Starting phenix.real_space_refine on Wed May 21 09:06:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ex7_50032/05_2025/9ex7_50032.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ex7_50032/05_2025/9ex7_50032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ex7_50032/05_2025/9ex7_50032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ex7_50032/05_2025/9ex7_50032.map" model { file = "/net/cci-nas-00/data/ceres_data/9ex7_50032/05_2025/9ex7_50032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ex7_50032/05_2025/9ex7_50032.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 Mg 2 5.21 5 S 93 5.16 5 C 13398 2.51 5 N 3552 2.21 5 O 4010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21055 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9548 Classifications: {'peptide': 1181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1140} Chain breaks: 1 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "A" Number of atoms: 9544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9544 Classifications: {'peptide': 1181} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1140} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.75, per 1000 atoms: 0.65 Number of scatterers: 21055 At special positions: 0 Unit cell: (97.24, 126.48, 201.96, 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 93 16.00 Mg 2 11.99 O 4010 8.00 N 3552 7.00 C 13398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.8 seconds 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4914 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 9 sheets defined 56.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'B' and resid 1 through 29 removed outlier: 4.481A pdb=" N ILE B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.509A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 101 removed outlier: 3.524A pdb=" N HIS B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 137 through 148 removed outlier: 3.761A pdb=" N GLY B 148 " --> pdb=" O MET B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 168 removed outlier: 3.610A pdb=" N GLN B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.647A pdb=" N LEU B 185 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 4.035A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 removed outlier: 3.816A pdb=" N TRP B 208 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.512A pdb=" N TYR B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.595A pdb=" N THR B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 258 removed outlier: 3.608A pdb=" N VAL B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 258 " --> pdb=" O TYR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.913A pdb=" N ILE B 307 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.820A pdb=" N THR B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.602A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.513A pdb=" N ALA B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.627A pdb=" N LEU B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 499 Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 518 through 529 Processing helix chain 'B' and resid 530 through 533 removed outlier: 4.095A pdb=" N LYS B 533 " --> pdb=" O PRO B 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 530 through 533' Processing helix chain 'B' and resid 536 through 547 Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 568 through 576 Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 626 through 637 Processing helix chain 'B' and resid 646 through 651 Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'B' and resid 688 through 691 removed outlier: 3.511A pdb=" N VAL B 691 " --> pdb=" O SER B 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 688 through 691' Processing helix chain 'B' and resid 695 through 699 removed outlier: 3.715A pdb=" N VAL B 699 " --> pdb=" O TRP B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 740 Processing helix chain 'B' and resid 741 through 746 removed outlier: 3.797A pdb=" N ASN B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.681A pdb=" N TYR B 756 " --> pdb=" O LYS B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 Processing helix chain 'B' and resid 808 through 819 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 838 through 856 removed outlier: 4.201A pdb=" N ASP B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 872 removed outlier: 3.688A pdb=" N HIS B 872 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 909 removed outlier: 3.737A pdb=" N LYS B 899 " --> pdb=" O VAL B 895 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN B 902 " --> pdb=" O GLU B 898 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 907 " --> pdb=" O ASN B 903 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 933 Processing helix chain 'B' and resid 937 through 963 removed outlier: 3.846A pdb=" N ASN B 943 " --> pdb=" O ASP B 939 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 989 removed outlier: 3.577A pdb=" N GLY B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1026 Processing helix chain 'B' and resid 1030 through 1043 removed outlier: 3.510A pdb=" N CYS B1043 " --> pdb=" O ALA B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1066 Processing helix chain 'B' and resid 1067 through 1075 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1104 through 1114 removed outlier: 4.134A pdb=" N ARG B1108 " --> pdb=" O ALA B1104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B1114 " --> pdb=" O ARG B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1135 removed outlier: 3.651A pdb=" N GLN B1131 " --> pdb=" O ARG B1127 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B1132 " --> pdb=" O LEU B1128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B1133 " --> pdb=" O ASN B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1169 removed outlier: 3.578A pdb=" N LYS B1144 " --> pdb=" O ALA B1140 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B1149 " --> pdb=" O ARG B1145 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B1151 " --> pdb=" O ARG B1147 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B1152 " --> pdb=" O ASP B1148 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1184 Processing helix chain 'B' and resid 1193 through 1199 removed outlier: 3.585A pdb=" N ILE B1197 " --> pdb=" O ASP B1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.633A pdb=" N VAL C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 44 removed outlier: 3.674A pdb=" N ALA C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.711A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.609A pdb=" N LEU C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 68 through 72' Processing helix chain 'C' and resid 77 through 97 removed outlier: 4.199A pdb=" N ILE C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.641A pdb=" N LEU C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.626A pdb=" N VAL D 11 " --> pdb=" O THR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 44 removed outlier: 4.471A pdb=" N ALA D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.571A pdb=" N ALA D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.711A pdb=" N LEU D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 68 through 72' Processing helix chain 'D' and resid 78 through 97 removed outlier: 3.855A pdb=" N ASP D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 111 removed outlier: 3.675A pdb=" N LEU D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 removed outlier: 6.248A pdb=" N ASP D 115 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 29 removed outlier: 4.150A pdb=" N ILE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 60 through 75 removed outlier: 4.450A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.511A pdb=" N ASP A 124 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 194 through 203 removed outlier: 4.140A pdb=" N GLY A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.735A pdb=" N TYR A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.600A pdb=" N VAL A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.803A pdb=" N TYR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.926A pdb=" N LYS A 274 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.178A pdb=" N ILE A 307 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 335 Processing helix chain 'A' and resid 339 through 349 removed outlier: 4.363A pdb=" N GLN A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 432 through 443 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.292A pdb=" N LEU A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 456 through 459 removed outlier: 3.577A pdb=" N ASP A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 456 through 459' Processing helix chain 'A' and resid 460 through 475 removed outlier: 4.478A pdb=" N VAL A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 499 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 535 through 547 removed outlier: 3.670A pdb=" N MET A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 626 through 637 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 662 through 670 removed outlier: 3.981A pdb=" N LEU A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.635A pdb=" N GLU A 698 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 699 " --> pdb=" O TRP A 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 695 through 699' Processing helix chain 'A' and resid 737 through 740 Processing helix chain 'A' and resid 798 through 807 Processing helix chain 'A' and resid 808 through 819 Processing helix chain 'A' and resid 838 through 856 removed outlier: 4.231A pdb=" N ASP A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 905 removed outlier: 4.359A pdb=" N ILE A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 909 removed outlier: 3.749A pdb=" N LEU A 909 " --> pdb=" O GLU A 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 917 through 921 Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'A' and resid 940 through 962 removed outlier: 4.379A pdb=" N ARG A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 1013 through 1027 Processing helix chain 'A' and resid 1030 through 1043 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1099 through 1101 No H-bonds generated for 'chain 'A' and resid 1099 through 1101' Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 4.079A pdb=" N ARG A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1134 removed outlier: 3.778A pdb=" N ASP A1126 " --> pdb=" O GLN A1122 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A1127 " --> pdb=" O ALA A1123 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1128 " --> pdb=" O ASN A1124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A1129 " --> pdb=" O ILE A1125 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A1130 " --> pdb=" O ASP A1126 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A1131 " --> pdb=" O ARG A1127 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1141 removed outlier: 3.969A pdb=" N THR A1141 " --> pdb=" O GLY A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1170 removed outlier: 3.631A pdb=" N ILE A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A1152 " --> pdb=" O ASP A1148 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A1155 " --> pdb=" O ILE A1151 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET A1170 " --> pdb=" O HIS A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1184 Processing helix chain 'A' and resid 1193 through 1199 removed outlier: 3.590A pdb=" N ILE A1197 " --> pdb=" O ASP A1193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.324A pdb=" N VAL B 309 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU B 353 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP B 311 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL B 388 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY B 352 " --> pdb=" O VAL B 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 502 through 507 removed outlier: 6.980A pdb=" N TYR B 502 " --> pdb=" O LYS B 549 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN B 551 " --> pdb=" O TYR B 502 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 504 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE B 553 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 506 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA B 555 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR B 602 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 583 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 608 " --> pdb=" O PHE B 581 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 581 " --> pdb=" O LYS B 608 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 679 through 680 removed outlier: 3.678A pdb=" N ALA B 788 " --> pdb=" O VAL B 680 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 693 through 694 Processing sheet with id=AA5, first strand: chain 'B' and resid 1001 through 1003 Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 310 removed outlier: 3.551A pdb=" N VAL A 506 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 505 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 557 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA A 507 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N MET A 559 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 604 " --> pdb=" O HIS A 586 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N HIS A 586 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 606 " --> pdb=" O MET A 584 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N MET A 584 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS A 608 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 582 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 618 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 619 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680 Processing sheet with id=AA8, first strand: chain 'A' and resid 733 through 735 Processing sheet with id=AA9, first strand: chain 'A' and resid 1001 through 1003 941 hydrogen bonds defined for protein. 2703 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: 7.34 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6973 1.34 - 1.46: 4300 1.46 - 1.58: 10077 1.58 - 1.69: 0 1.69 - 1.81: 163 Bond restraints: 21513 Sorted by residual: bond pdb=" C2 SAM B1302 " pdb=" N3 SAM B1302 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" C8 SAM B1302 " pdb=" N7 SAM B1302 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" C2 SAM B1302 " pdb=" N1 SAM B1302 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C6 SAM B1302 " pdb=" N1 SAM B1302 " ideal model delta sigma weight residual 1.337 1.377 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C SAM B1302 " pdb=" OXT SAM B1302 " ideal model delta sigma weight residual 1.256 1.230 0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 21508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 28803 1.75 - 3.49: 246 3.49 - 5.24: 35 5.24 - 6.98: 14 6.98 - 8.73: 4 Bond angle restraints: 29102 Sorted by residual: angle pdb=" C LYS B 725 " pdb=" N TRP B 726 " pdb=" CA TRP B 726 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" CA TYR B 86 " pdb=" CB TYR B 86 " pdb=" CG TYR B 86 " ideal model delta sigma weight residual 113.90 119.33 -5.43 1.80e+00 3.09e-01 9.11e+00 angle pdb=" O SAM B1302 " pdb=" C SAM B1302 " pdb=" OXT SAM B1302 " ideal model delta sigma weight residual 126.77 118.07 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" N VAL B 260 " pdb=" CA VAL B 260 " pdb=" C VAL B 260 " ideal model delta sigma weight residual 111.67 109.06 2.61 9.50e-01 1.11e+00 7.56e+00 angle pdb=" N1 SAM B1302 " pdb=" C2 SAM B1302 " pdb=" N3 SAM B1302 " ideal model delta sigma weight residual 128.51 120.28 8.23 3.00e+00 1.11e-01 7.53e+00 ... (remaining 29097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 12297 17.77 - 35.53: 560 35.53 - 53.30: 75 53.30 - 71.06: 5 71.06 - 88.83: 3 Dihedral angle restraints: 12940 sinusoidal: 5316 harmonic: 7624 Sorted by residual: dihedral pdb=" CB LYS B1144 " pdb=" CG LYS B1144 " pdb=" CD LYS B1144 " pdb=" CE LYS B1144 " ideal model delta sinusoidal sigma weight residual 180.00 121.72 58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ARG B 71 " pdb=" CB ARG B 71 " pdb=" CG ARG B 71 " pdb=" CD ARG B 71 " ideal model delta sinusoidal sigma weight residual -180.00 -126.69 -53.31 3 1.50e+01 4.44e-03 9.19e+00 dihedral pdb=" N MET D 40 " pdb=" CA MET D 40 " pdb=" CB MET D 40 " pdb=" CG MET D 40 " ideal model delta sinusoidal sigma weight residual -60.00 -112.92 52.92 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 12937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2057 0.031 - 0.063: 780 0.063 - 0.094: 187 0.094 - 0.125: 95 0.125 - 0.157: 10 Chirality restraints: 3129 Sorted by residual: chirality pdb=" C2' SAM B1302 " pdb=" C1' SAM B1302 " pdb=" C3' SAM B1302 " pdb=" O2' SAM B1302 " both_signs ideal model delta sigma weight residual False -2.76 -2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA TYR B 86 " pdb=" N TYR B 86 " pdb=" C TYR B 86 " pdb=" CB TYR B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" C1' SAM B1302 " pdb=" C2' SAM B1302 " pdb=" N9 SAM B1302 " pdb=" O4' SAM B1302 " both_signs ideal model delta sigma weight residual False 2.30 2.44 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 3126 not shown) Planarity restraints: 3789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 203 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO B 204 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1144 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LYS A1144 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS A1144 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A1145 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 57 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 58 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.020 5.00e-02 4.00e+02 ... (remaining 3786 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 126 2.54 - 3.13: 16202 3.13 - 3.72: 31365 3.72 - 4.31: 41703 4.31 - 4.90: 71540 Nonbonded interactions: 160936 Sorted by model distance: nonbonded pdb=" OD2 ASP A 999 " pdb="MG MG A1301 " model vdw 1.950 2.170 nonbonded pdb=" OD2 ASP B 999 " pdb="MG MG B1301 " model vdw 1.968 2.170 nonbonded pdb=" OD1 ASP A 999 " pdb="MG MG A1301 " model vdw 1.985 2.170 nonbonded pdb=" OD1 ASP B 999 " pdb="MG MG B1301 " model vdw 2.017 2.170 nonbonded pdb=" OD2 ASP A 997 " pdb="MG MG A1301 " model vdw 2.055 2.170 ... (remaining 160931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 1124 or (resid 1125 and (name N or name CA or na \ me C or name O or name CB )) or resid 1126 through 1204 or (resid 1205 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 \ )) or resid 1301)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.510 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: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 46.680 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 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:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 0.056 21513 Z= 0.125 Angle : 0.471 8.726 29102 Z= 0.249 Chirality : 0.038 0.157 3129 Planarity : 0.003 0.046 3789 Dihedral : 9.799 88.831 8026 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.71 % Allowed : 5.12 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2584 helix: 1.85 (0.15), residues: 1249 sheet: 0.03 (0.47), residues: 139 loop : -1.43 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 862 HIS 0.003 0.001 HIS B 945 PHE 0.013 0.001 PHE B1021 TYR 0.025 0.001 TYR B 86 ARG 0.002 0.000 ARG B 931 Details of bonding type rmsd hydrogen bonds : bond 0.16298 ( 941) hydrogen bonds : angle 5.26103 ( 2703) covalent geometry : bond 0.00273 (21513) covalent geometry : angle 0.47135 (29102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.8440 (mpp) cc_final: 0.8210 (mtt) REVERT: B 337 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7525 (ttt-90) REVERT: A 766 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7408 (m) REVERT: A 904 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7651 (mm) outliers start: 16 outliers final: 7 residues processed: 163 average time/residue: 1.6183 time to fit residues: 294.0714 Evaluate side-chains 110 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 904 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 918 ASN D 44 ASN A 457 GLN A 554 ASN A 556 GLN A 633 ASN A1183 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.083729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056248 restraints weight = 84447.322| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.10 r_work: 0.2922 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21513 Z= 0.191 Angle : 0.552 7.075 29102 Z= 0.291 Chirality : 0.041 0.155 3129 Planarity : 0.004 0.088 3789 Dihedral : 5.076 53.214 2889 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.51 % Allowed : 8.46 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2584 helix: 1.81 (0.15), residues: 1287 sheet: -0.21 (0.47), residues: 132 loop : -1.55 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 862 HIS 0.004 0.001 HIS B 125 PHE 0.017 0.001 PHE B 864 TYR 0.025 0.002 TYR B 86 ARG 0.009 0.001 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.05815 ( 941) hydrogen bonds : angle 4.21481 ( 2703) covalent geometry : bond 0.00459 (21513) covalent geometry : angle 0.55161 (29102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7258 (p90) cc_final: 0.6593 (p-90) REVERT: B 517 MET cc_start: 0.8085 (mtt) cc_final: 0.7883 (mtt) REVERT: B 1005 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7469 (mtm) REVERT: C 18 MET cc_start: 0.8402 (mtt) cc_final: 0.8062 (mtt) REVERT: C 22 ASN cc_start: 0.8653 (m-40) cc_final: 0.8263 (m110) REVERT: A 638 MET cc_start: 0.5561 (ptp) cc_final: 0.5215 (pmm) REVERT: A 659 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6296 (p90) REVERT: A 666 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8947 (tp) REVERT: A 773 MET cc_start: 0.8883 (ttt) cc_final: 0.8543 (ttm) REVERT: A 904 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7317 (mp) outliers start: 34 outliers final: 11 residues processed: 131 average time/residue: 1.4005 time to fit residues: 208.9101 Evaluate side-chains 113 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 1072 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 62 optimal weight: 0.9990 chunk 184 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 85 optimal weight: 0.1980 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.083934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056635 restraints weight = 83280.624| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 4.10 r_work: 0.2938 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21513 Z= 0.138 Angle : 0.504 7.207 29102 Z= 0.265 Chirality : 0.039 0.143 3129 Planarity : 0.003 0.070 3789 Dihedral : 4.928 54.096 2886 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.38 % Allowed : 9.48 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2584 helix: 1.87 (0.15), residues: 1288 sheet: -0.41 (0.47), residues: 128 loop : -1.60 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 862 HIS 0.003 0.001 HIS B 113 PHE 0.012 0.001 PHE B 864 TYR 0.022 0.001 TYR B 86 ARG 0.008 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 941) hydrogen bonds : angle 3.99329 ( 2703) covalent geometry : bond 0.00322 (21513) covalent geometry : angle 0.50416 (29102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 339 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8265 (mmm160) REVERT: B 401 TRP cc_start: 0.7236 (p90) cc_final: 0.6553 (p-90) REVERT: B 517 MET cc_start: 0.8121 (mtt) cc_final: 0.7888 (mtt) REVERT: B 934 GLN cc_start: 0.8901 (tt0) cc_final: 0.8682 (tp-100) REVERT: B 1005 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7495 (mtm) REVERT: C 18 MET cc_start: 0.8408 (mtt) cc_final: 0.8068 (mtt) REVERT: C 22 ASN cc_start: 0.8662 (m-40) cc_final: 0.8256 (m110) REVERT: A 488 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6577 (tm) REVERT: A 563 MET cc_start: 0.7248 (ptm) cc_final: 0.7038 (ptm) REVERT: A 638 MET cc_start: 0.5437 (ptp) cc_final: 0.4950 (pmm) REVERT: A 659 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6161 (p90) REVERT: A 666 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8948 (tp) REVERT: A 773 MET cc_start: 0.8854 (ttt) cc_final: 0.8430 (ttm) outliers start: 31 outliers final: 9 residues processed: 124 average time/residue: 1.4690 time to fit residues: 206.8569 Evaluate side-chains 114 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 102 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.083949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056472 restraints weight = 84374.667| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.00 r_work: 0.2947 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21513 Z= 0.133 Angle : 0.503 8.323 29102 Z= 0.263 Chirality : 0.039 0.141 3129 Planarity : 0.003 0.046 3789 Dihedral : 4.801 54.090 2882 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.38 % Allowed : 9.97 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2584 helix: 1.90 (0.15), residues: 1289 sheet: -0.38 (0.48), residues: 124 loop : -1.59 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 216 HIS 0.004 0.001 HIS A 945 PHE 0.014 0.001 PHE A 77 TYR 0.022 0.001 TYR B 86 ARG 0.011 0.000 ARG B1127 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 941) hydrogen bonds : angle 3.90146 ( 2703) covalent geometry : bond 0.00310 (21513) covalent geometry : angle 0.50260 (29102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 517 MET cc_start: 0.8095 (mtt) cc_final: 0.7846 (mtt) REVERT: B 1005 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7475 (mtm) REVERT: C 18 MET cc_start: 0.8414 (mtt) cc_final: 0.8080 (mtt) REVERT: C 22 ASN cc_start: 0.8663 (m-40) cc_final: 0.8255 (m110) REVERT: A 110 MET cc_start: 0.0786 (tpt) cc_final: 0.0516 (tpp) REVERT: A 638 MET cc_start: 0.5322 (ptp) cc_final: 0.4904 (pmm) REVERT: A 659 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6115 (p90) REVERT: A 666 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8943 (tp) REVERT: A 766 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6969 (m) REVERT: A 773 MET cc_start: 0.8825 (ttt) cc_final: 0.8400 (ttm) outliers start: 31 outliers final: 13 residues processed: 123 average time/residue: 1.5739 time to fit residues: 217.9351 Evaluate side-chains 116 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 999 ASP Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 1072 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 173 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 135 optimal weight: 0.0030 chunk 152 optimal weight: 5.9990 chunk 239 optimal weight: 0.5980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.084316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057068 restraints weight = 84489.709| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.12 r_work: 0.2954 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21513 Z= 0.108 Angle : 0.492 9.031 29102 Z= 0.256 Chirality : 0.038 0.135 3129 Planarity : 0.003 0.047 3789 Dihedral : 4.686 54.810 2882 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.34 % Allowed : 10.50 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2584 helix: 1.92 (0.15), residues: 1290 sheet: -0.35 (0.48), residues: 124 loop : -1.55 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 862 HIS 0.003 0.000 HIS B1166 PHE 0.018 0.001 PHE A 466 TYR 0.024 0.001 TYR C 112 ARG 0.010 0.000 ARG B1127 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 941) hydrogen bonds : angle 3.81075 ( 2703) covalent geometry : bond 0.00241 (21513) covalent geometry : angle 0.49191 (29102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 2.237 Fit side-chains revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7215 (p90) cc_final: 0.6774 (p-90) REVERT: B 517 MET cc_start: 0.8099 (mtt) cc_final: 0.7825 (mtt) REVERT: B 1005 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: C 18 MET cc_start: 0.8390 (mtt) cc_final: 0.8062 (mtt) REVERT: C 22 ASN cc_start: 0.8639 (m-40) cc_final: 0.8229 (m110) REVERT: D 40 MET cc_start: 0.7990 (tpt) cc_final: 0.7492 (ttm) REVERT: A 277 MET cc_start: 0.4565 (mmt) cc_final: 0.4109 (mmm) REVERT: A 638 MET cc_start: 0.5321 (ptp) cc_final: 0.4909 (pmm) REVERT: A 659 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6040 (p90) REVERT: A 666 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8945 (tp) REVERT: A 766 VAL cc_start: 0.7126 (OUTLIER) cc_final: 0.6838 (m) REVERT: A 773 MET cc_start: 0.8807 (ttt) cc_final: 0.8383 (ttm) REVERT: A 829 VAL cc_start: 0.7544 (OUTLIER) cc_final: 0.7038 (m) outliers start: 30 outliers final: 12 residues processed: 124 average time/residue: 1.4434 time to fit residues: 204.7843 Evaluate side-chains 115 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 999 ASP Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 188 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 209 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 148 optimal weight: 40.0000 chunk 228 optimal weight: 10.0000 chunk 180 optimal weight: 30.0000 chunk 140 optimal weight: 50.0000 chunk 208 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.083515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056147 restraints weight = 84268.623| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.03 r_work: 0.2933 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21513 Z= 0.151 Angle : 0.521 9.698 29102 Z= 0.271 Chirality : 0.039 0.145 3129 Planarity : 0.003 0.066 3789 Dihedral : 4.776 53.705 2882 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.42 % Allowed : 10.59 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2584 helix: 1.88 (0.15), residues: 1287 sheet: -0.46 (0.47), residues: 128 loop : -1.61 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 862 HIS 0.004 0.001 HIS A 945 PHE 0.015 0.001 PHE A 466 TYR 0.023 0.001 TYR B 86 ARG 0.014 0.000 ARG B1127 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 941) hydrogen bonds : angle 3.85002 ( 2703) covalent geometry : bond 0.00360 (21513) covalent geometry : angle 0.52127 (29102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7289 (p90) cc_final: 0.6675 (p-90) REVERT: B 1005 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7517 (mtm) REVERT: C 18 MET cc_start: 0.8476 (mtt) cc_final: 0.8149 (mtt) REVERT: C 22 ASN cc_start: 0.8679 (m-40) cc_final: 0.8260 (m110) REVERT: D 18 MET cc_start: 0.7669 (mmm) cc_final: 0.7356 (mtt) REVERT: D 40 MET cc_start: 0.7818 (tpt) cc_final: 0.7489 (tmm) REVERT: A 110 MET cc_start: 0.0839 (tpt) cc_final: 0.0604 (tpp) REVERT: A 277 MET cc_start: 0.4943 (mmt) cc_final: 0.4589 (mmm) REVERT: A 333 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: A 369 MET cc_start: 0.2875 (tmm) cc_final: 0.2649 (tmt) REVERT: A 587 LEU cc_start: 0.7294 (mt) cc_final: 0.7034 (tm) REVERT: A 638 MET cc_start: 0.5311 (ptp) cc_final: 0.5035 (pmm) REVERT: A 659 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6095 (p90) REVERT: A 666 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8947 (tp) REVERT: A 766 VAL cc_start: 0.7191 (OUTLIER) cc_final: 0.6922 (m) REVERT: A 773 MET cc_start: 0.8845 (ttt) cc_final: 0.8416 (ttm) REVERT: A 829 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7074 (m) outliers start: 32 outliers final: 14 residues processed: 119 average time/residue: 1.3319 time to fit residues: 180.9597 Evaluate side-chains 115 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 999 ASP Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.084348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057320 restraints weight = 84042.742| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.17 r_work: 0.2959 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21513 Z= 0.099 Angle : 0.486 10.598 29102 Z= 0.250 Chirality : 0.038 0.135 3129 Planarity : 0.003 0.042 3789 Dihedral : 4.616 54.709 2882 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.20 % Allowed : 10.90 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2584 helix: 1.92 (0.15), residues: 1290 sheet: -0.39 (0.48), residues: 124 loop : -1.55 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 862 HIS 0.003 0.000 HIS B1166 PHE 0.013 0.001 PHE A 466 TYR 0.021 0.001 TYR B 86 ARG 0.003 0.000 ARG B1127 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 941) hydrogen bonds : angle 3.72031 ( 2703) covalent geometry : bond 0.00218 (21513) covalent geometry : angle 0.48583 (29102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7253 (p90) cc_final: 0.6620 (p-90) REVERT: B 517 MET cc_start: 0.8101 (mtt) cc_final: 0.7887 (mtp) REVERT: B 1005 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7378 (mtm) REVERT: C 18 MET cc_start: 0.8446 (mtt) cc_final: 0.8129 (mtt) REVERT: C 22 ASN cc_start: 0.8670 (m-40) cc_final: 0.8259 (m110) REVERT: D 40 MET cc_start: 0.7724 (tpt) cc_final: 0.7319 (tmm) REVERT: A 1 MET cc_start: 0.7396 (tpt) cc_final: 0.7156 (tpt) REVERT: A 110 MET cc_start: 0.0838 (tpt) cc_final: 0.0612 (tpp) REVERT: A 277 MET cc_start: 0.5103 (mmt) cc_final: 0.4782 (mmm) REVERT: A 333 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: A 587 LEU cc_start: 0.7329 (mt) cc_final: 0.7038 (tm) REVERT: A 638 MET cc_start: 0.5286 (ptp) cc_final: 0.5032 (pmm) REVERT: A 659 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6219 (p90) REVERT: A 666 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8949 (tp) REVERT: A 766 VAL cc_start: 0.7145 (OUTLIER) cc_final: 0.6872 (m) REVERT: A 773 MET cc_start: 0.8840 (ttt) cc_final: 0.8421 (ttm) REVERT: A 829 VAL cc_start: 0.7583 (OUTLIER) cc_final: 0.7072 (m) outliers start: 27 outliers final: 10 residues processed: 121 average time/residue: 1.4218 time to fit residues: 196.3792 Evaluate side-chains 113 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 164 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.083029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055607 restraints weight = 84387.482| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 4.12 r_work: 0.2901 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21513 Z= 0.182 Angle : 0.549 10.933 29102 Z= 0.284 Chirality : 0.040 0.152 3129 Planarity : 0.003 0.044 3789 Dihedral : 4.861 52.435 2882 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.34 % Allowed : 11.04 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2584 helix: 1.84 (0.15), residues: 1288 sheet: -0.56 (0.48), residues: 122 loop : -1.63 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 862 HIS 0.005 0.001 HIS A 945 PHE 0.016 0.001 PHE B 864 TYR 0.023 0.001 TYR B 86 ARG 0.016 0.000 ARG B1127 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 941) hydrogen bonds : angle 3.87634 ( 2703) covalent geometry : bond 0.00441 (21513) covalent geometry : angle 0.54916 (29102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7366 (p90) cc_final: 0.7157 (p90) REVERT: B 1005 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7386 (mtm) REVERT: C 18 MET cc_start: 0.8463 (mtt) cc_final: 0.8251 (mtt) REVERT: C 22 ASN cc_start: 0.8679 (m-40) cc_final: 0.8400 (m110) REVERT: D 18 MET cc_start: 0.7652 (mmm) cc_final: 0.7411 (mtt) REVERT: D 40 MET cc_start: 0.7686 (tpt) cc_final: 0.7443 (ttm) REVERT: A 1 MET cc_start: 0.7404 (tpt) cc_final: 0.7152 (tpt) REVERT: A 110 MET cc_start: 0.0807 (tpt) cc_final: 0.0538 (tpp) REVERT: A 277 MET cc_start: 0.5125 (mmt) cc_final: 0.4816 (mmm) REVERT: A 333 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: A 587 LEU cc_start: 0.7317 (mt) cc_final: 0.7018 (tm) REVERT: A 638 MET cc_start: 0.5304 (ptp) cc_final: 0.5071 (pmm) REVERT: A 659 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.6191 (p90) REVERT: A 666 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8954 (tp) REVERT: A 766 VAL cc_start: 0.7198 (OUTLIER) cc_final: 0.6946 (m) REVERT: A 829 VAL cc_start: 0.7582 (OUTLIER) cc_final: 0.7079 (m) outliers start: 30 outliers final: 12 residues processed: 120 average time/residue: 1.4602 time to fit residues: 200.5315 Evaluate side-chains 116 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 191 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 178 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.083825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056659 restraints weight = 84620.618| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.10 r_work: 0.2938 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21513 Z= 0.116 Angle : 0.508 11.816 29102 Z= 0.261 Chirality : 0.038 0.137 3129 Planarity : 0.003 0.041 3789 Dihedral : 4.731 52.945 2882 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.16 % Allowed : 11.39 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2584 helix: 1.89 (0.15), residues: 1288 sheet: -0.44 (0.47), residues: 124 loop : -1.59 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 862 HIS 0.003 0.001 HIS A 945 PHE 0.012 0.001 PHE A 466 TYR 0.021 0.001 TYR B 86 ARG 0.003 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 941) hydrogen bonds : angle 3.75185 ( 2703) covalent geometry : bond 0.00268 (21513) covalent geometry : angle 0.50832 (29102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7313 (p90) cc_final: 0.7095 (p90) REVERT: B 645 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8636 (mp) REVERT: B 1005 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7352 (mtm) REVERT: C 18 MET cc_start: 0.8458 (mtt) cc_final: 0.8152 (mtt) REVERT: C 22 ASN cc_start: 0.8670 (m-40) cc_final: 0.8261 (m110) REVERT: A 1 MET cc_start: 0.7406 (tpt) cc_final: 0.7146 (tpt) REVERT: A 110 MET cc_start: 0.0848 (tpt) cc_final: 0.0597 (tpp) REVERT: A 277 MET cc_start: 0.5122 (mmt) cc_final: 0.4813 (mmm) REVERT: A 512 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5810 (ttm) REVERT: A 587 LEU cc_start: 0.7301 (mt) cc_final: 0.6986 (tm) REVERT: A 659 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6159 (p90) REVERT: A 666 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8964 (tp) REVERT: A 766 VAL cc_start: 0.7211 (OUTLIER) cc_final: 0.6952 (m) REVERT: A 773 MET cc_start: 0.8878 (ttt) cc_final: 0.8561 (ttm) REVERT: A 796 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.9053 (pp20) REVERT: A 829 VAL cc_start: 0.7561 (OUTLIER) cc_final: 0.7030 (m) outliers start: 26 outliers final: 13 residues processed: 117 average time/residue: 1.3730 time to fit residues: 183.3049 Evaluate side-chains 118 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 52 optimal weight: 0.0170 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 239 optimal weight: 0.5980 chunk 195 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.084246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057230 restraints weight = 84650.234| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.11 r_work: 0.2960 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21513 Z= 0.101 Angle : 0.514 12.400 29102 Z= 0.260 Chirality : 0.038 0.134 3129 Planarity : 0.003 0.083 3789 Dihedral : 4.603 54.375 2882 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.11 % Allowed : 11.53 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2584 helix: 1.92 (0.15), residues: 1288 sheet: -0.38 (0.48), residues: 124 loop : -1.53 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 88 HIS 0.003 0.000 HIS B1166 PHE 0.012 0.001 PHE A 77 TYR 0.022 0.001 TYR B 86 ARG 0.021 0.000 ARG B1127 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 941) hydrogen bonds : angle 3.69103 ( 2703) covalent geometry : bond 0.00227 (21513) covalent geometry : angle 0.51388 (29102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8585 (mp) REVERT: B 1005 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7369 (mtm) REVERT: C 18 MET cc_start: 0.8445 (mtt) cc_final: 0.8139 (mtt) REVERT: C 22 ASN cc_start: 0.8669 (m-40) cc_final: 0.8261 (m110) REVERT: A 1 MET cc_start: 0.7497 (tpt) cc_final: 0.7267 (tpt) REVERT: A 110 MET cc_start: 0.0888 (tpt) cc_final: 0.0659 (tpp) REVERT: A 277 MET cc_start: 0.5187 (mmt) cc_final: 0.4962 (mmm) REVERT: A 512 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5615 (ttm) REVERT: A 559 MET cc_start: 0.4337 (pmm) cc_final: 0.4069 (pmm) REVERT: A 587 LEU cc_start: 0.7285 (mt) cc_final: 0.6967 (tm) REVERT: A 659 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6108 (p90) REVERT: A 666 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8961 (tp) REVERT: A 766 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.6968 (m) REVERT: A 773 MET cc_start: 0.8862 (ttt) cc_final: 0.8538 (ttm) REVERT: A 829 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7038 (m) outliers start: 25 outliers final: 12 residues processed: 121 average time/residue: 1.4133 time to fit residues: 194.6465 Evaluate side-chains 117 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 38 optimal weight: 8.9990 chunk 46 optimal weight: 0.2980 chunk 127 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 245 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.082989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055652 restraints weight = 84059.428| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.06 r_work: 0.2910 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21513 Z= 0.181 Angle : 0.567 12.309 29102 Z= 0.292 Chirality : 0.040 0.190 3129 Planarity : 0.003 0.058 3789 Dihedral : 4.843 52.266 2882 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.02 % Allowed : 11.84 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2584 helix: 1.82 (0.15), residues: 1287 sheet: -0.50 (0.49), residues: 118 loop : -1.62 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 862 HIS 0.004 0.001 HIS A 945 PHE 0.016 0.001 PHE B 864 TYR 0.023 0.001 TYR B 86 ARG 0.012 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.05247 ( 941) hydrogen bonds : angle 3.86749 ( 2703) covalent geometry : bond 0.00437 (21513) covalent geometry : angle 0.56717 (29102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17368.53 seconds wall clock time: 299 minutes 4.29 seconds (17944.29 seconds total)