Starting phenix.real_space_refine on Mon Oct 26 04:25:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i9y_52772/10_2026/9i9y_52772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i9y_52772/10_2026/9i9y_52772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i9y_52772/10_2026/9i9y_52772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i9y_52772/10_2026/9i9y_52772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i9y_52772/10_2026/9i9y_52772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i9y_52772/10_2026/9i9y_52772.map" } resolution = 2.22 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 5983 2.51 5 N 1822 2.21 5 O 1805 1.98 5 H 9268 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 18898 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 262 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 17} Chain: "B" Number of atoms: 16424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 16424 Classifications: {'peptide': 1058} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 1010} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2212 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 143} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.34, per 1000 atoms: 0.18 Number of scatterers: 18898 At special positions: 0 Unit cell: (76.8978, 80.775, 118.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1805 8.00 N 1822 7.00 C 5983 6.00 H 9268 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS C1305 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 566.3 milliseconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 6.9% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.518A pdb=" N GLN B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 164' Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 360 through 364 removed outlier: 3.509A pdb=" N ARG B 364 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1107 removed outlier: 3.541A pdb=" N GLN B1107 " --> pdb=" O PRO B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1148 Processing helix chain 'B' and resid 1154 through 1158 Processing helix chain 'C' and resid 1171 through 1185 removed outlier: 3.534A pdb=" N ILE C1175 " --> pdb=" O PRO C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1188 No H-bonds generated for 'chain 'C' and resid 1186 through 1188' Processing helix chain 'C' and resid 1189 through 1204 removed outlier: 3.786A pdb=" N GLY C1204 " --> pdb=" O LYS C1200 " (cutoff:3.500A) Processing helix chain 'C' and resid 1248 through 1255 Processing helix chain 'C' and resid 1255 through 1262 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.679A pdb=" N LEU A 34 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 119 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 100 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP B 188 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS B 179 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER B 193 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 177 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.679A pdb=" N LEU A 34 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 119 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 100 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP B 188 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 11.430A pdb=" N ARG B 189 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N TRP B 205 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLN B 191 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR B 212 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER B 221 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 243 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN B 227 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 241 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG B 240 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N PHE B 272 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 242 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 246 " --> pdb=" O TRP B 266 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP B 266 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE B 279 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 291 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 281 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG B 295 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N MET B 298 " --> pdb=" O TRP B 314 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N TRP B 314 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL B 300 " --> pdb=" O TYR B 312 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU B 309 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLU B 328 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 311 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN B 326 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU B 313 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL B 324 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 358 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP B 366 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N ARG B 365 " --> pdb=" O TYR B 381 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR B 381 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR B 367 " --> pdb=" O PHE B 379 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU B 378 " --> pdb=" O MET B 390 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET B 390 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 380 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL B 388 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 409 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 431 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR B 452 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 486 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 498 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU B 488 " --> pdb=" O ALA B 496 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA B 496 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL B 517 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG B 528 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU B 540 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG B 530 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE B 538 " --> pdb=" O TYR B 550 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 547 " --> pdb=" O ASP B 563 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP B 563 " --> pdb=" O ALA B 547 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 549 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 561 " --> pdb=" O SER B 549 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU B 551 " --> pdb=" O THR B 559 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR B 559 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA B 580 " --> pdb=" O TYR B 592 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER B 591 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU B 603 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 593 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL B 601 " --> pdb=" O PHE B 613 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL B 622 " --> pdb=" O TYR B 634 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE B 643 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLU B 652 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL B 668 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 654 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE B 666 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 656 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA B 664 " --> pdb=" O TYR B 681 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA B 690 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG B 710 " --> pdb=" O HIS B 726 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER B 723 " --> pdb=" O TYR B 739 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR B 739 " --> pdb=" O SER B 723 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU B 725 " --> pdb=" O SER B 737 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER B 737 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER B 727 " --> pdb=" O GLN B 735 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLN B 735 " --> pdb=" O TRP B 747 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 746 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA B 758 " --> pdb=" O ALA B 746 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 748 " --> pdb=" O HIS B 756 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N HIS B 754 " --> pdb=" O ARG B 769 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ARG B 769 " --> pdb=" O HIS B 754 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS B 756 " --> pdb=" O PHE B 767 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU B 764 " --> pdb=" O ALA B 780 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA B 780 " --> pdb=" O GLU B 764 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 766 " --> pdb=" O ARG B 778 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG B 778 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU B 768 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 776 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 790 " --> pdb=" O ALA B 780 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B 791 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU B 807 " --> pdb=" O THR B 791 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU B 793 " --> pdb=" O SER B 805 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 805 " --> pdb=" O GLU B 793 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 795 " --> pdb=" O GLN B 803 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 801 " --> pdb=" O ALA B 797 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N ARG B 801 " --> pdb=" O TYR B 821 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N TYR B 821 " --> pdb=" O ARG B 801 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 803 " --> pdb=" O TYR B 819 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL B 828 " --> pdb=" O TYR B 840 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 66 removed outlier: 4.475A pdb=" N GLU B 60 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG B 76 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL B 62 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE B 74 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 64 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 72 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.533A pdb=" N GLY B 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 862 through 863 removed outlier: 4.375A pdb=" N ARG B 862 " --> pdb=" O LEU B 870 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 919 through 920 removed outlier: 5.065A pdb=" N VAL B 934 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL B 955 " --> pdb=" O TYR B 971 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ARG B 966 " --> pdb=" O ARG B 986 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG B 986 " --> pdb=" O ARG B 966 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU B 968 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 984 " --> pdb=" O GLU B 968 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG B 970 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS B 982 " --> pdb=" O ARG B 970 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG B 972 " --> pdb=" O ILE B 980 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE B 980 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG B 994 " --> pdb=" O GLU B1005 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B1005 " --> pdb=" O ARG B 994 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY B 996 " --> pdb=" O CYS B1003 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N ARG B1001 " --> pdb=" O HIS B1016 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N HIS B1016 " --> pdb=" O ARG B1001 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N CYS B1003 " --> pdb=" O THR B1014 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU B1024 " --> pdb=" O PHE B1068 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU B1077 " --> pdb=" O GLN B1089 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN B1089 " --> pdb=" O LEU B1077 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B1079 " --> pdb=" O ARG B1087 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1115 through 1116 removed outlier: 3.520A pdb=" N ARG B1136 " --> pdb=" O LEU B1131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1224 through 1226 317 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9257 1.03 - 1.23: 14 1.23 - 1.42: 4352 1.42 - 1.61: 5460 1.61 - 1.81: 29 Bond restraints: 19112 Sorted by residual: bond pdb=" C PRO C1315 " pdb=" N PRO C1316 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.34e-01 bond pdb=" CB ARG B 801 " pdb=" CG ARG B 801 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.43e-01 bond pdb=" N GLN B1107 " pdb=" CA GLN B1107 " ideal model delta sigma weight residual 1.463 1.454 0.008 9.30e-03 1.16e+04 8.04e-01 bond pdb=" CA TRP C1221 " pdb=" CB TRP C1221 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.02e-01 bond pdb=" CA ALA B1097 " pdb=" CB ALA B1097 " ideal model delta sigma weight residual 1.541 1.531 0.010 1.20e-02 6.94e+03 7.42e-01 ... (remaining 19107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 32067 1.10 - 2.21: 1978 2.21 - 3.31: 162 3.31 - 4.41: 46 4.41 - 5.51: 8 Bond angle restraints: 34261 Sorted by residual: angle pdb=" N ALA B1097 " pdb=" CA ALA B1097 " pdb=" CB ALA B1097 " ideal model delta sigma weight residual 114.17 110.80 3.37 1.14e+00 7.69e-01 8.73e+00 angle pdb=" CA TRP C1221 " pdb=" CB TRP C1221 " pdb=" CG TRP C1221 " ideal model delta sigma weight residual 113.60 117.99 -4.39 1.90e+00 2.77e-01 5.33e+00 angle pdb=" CA GLN B1103 " pdb=" CB GLN B1103 " pdb=" CG GLN B1103 " ideal model delta sigma weight residual 114.10 118.38 -4.28 2.00e+00 2.50e-01 4.59e+00 angle pdb=" CA TRP B 93 " pdb=" CB TRP B 93 " pdb=" CG TRP B 93 " ideal model delta sigma weight residual 113.60 117.48 -3.88 1.90e+00 2.77e-01 4.18e+00 angle pdb=" CA GLN B1107 " pdb=" C GLN B1107 " pdb=" N PRO B1108 " ideal model delta sigma weight residual 117.67 119.46 -1.79 8.80e-01 1.29e+00 4.12e+00 ... (remaining 34256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 8154 17.59 - 35.18: 574 35.18 - 52.76: 168 52.76 - 70.35: 50 70.35 - 87.94: 8 Dihedral angle restraints: 8954 sinusoidal: 4889 harmonic: 4065 Sorted by residual: dihedral pdb=" CA CYS A 41 " pdb=" CB CYS A 41 " pdb=" SG CYS A 41 " pdb=" SG CYS C1305 " ideal model delta sinusoidal sigma weight residual -73.00 -3.04 -69.96 1 2.00e+01 2.50e-03 1.58e+01 dihedral pdb=" CA ASP C1284 " pdb=" C ASP C1284 " pdb=" N THR C1285 " pdb=" CA THR C1285 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ILE C1219 " pdb=" C ILE C1219 " pdb=" N LYS C1220 " pdb=" CA LYS C1220 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 8951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 782 0.031 - 0.062: 438 0.062 - 0.093: 62 0.093 - 0.124: 72 0.124 - 0.155: 9 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CA VAL B 668 " pdb=" N VAL B 668 " pdb=" C VAL B 668 " pdb=" CB VAL B 668 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE B 561 " pdb=" N ILE B 561 " pdb=" C ILE B 561 " pdb=" CB ILE B 561 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA VAL B1098 " pdb=" N VAL B1098 " pdb=" C VAL B1098 " pdb=" CB VAL B1098 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1360 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 183 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO B 184 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 184 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 184 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 521 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B 522 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 797 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO B 798 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 798 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 798 " -0.020 5.00e-02 4.00e+02 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2136 2.24 - 2.83: 41509 2.83 - 3.42: 48311 3.42 - 4.01: 71611 4.01 - 4.60: 107224 Nonbonded interactions: 270791 Sorted by model distance: nonbonded pdb=" O ALA B 67 " pdb="HH21 ARG B 220 " model vdw 1.651 2.450 nonbonded pdb=" O ARG B 154 " pdb=" HH TYR B 177 " model vdw 1.678 2.450 nonbonded pdb=" OG SER B 727 " pdb=" HG1 THR B 736 " model vdw 1.697 2.450 nonbonded pdb="HH22 ARG B 986 " pdb=" OE1 GLU B1118 " model vdw 1.699 2.450 nonbonded pdb=" O ASN B 50 " pdb=" H GLY B 54 " model vdw 1.700 2.450 ... (remaining 270786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 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: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.910 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9845 Z= 0.124 Angle : 0.568 23.233 13332 Z= 0.297 Chirality : 0.042 0.155 1363 Planarity : 0.004 0.058 1801 Dihedral : 12.718 87.938 3646 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.65 (0.24), residues: 1216 helix: 1.73 (0.79), residues: 49 sheet: 0.96 (0.28), residues: 329 loop : 0.20 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 801 TYR 0.014 0.001 TYR B 419 PHE 0.010 0.001 PHE B 120 TRP 0.016 0.001 TRP C1221 HIS 0.005 0.001 HIS C1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 9844) covalent geometry : angle 0.52806 / 0.28 (13330) SS BOND : bond 0.00277 / 0.15 ( 1) SS BOND : angle 17.05214 / 9.05 ( 2) hydrogen bonds : bond 0.12036 / 8.01 ( 309) hydrogen bonds : angle 6.79848 / 4.60 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.476 Fit side-chains REVERT: C 1181 ARG cc_start: 0.8595 (mtt90) cc_final: 0.8181 (mtt180) REVERT: C 1230 HIS cc_start: 0.8349 (t70) cc_final: 0.8028 (t70) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.6633 time to fit residues: 161.4611 Evaluate side-chains 69 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.0970 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.077621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.059210 restraints weight = 42364.312| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.19 r_work: 0.2544 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9845 Z= 0.095 Angle : 0.457 4.349 13332 Z= 0.242 Chirality : 0.041 0.134 1363 Planarity : 0.004 0.052 1801 Dihedral : 3.861 18.067 1418 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.75 (0.25), residues: 1216 helix: 1.98 (0.83), residues: 50 sheet: 0.92 (0.27), residues: 348 loop : 0.29 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 204 TYR 0.012 0.001 TYR B 419 PHE 0.008 0.001 PHE B 120 TRP 0.013 0.001 TRP C1221 HIS 0.002 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 ( 9844) covalent geometry : angle 0.45625 / 0.24 (13330) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 2.20384 / 1.16 ( 2) hydrogen bonds : bond 0.03390 / 2.29 ( 309) hydrogen bonds : angle 5.83388 / 4.00 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.657 Fit side-chains REVERT: C 1181 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8242 (mtt-85) REVERT: C 1193 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8402 (tt0) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 1.4869 time to fit residues: 118.6694 Evaluate side-chains 72 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [25, 101, 13, 16, 92, 10, 78, 7, 113, 73, 72] chunk 25 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.074655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.056028 restraints weight = 42541.818| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 2.20 r_work: 0.2478 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9845 Z= 0.183 Angle : 0.488 4.805 13332 Z= 0.261 Chirality : 0.041 0.135 1363 Planarity : 0.004 0.051 1801 Dihedral : 4.158 19.598 1418 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.21 % Allowed : 4.21 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.84 (0.24), residues: 1216 helix: 2.18 (0.82), residues: 50 sheet: 0.95 (0.26), residues: 370 loop : 0.35 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 801 TYR 0.012 0.001 TYR B 419 PHE 0.013 0.001 PHE B 120 TRP 0.011 0.001 TRP B 93 HIS 0.004 0.001 HIS C1230 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 9844) covalent geometry : angle 0.48747 / 0.26 (13330) SS BOND : bond 0.00443 / 0.23 ( 1) SS BOND : angle 2.27887 / 1.20 ( 2) hydrogen bonds : bond 0.03645 / 2.43 ( 309) hydrogen bonds : angle 5.79377 / 3.96 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.513 Fit side-chains REVERT: C 1181 ARG cc_start: 0.8472 (mtt90) cc_final: 0.8229 (mtt-85) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 1.6287 time to fit residues: 120.6643 Evaluate side-chains 71 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain C residue 1244 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [77, 48, 7, 82, 71, 28, 116, 21, 39, 29, 112] chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1107 GLN C1209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.074620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.055988 restraints weight = 42595.566| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 2.21 r_work: 0.2477 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9845 Z= 0.169 Angle : 0.479 4.306 13332 Z= 0.256 Chirality : 0.041 0.135 1363 Planarity : 0.004 0.049 1801 Dihedral : 4.145 19.084 1418 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.32 % Allowed : 5.27 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.78 (0.24), residues: 1216 helix: 2.32 (0.83), residues: 50 sheet: 0.89 (0.26), residues: 362 loop : 0.31 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 801 TYR 0.013 0.001 TYR B 419 PHE 0.012 0.001 PHE B 120 TRP 0.011 0.001 TRP C1221 HIS 0.004 0.001 HIS C1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 9844) covalent geometry : angle 0.47814 / 0.26 (13330) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 1.96767 / 1.04 ( 2) hydrogen bonds : bond 0.03368 / 2.25 ( 309) hydrogen bonds : angle 5.75765 / 3.93 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.507 Fit side-chains REVERT: C 1181 ARG cc_start: 0.8461 (mtt90) cc_final: 0.8220 (mtt-85) outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 1.7482 time to fit residues: 129.1031 Evaluate side-chains 70 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain C residue 1244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [54, 37, 105, 1, 22, 96, 112, 21, 100, 49, 72] chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.057067 restraints weight = 42347.491| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 2.20 r_work: 0.2502 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9845 Z= 0.108 Angle : 0.449 4.139 13332 Z= 0.239 Chirality : 0.040 0.132 1363 Planarity : 0.004 0.048 1801 Dihedral : 3.955 18.520 1418 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.32 % Allowed : 5.69 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.81 (0.24), residues: 1216 helix: 2.59 (0.84), residues: 50 sheet: 0.81 (0.26), residues: 362 loop : 0.37 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 801 TYR 0.012 0.001 TYR B 419 PHE 0.009 0.001 PHE B 120 TRP 0.012 0.001 TRP B 93 HIS 0.003 0.001 HIS C1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9844) covalent geometry : angle 0.44861 / 0.24 (13330) SS BOND : bond 0.00306 / 0.16 ( 1) SS BOND : angle 1.77801 / 0.94 ( 2) hydrogen bonds : bond 0.02931 / 1.96 ( 309) hydrogen bonds : angle 5.56566 / 3.79 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: C 1181 ARG cc_start: 0.8438 (mtt90) cc_final: 0.8182 (mtt-85) outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 1.6965 time to fit residues: 127.4568 Evaluate side-chains 72 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain C residue 1244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [107, 28, 45, 18, 44, 33, 31, 87, 22, 111, 93] chunk 107 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.057282 restraints weight = 42275.929| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 2.20 r_work: 0.2502 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9845 Z= 0.117 Angle : 0.449 4.117 13332 Z= 0.239 Chirality : 0.040 0.132 1363 Planarity : 0.004 0.047 1801 Dihedral : 3.936 18.109 1418 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.42 % Allowed : 6.01 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.87 (0.25), residues: 1216 helix: 2.70 (0.84), residues: 50 sheet: 0.82 (0.26), residues: 372 loop : 0.42 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 801 TYR 0.011 0.001 TYR B 419 PHE 0.010 0.001 PHE B 120 TRP 0.011 0.001 TRP B 93 HIS 0.003 0.001 HIS C1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9844) covalent geometry : angle 0.44882 / 0.24 (13330) SS BOND : bond 0.00293 / 0.15 ( 1) SS BOND : angle 1.78811 / 0.95 ( 2) hydrogen bonds : bond 0.02951 / 1.97 ( 309) hydrogen bonds : angle 5.52715 / 3.76 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: C 1181 ARG cc_start: 0.8425 (mtt90) cc_final: 0.8161 (mtt-85) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 1.6963 time to fit residues: 127.1397 Evaluate side-chains 71 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain C residue 1244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [107, 30, 9, 109, 63, 117, 31, 17, 93, 97, 34] chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 117 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.075314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.056841 restraints weight = 42302.568| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 2.20 r_work: 0.2496 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2382 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9845 Z= 0.129 Angle : 0.455 4.440 13332 Z= 0.242 Chirality : 0.040 0.132 1363 Planarity : 0.004 0.047 1801 Dihedral : 3.958 18.197 1418 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.42 % Allowed : 6.22 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.85 (0.24), residues: 1216 helix: 2.72 (0.84), residues: 50 sheet: 0.85 (0.26), residues: 360 loop : 0.39 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 801 TYR 0.011 0.001 TYR B 419 PHE 0.010 0.001 PHE B 120 TRP 0.010 0.001 TRP B 93 HIS 0.003 0.001 HIS C1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9844) covalent geometry : angle 0.45470 / 0.24 (13330) SS BOND : bond 0.00317 / 0.17 ( 1) SS BOND : angle 1.77678 / 0.94 ( 2) hydrogen bonds : bond 0.03009 / 2.00 ( 309) hydrogen bonds : angle 5.53106 / 3.77 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: C 1181 ARG cc_start: 0.8439 (mtt90) cc_final: 0.8168 (mtt-85) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 1.6548 time to fit residues: 124.4017 Evaluate side-chains 72 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain C residue 1244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [81, 20, 112, 29, 10, 86, 72, 41, 16, 62, 37] chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1205 GLN C1209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.073864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.055340 restraints weight = 42515.622| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 2.20 r_work: 0.2464 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9845 Z= 0.194 Angle : 0.494 4.748 13332 Z= 0.264 Chirality : 0.041 0.138 1363 Planarity : 0.005 0.048 1801 Dihedral : 4.197 19.545 1418 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.53 % Allowed : 6.22 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.79 (0.24), residues: 1216 helix: 2.64 (0.84), residues: 50 sheet: 0.84 (0.26), residues: 360 loop : 0.33 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 801 TYR 0.012 0.001 TYR B 419 PHE 0.012 0.001 PHE B 120 TRP 0.009 0.001 TRP B 93 HIS 0.004 0.001 HIS C1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 9844) covalent geometry : angle 0.49371 / 0.26 (13330) SS BOND : bond 0.00345 / 0.18 ( 1) SS BOND : angle 1.95668 / 1.04 ( 2) hydrogen bonds : bond 0.03443 / 2.29 ( 309) hydrogen bonds : angle 5.73667 / 3.91 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: C 1181 ARG cc_start: 0.8440 (mtt90) cc_final: 0.8165 (mtt-85) REVERT: C 1313 GLU cc_start: 0.7609 (mp0) cc_final: 0.7376 (mp0) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 1.7055 time to fit residues: 127.9652 Evaluate side-chains 71 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 1244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [63, 72, 44, 117, 31, 60, 80, 110, 62, 104, 46] chunk 63 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 117 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.074296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.055815 restraints weight = 41318.264| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 2.22 r_work: 0.2479 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2358 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9845 Z= 0.112 Angle : 0.461 5.013 13332 Z= 0.246 Chirality : 0.040 0.141 1363 Planarity : 0.004 0.047 1801 Dihedral : 4.002 18.371 1418 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.32 % Allowed : 6.64 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.81 (0.24), residues: 1216 helix: 2.71 (0.84), residues: 50 sheet: 0.82 (0.26), residues: 360 loop : 0.35 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 801 TYR 0.012 0.001 TYR B 419 PHE 0.010 0.001 PHE B 120 TRP 0.012 0.001 TRP C1221 HIS 0.003 0.001 HIS C1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9844) covalent geometry : angle 0.46032 / 0.25 (13330) SS BOND : bond 0.00303 / 0.16 ( 1) SS BOND : angle 1.68983 / 0.90 ( 2) hydrogen bonds : bond 0.02951 / 1.97 ( 309) hydrogen bonds : angle 5.55727 / 3.78 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: C 1181 ARG cc_start: 0.8426 (mtt90) cc_final: 0.8154 (mtt-85) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 1.8133 time to fit residues: 130.1140 Evaluate side-chains 71 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 1244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [36, 12, 69, 13, 28, 16, 48, 86, 38, 80, 102] chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.074017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.055598 restraints weight = 41350.970| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 2.20 r_work: 0.2475 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2355 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9845 Z= 0.129 Angle : 0.463 5.253 13332 Z= 0.246 Chirality : 0.041 0.134 1363 Planarity : 0.004 0.048 1801 Dihedral : 4.000 18.188 1418 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.32 % Allowed : 6.74 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.83 (0.24), residues: 1216 helix: 2.73 (0.84), residues: 50 sheet: 0.82 (0.26), residues: 362 loop : 0.37 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 801 TYR 0.012 0.001 TYR B 419 PHE 0.010 0.001 PHE B 120 TRP 0.010 0.001 TRP B 93 HIS 0.003 0.001 HIS C1282 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9844) covalent geometry : angle 0.46214 / 0.25 (13330) SS BOND : bond 0.00313 / 0.16 ( 1) SS BOND : angle 1.76104 / 0.93 ( 2) hydrogen bonds : bond 0.03016 / 2.01 ( 309) hydrogen bonds : angle 5.54153 / 3.77 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1231 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: C 1181 ARG cc_start: 0.8429 (mtt90) cc_final: 0.8155 (mtt-85) outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 1.7770 time to fit residues: 131.2931 Evaluate side-chains 72 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 1244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [42, 91, 96, 23, 77, 87, 31, 24, 94, 61, 67] chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.074630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.056138 restraints weight = 42411.352| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 2.19 r_work: 0.2480 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2364 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9845 Z= 0.160 Angle : 0.477 5.029 13332 Z= 0.255 Chirality : 0.041 0.134 1363 Planarity : 0.004 0.048 1801 Dihedral : 4.086 18.874 1418 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.32 % Allowed : 6.64 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.80 (0.24), residues: 1216 helix: 2.68 (0.84), residues: 50 sheet: 0.82 (0.26), residues: 362 loop : 0.34 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 801 TYR 0.012 0.001 TYR B 419 PHE 0.011 0.001 PHE B 120 TRP 0.010 0.001 TRP B 93 HIS 0.004 0.001 HIS C1230 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 9844) covalent geometry : angle 0.47674 / 0.25 (13330) SS BOND : bond 0.00323 / 0.17 ( 1) SS BOND : angle 1.84430 / 0.98 ( 2) hydrogen bonds : bond 0.03196 / 2.13 ( 309) hydrogen bonds : angle 5.61883 / 3.82 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6247.13 seconds wall clock time: 106 minutes 8.19 seconds (6368.19 seconds total)