (pt0) REVERT: A 946 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8175 (mp) REVERT: A 1194 GLU cc_start: 0.7287 (pt0) cc_final: 0.6770 (tm-30) REVERT: A 1206 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 1229 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7008 (t80) REVERT: B 86 GLN cc_start: 0.8530 (tt0) cc_final: 0.8254 (tp-100) REVERT: B 101 GLU cc_start: 0.8370 (tt0) cc_final: 0.8041 (tt0) REVERT: B 126 ASP cc_start: 0.7105 (t0) cc_final: 0.6856 (m-30) REVERT: B 243 ASN cc_start: 0.6841 (t0) cc_final: 0.6404 (m-40) REVERT: B 272 ASP cc_start: 0.7259 (p0) cc_final: 0.6665 (p0) REVERT: B 293 GLN cc_start: 0.6643 (mm-40) cc_final: 0.6230 (mm-40) REVERT: B 396 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.5947 (ttp-170) REVERT: C 52 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7229 (mtmm) REVERT: C 57 TYR cc_start: 0.6417 (t80) cc_final: 0.6111 (t80) REVERT: C 104 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7612 (mmt90) REVERT: C 112 GLU cc_start: 0.8594 (tp30) cc_final: 0.8345 (mm-30) REVERT: C 218 TRP cc_start: 0.7557 (t60) cc_final: 0.6803 (t60) REVERT: C 221 GLN cc_start: 0.8804 (mp10) cc_final: 0.8576 (pm20) outliers start: 18 outliers final: 10 residues processed: 173 average time/residue: 0.1472 time to fit residues: 35.8601 Evaluate side-chains 170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [22, 7, 151, 37, 92, 28, 99, 14, 26, 46, 122] chunk 22 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS C 120 GLN C 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089794 restraints weight = 34215.715| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.10 r_work: 0.2986 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15152 Z= 0.230 Angle : 0.636 10.455 20971 Z= 0.344 Chirality : 0.041 0.179 2329 Planarity : 0.005 0.045 2324 Dihedral : 20.272 133.439 2901 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 1.50 % Allowed : 14.29 % Favored : 84.21 % 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 are not related in a simple way. whole: 1.47 (0.21), residues: 1555 helix: 2.04 (0.17), residues: 923 sheet: -0.16 (0.48), residues: 94 loop : -0.70 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 83 TYR 0.023 0.002 TYR B 74 PHE 0.031 0.002 PHE C 60 TRP 0.015 0.002 TRP A 553 HIS 0.007 0.001 HIS A1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (15150) covalent geometry : angle 0.63594 / 0.34 (20971) hydrogen bonds : bond 0.06055 / 4.02 ( 803) hydrogen bonds : angle 3.68146 / 2.73 ( 2229) Misc. bond : bond 0.00176 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8589 (mp0) cc_final: 0.8089 (mt-10) REVERT: A 503 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7428 (mt-10) REVERT: A 771 GLU cc_start: 0.7733 (mm-30) cc_final: 0.6569 (pt0) REVERT: A 946 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 1041 GLN cc_start: 0.7919 (pm20) cc_final: 0.7607 (pm20) REVERT: A 1206 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: A 1229 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7113 (t80) REVERT: B 86 GLN cc_start: 0.8566 (tt0) cc_final: 0.8277 (tp-100) REVERT: B 101 GLU cc_start: 0.8519 (tt0) cc_final: 0.8202 (tt0) REVERT: B 126 ASP cc_start: 0.7140 (t0) cc_final: 0.6573 (t0) REVERT: B 243 ASN cc_start: 0.7126 (t0) cc_final: 0.6693 (m-40) REVERT: B 272 ASP cc_start: 0.7075 (p0) cc_final: 0.6488 (p0) REVERT: B 396 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6315 (ttp-170) REVERT: C 52 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7338 (mtmm) REVERT: C 57 TYR cc_start: 0.6599 (t80) cc_final: 0.6175 (t80) REVERT: C 82 ARG cc_start: 0.8552 (tpp-160) cc_final: 0.7766 (mmt90) REVERT: C 83 ARG cc_start: 0.8018 (mmp80) cc_final: 0.7543 (mtp85) REVERT: C 218 TRP cc_start: 0.7438 (t60) cc_final: 0.6821 (t60) REVERT: C 221 GLN cc_start: 0.8851 (mp10) cc_final: 0.8614 (pm20) outliers start: 19 outliers final: 11 residues processed: 166 average time/residue: 0.1458 time to fit residues: 33.8552 Evaluate side-chains 166 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [95, 29, 54, 65, 98, 82, 149, 75, 143, 114, 153] chunk 95 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 114 optimal weight: 50.0000 chunk 153 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093854 restraints weight = 26250.357| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.76 r_work: 0.3064 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15152 Z= 0.131 Angle : 0.554 7.731 20971 Z= 0.305 Chirality : 0.037 0.168 2329 Planarity : 0.004 0.040 2324 Dihedral : 20.171 134.247 2901 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % Rotamer: Outliers : 1.05 % Allowed : 14.29 % Favored : 84.66 % 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 are not related in a simple way. whole: 1.71 (0.21), residues: 1555 helix: 2.26 (0.17), residues: 923 sheet: -0.21 (0.48), residues: 99 loop : -0.62 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 83 TYR 0.021 0.001 TYR B 74 PHE 0.030 0.001 PHE C 60 TRP 0.023 0.001 TRP B 387 HIS 0.004 0.001 HIS A1125 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (15150) covalent geometry : angle 0.55407 / 0.30 (20971) hydrogen bonds : bond 0.04891 / 3.27 ( 803) hydrogen bonds : angle 3.45064 / 2.55 ( 2229) Misc. bond : bond 0.00098 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.1868 (tpt) cc_final: 0.1631 (tmm) REVERT: A 188 GLU cc_start: 0.8647 (mp0) cc_final: 0.8160 (mt-10) REVERT: A 503 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7410 (mt-10) REVERT: A 946 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8182 (mp) REVERT: A 1194 GLU cc_start: 0.7258 (pt0) cc_final: 0.6750 (tm-30) REVERT: A 1206 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 1229 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7038 (t80) REVERT: B 86 GLN cc_start: 0.8539 (tt0) cc_final: 0.8250 (tp-100) REVERT: B 101 GLU cc_start: 0.8437 (tt0) cc_final: 0.8127 (tt0) REVERT: B 126 ASP cc_start: 0.7109 (t0) cc_final: 0.6551 (t0) REVERT: B 243 ASN cc_start: 0.6961 (t0) cc_final: 0.6501 (m-40) REVERT: B 272 ASP cc_start: 0.7221 (p0) cc_final: 0.6618 (p0) REVERT: B 396 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6073 (ttp-170) REVERT: C 52 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7345 (mtmm) REVERT: C 57 TYR cc_start: 0.6598 (t80) cc_final: 0.6244 (t80) REVERT: C 82 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8268 (mpt-90) REVERT: C 104 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7667 (mmt90) REVERT: C 112 GLU cc_start: 0.8571 (tp30) cc_final: 0.8328 (mm-30) REVERT: C 218 TRP cc_start: 0.7392 (t60) cc_final: 0.6804 (t60) REVERT: C 221 GLN cc_start: 0.8850 (mp10) cc_final: 0.8604 (pm20) outliers start: 13 outliers final: 9 residues processed: 162 average time/residue: 0.1426 time to fit residues: 32.4332 Evaluate side-chains 162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: [110, 150, 164, 72, 36, 156, 98, 19, 71, 92, 132] chunk 110 optimal weight: 50.0000 chunk 150 optimal weight: 9.9990 chunk 164 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN C 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.149407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090789 restraints weight = 39107.455| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.33 r_work: 0.2999 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15152 Z= 0.173 Angle : 0.578 8.000 20971 Z= 0.316 Chirality : 0.039 0.157 2329 Planarity : 0.005 0.043 2324 Dihedral : 20.161 133.047 2901 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 1.50 % Allowed : 14.21 % Favored : 84.29 % 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 are not related in a simple way. whole: 1.61 (0.21), residues: 1555 helix: 2.17 (0.17), residues: 923 sheet: -0.18 (0.49), residues: 99 loop : -0.67 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 805 TYR 0.026 0.002 TYR B 74 PHE 0.030 0.002 PHE C 60 TRP 0.026 0.001 TRP C 107 HIS 0.005 0.001 HIS A1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (15150) covalent geometry : angle 0.57849 / 0.32 (20971) hydrogen bonds : bond 0.05367 / 3.58 ( 803) hydrogen bonds : angle 3.53957 / 2.62 ( 2229) Misc. bond : bond 0.00117 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4043.04 seconds wall clock time: 69 minutes 36.50 seconds (4176.50 seconds total)