Starting phenix.real_space_refine on Sat Sep 12 03:56:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qee_4536/09_2026/6qee_4536.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qee_4536/09_2026/6qee_4536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6qee_4536/09_2026/6qee_4536.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qee_4536/09_2026/6qee_4536.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qee_4536/09_2026/6qee_4536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qee_4536/09_2026/6qee_4536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qee_4536/09_2026/6qee_4536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qee_4536/09_2026/6qee_4536.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 8388 2.51 5 N 2131 2.21 5 O 2396 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12975 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9184 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 27, 'TRANS': 1154} Chain breaks: 1 Chain: "B" Number of atoms: 1713 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} bond proxies already assigned to first conformer: 1747 Chain: "C" Number of atoms: 1720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Conformer: "B" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} bond proxies already assigned to first conformer: 1763 Chain: "A" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 358 Unusual residues: {'3PE': 1, 'CLR': 7, 'NAG': 3, 'ZQU': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.37, per 1000 atoms: 0.26 Number of scatterers: 12975 At special positions: 0 Unit cell: (178.08, 134.4, 145.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 1 15.00 F 4 9.00 O 2396 8.00 N 2131 7.00 C 8388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG BCYS C 204 " distance=2.08 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 Links applied NAG-ASN " NAG A1401 " - " ASN A 93 " " NAG A1402 " - " ASN A 90 " " NAG A1403 " - " ASN A 98 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 796.8 milliseconds 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3002 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 49.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.989A pdb=" N MET A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 39' Processing helix chain 'A' and resid 44 through 62 removed outlier: 3.772A pdb=" N LEU A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 90 removed outlier: 3.670A pdb=" N GLY A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 137 removed outlier: 3.568A pdb=" N PHE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TRP A 135 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 removed outlier: 4.015A pdb=" N GLN A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.686A pdb=" N VAL A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 removed outlier: 3.577A pdb=" N ILE A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 210 removed outlier: 3.824A pdb=" N GLY A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.894A pdb=" N THR A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 237 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.547A pdb=" N ALA A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 320 removed outlier: 4.212A pdb=" N ASN A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 326 through 347 Processing helix chain 'A' and resid 348 through 370 removed outlier: 4.223A pdb=" N PHE A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.800A pdb=" N ILE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.722A pdb=" N ILE A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.694A pdb=" N ALA A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 618 removed outlier: 3.702A pdb=" N LYS A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 628 removed outlier: 3.762A pdb=" N LYS A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 706 through 721 removed outlier: 4.453A pdb=" N VAL A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 737 removed outlier: 3.885A pdb=" N ALA A 726 " --> pdb=" O GLY A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 797 removed outlier: 3.680A pdb=" N LYS A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 783 " --> pdb=" O ALA A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.906A pdb=" N ASP A 805 " --> pdb=" O TRP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.966A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 879 removed outlier: 3.648A pdb=" N THR A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Proline residue: A 865 - end of helix removed outlier: 3.809A pdb=" N SER A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 890 through 902 removed outlier: 3.569A pdb=" N LYS A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 897 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 901 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN A 902 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 910 removed outlier: 3.591A pdb=" N VAL A 906 " --> pdb=" O ASN A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 964 removed outlier: 3.882A pdb=" N PHE A 915 " --> pdb=" O ARG A 911 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 922 " --> pdb=" O MET A 918 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 4.112A pdb=" N ILE A 939 " --> pdb=" O HIS A 935 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 952 " --> pdb=" O MET A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 994 removed outlier: 5.164A pdb=" N ALA A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.973A pdb=" N GLU A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 4.081A pdb=" N GLU A1083 " --> pdb=" O VAL A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1111 Processing helix chain 'A' and resid 1125 through 1131 Processing helix chain 'A' and resid 1132 through 1134 No H-bonds generated for 'chain 'A' and resid 1132 through 1134' Processing helix chain 'A' and resid 1140 through 1150 removed outlier: 3.678A pdb=" N ILE A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1159 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1209 through 1221 Processing helix chain 'A' and resid 1255 through 1262 Processing helix chain 'A' and resid 1264 through 1275 removed outlier: 3.694A pdb=" N SER A1268 " --> pdb=" O GLY A1264 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A1275 " --> pdb=" O SER A1271 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.701A pdb=" N ARG B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS B 195 " --> pdb=" O TYR B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 195' Processing helix chain 'C' and resid 162 through 166 removed outlier: 3.724A pdb=" N SER C 165 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.825A pdb=" N VAL A 416 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 391 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 396 through 399 removed outlier: 5.244A pdb=" N ILE A 396 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 471 through 472 removed outlier: 6.830A pdb=" N VAL A 472 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 553 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 422 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 599 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A 607 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1055 through 1058 removed outlier: 4.402A pdb=" N LEU A1055 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY A1038 " --> pdb=" O SER A1092 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER A1092 " --> pdb=" O GLY A1038 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1064 through 1066 removed outlier: 3.598A pdb=" N VAL A1228 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A1229 " --> pdb=" O LEU A1198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1245 through 1246 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 23 removed outlier: 3.513A pdb=" N ALA B 19 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 77 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 53 removed outlier: 5.306A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.697A pdb=" N ASN B 143 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 139 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.641A pdb=" N ASN B 151 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 203 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 213 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.828A pdb=" N GLN C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 18 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.319A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 34 " --> pdb=" O ILE C 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.593A pdb=" N LYS C 152 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.593A pdb=" N LYS C 152 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 206 through 208 631 hydrogen bonds defined for protein. 1814 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: 2.82 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2090 1.31 - 1.46: 4932 1.46 - 1.61: 6156 1.61 - 1.76: 3 1.76 - 1.90: 89 Bond restraints: 13270 Sorted by residual: bond pdb=" C7 NAG A1403 " pdb=" N2 NAG A1403 " ideal model delta sigma weight residual 1.346 1.488 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C7 NAG A1402 " pdb=" N2 NAG A1402 " ideal model delta sigma weight residual 1.346 1.483 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C7 NAG A1401 " pdb=" N2 NAG A1401 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C1 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.406 1.524 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.24e+01 ... (remaining 13265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 17794 4.64 - 9.29: 206 9.29 - 13.93: 20 13.93 - 18.58: 0 18.58 - 23.22: 1 Bond angle restraints: 18021 Sorted by residual: angle pdb=" O12 3PE A1413 " pdb=" P 3PE A1413 " pdb=" O14 3PE A1413 " ideal model delta sigma weight residual 123.79 100.57 23.22 3.00e+00 1.11e-01 5.99e+01 angle pdb=" CA THR A 100 " pdb=" C THR A 100 " pdb=" O THR A 100 " ideal model delta sigma weight residual 120.31 113.94 6.37 1.25e+00 6.40e-01 2.59e+01 angle pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " pdb=" CG1 ILE A 91 " ideal model delta sigma weight residual 110.40 118.70 -8.30 1.70e+00 3.46e-01 2.39e+01 angle pdb=" N VAL A 864 " pdb=" CA VAL A 864 " pdb=" C VAL A 864 " ideal model delta sigma weight residual 108.88 119.01 -10.13 2.16e+00 2.14e-01 2.20e+01 angle pdb=" N VAL B 56 " pdb=" CA VAL B 56 " pdb=" C VAL B 56 " ideal model delta sigma weight residual 109.34 119.07 -9.73 2.08e+00 2.31e-01 2.19e+01 ... (remaining 18016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6974 17.84 - 35.69: 688 35.69 - 53.53: 128 53.53 - 71.37: 29 71.37 - 89.21: 11 Dihedral angle restraints: 7830 sinusoidal: 3144 harmonic: 4686 Sorted by residual: dihedral pdb=" CA SER B 7 " pdb=" C SER B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual 180.00 131.98 48.02 0 5.00e+00 4.00e-02 9.22e+01 dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N VAL B 56 " pdb=" CA VAL B 56 " ideal model delta harmonic sigma weight residual -180.00 -132.19 -47.81 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " pdb=" SG BCYS C 204 " pdb=" CB BCYS C 204 " ideal model delta sinusoidal sigma weight residual 93.00 156.16 -63.16 1 1.00e+01 1.00e-02 5.27e+01 ... (remaining 7827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.542: 2070 0.542 - 1.085: 1 1.085 - 1.627: 0 1.627 - 2.169: 0 2.169 - 2.711: 1 Chirality restraints: 2072 Sorted by residual: chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A 98 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 0.31 -2.71 2.00e-01 2.50e+01 1.84e+02 chirality pdb=" C1 NAG A1401 " pdb=" ND2 ASN A 93 " pdb=" C2 NAG A1401 " pdb=" O5 NAG A1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" C14 CLR A1408 " pdb=" C13 CLR A1408 " pdb=" C15 CLR A1408 " pdb=" C8 CLR A1408 " both_signs ideal model delta sigma weight residual False -2.32 -2.83 0.51 2.00e-01 2.50e+01 6.49e+00 ... (remaining 2069 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 93 " 0.139 2.00e-02 2.50e+03 1.64e-01 3.36e+02 pdb=" CG ASN A 93 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 93 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN A 93 " -0.264 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 90 " -0.148 2.00e-02 2.50e+03 1.59e-01 3.14e+02 pdb=" CG ASN A 90 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN A 90 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 90 " 0.266 2.00e-02 2.50e+03 pdb=" C1 NAG A1402 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.048 2.00e-02 2.50e+03 1.20e-01 1.79e+02 pdb=" CG ASN A 98 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " -0.072 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.222 2.00e-02 2.50e+03 pdb=" C1 NAG A1403 " -0.121 2.00e-02 2.50e+03 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2262 2.76 - 3.29: 11846 3.29 - 3.83: 20817 3.83 - 4.36: 23000 4.36 - 4.90: 40724 Nonbonded interactions: 98649 Sorted by model distance: nonbonded pdb=" OG SER A1125 " pdb=" OE1 GLU A1128 " model vdw 2.223 3.040 nonbonded pdb=" O ASP A 96 " pdb=" OG1 THR A 100 " model vdw 2.231 3.040 nonbonded pdb=" O LYS B 155 " pdb=" OG1 THR B 199 " model vdw 2.290 3.040 nonbonded pdb=" OG SER B 25 " pdb=" N SER B 26 " model vdw 2.291 3.120 nonbonded pdb=" NH2 ARG A 275 " pdb=" OD1 ASP A1123 " model vdw 2.294 3.120 ... (remaining 98644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.012 0.357 13277 Z= 0.530 Angle : 1.323 39.088 18038 Z= 0.633 Chirality : 0.098 2.711 2072 Planarity : 0.008 0.100 2227 Dihedral : 14.870 89.214 4816 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 1.09 % Allowed : 5.18 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.16), residues: 1621 helix: -2.61 (0.13), residues: 763 sheet: -2.22 (0.31), residues: 248 loop : -2.71 (0.20), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 94 TYR 0.025 0.003 TYR A 952 PHE 0.029 0.003 PHE A 731 TRP 0.028 0.003 TRP B 102 HIS 0.007 0.002 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.01107 / 0.48 (13270) covalent geometry : angle 1.25448 / 0.62 (18021) SS BOND : bond 0.02549 / 1.30 ( 4) SS BOND : angle 2.83952 / 1.21 ( 8) hydrogen bonds : bond 0.18961 / 12.26 ( 627) hydrogen bonds : angle 7.49199 / 5.38 ( 1814) link_NAG-ASN : bond 0.28846 / 16.66 ( 3) link_NAG-ASN : angle 18.70038 / 9.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7067 (mtt) cc_final: 0.6713 (mtt) REVERT: A 156 ASN cc_start: 0.8586 (t0) cc_final: 0.8286 (t0) REVERT: A 615 MET cc_start: 0.7563 (mmm) cc_final: 0.6313 (tpt) REVERT: A 715 PHE cc_start: 0.8353 (t80) cc_final: 0.7823 (t80) REVERT: C 89 GLU cc_start: 0.7656 (mp0) cc_final: 0.7404 (mp0) outliers start: 13 outliers final: 8 residues processed: 157 average time/residue: 0.1192 time to fit residues: 27.5722 Evaluate side-chains 95 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 72 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A1154 HIS A1247 ASN A1256 HIS B 31 HIS B 143 ASN B 144 ASN B 162 GLN B 204 HIS B 216 ASN C 39 GLN C 102 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.110284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.091826 restraints weight = 57757.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.092938 restraints weight = 91224.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094587 restraints weight = 31290.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094941 restraints weight = 18450.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095184 restraints weight = 13421.669| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13277 Z= 0.134 Angle : 0.660 8.308 18038 Z= 0.336 Chirality : 0.042 0.291 2072 Planarity : 0.005 0.077 2227 Dihedral : 7.482 59.348 1925 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.82 % Allowed : 11.67 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.19), residues: 1621 helix: -0.59 (0.17), residues: 779 sheet: -1.64 (0.32), residues: 247 loop : -2.31 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 82 TYR 0.023 0.002 TYR A 927 PHE 0.019 0.001 PHE A 398 TRP 0.013 0.001 TRP C 47 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (13270) covalent geometry : angle 0.65253 / 0.33 (18021) SS BOND : bond 0.01249 / 0.66 ( 4) SS BOND : angle 1.51427 / 0.62 ( 8) hydrogen bonds : bond 0.05943 / 3.87 ( 627) hydrogen bonds : angle 5.17194 / 3.73 ( 1814) link_NAG-ASN : bond 0.01062 / 0.68 ( 3) link_NAG-ASN : angle 4.15575 / 2.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LEU cc_start: 0.7428 (tp) cc_final: 0.7011 (tt) REVERT: A 515 LEU cc_start: 0.0542 (OUTLIER) cc_final: 0.0331 (pt) REVERT: A 615 MET cc_start: 0.6765 (mmm) cc_final: 0.5600 (tpt) REVERT: A 715 PHE cc_start: 0.8146 (t80) cc_final: 0.7485 (t80) REVERT: A 861 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 948 MET cc_start: 0.7739 (ttm) cc_final: 0.7434 (ttm) REVERT: A 1089 MET cc_start: 0.5351 (mpp) cc_final: 0.5138 (mpp) REVERT: B 219 GLU cc_start: 0.6914 (pm20) cc_final: 0.6067 (pm20) REVERT: C 202 ILE cc_start: 0.8043 (tp) cc_final: 0.7778 (mp) outliers start: 23 outliers final: 11 residues processed: 132 average time/residue: 0.1064 time to fit residues: 21.4221 Evaluate side-chains 98 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 72 optimal weight: 4.9990 chunk 157 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 720 ASN A1152 ASN A1154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.107587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089179 restraints weight = 56579.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090338 restraints weight = 94332.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091602 restraints weight = 31355.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.092037 restraints weight = 19788.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092207 restraints weight = 14591.432| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13277 Z= 0.167 Angle : 0.649 8.075 18038 Z= 0.330 Chirality : 0.044 0.266 2072 Planarity : 0.005 0.080 2227 Dihedral : 7.054 59.473 1921 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.04 % Allowed : 13.49 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.20), residues: 1621 helix: 0.17 (0.18), residues: 779 sheet: -1.30 (0.33), residues: 241 loop : -2.13 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.020 0.002 TYR A 927 PHE 0.016 0.001 PHE A 199 TRP 0.016 0.001 TRP B 102 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (13270) covalent geometry : angle 0.64584 / 0.33 (18021) SS BOND : bond 0.01256 / 0.65 ( 4) SS BOND : angle 1.69139 / 0.73 ( 8) hydrogen bonds : bond 0.05805 / 3.80 ( 627) hydrogen bonds : angle 4.91121 / 3.53 ( 1814) link_NAG-ASN : bond 0.00846 / 0.57 ( 3) link_NAG-ASN : angle 2.47559 / 1.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8340 (mmm) cc_final: 0.8134 (tpp) REVERT: A 615 MET cc_start: 0.6649 (mmm) cc_final: 0.5363 (tpt) REVERT: A 877 MET cc_start: 0.8850 (tmt) cc_final: 0.8462 (tmt) REVERT: A 948 MET cc_start: 0.7662 (ttm) cc_final: 0.7402 (ttm) REVERT: B 219 GLU cc_start: 0.6870 (pm20) cc_final: 0.5814 (pm20) outliers start: 26 outliers final: 17 residues processed: 118 average time/residue: 0.1043 time to fit residues: 18.7027 Evaluate side-chains 102 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 71 optimal weight: 0.2980 chunk 147 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.6744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.106998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081939 restraints weight = 36210.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.082557 restraints weight = 58370.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.083761 restraints weight = 36723.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.084084 restraints weight = 22649.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.084465 restraints weight = 21155.159| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13277 Z= 0.169 Angle : 0.633 8.176 18038 Z= 0.322 Chirality : 0.043 0.273 2072 Planarity : 0.004 0.073 2227 Dihedral : 6.840 59.692 1919 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.84 % Allowed : 14.81 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1621 helix: 0.44 (0.19), residues: 776 sheet: -1.24 (0.32), residues: 254 loop : -1.89 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 114 TYR 0.021 0.002 TYR A 927 PHE 0.015 0.001 PHE B 92 TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (13270) covalent geometry : angle 0.63122 / 0.32 (18021) SS BOND : bond 0.01126 / 0.58 ( 4) SS BOND : angle 1.63974 / 0.72 ( 8) hydrogen bonds : bond 0.05656 / 3.70 ( 627) hydrogen bonds : angle 4.79200 / 3.45 ( 1814) link_NAG-ASN : bond 0.00685 / 0.46 ( 3) link_NAG-ASN : angle 1.91074 / 1.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8524 (tp) REVERT: A 467 GLU cc_start: 0.6276 (tp30) cc_final: 0.6018 (tp30) REVERT: A 478 LEU cc_start: 0.7523 (tp) cc_final: 0.7249 (tp) REVERT: A 614 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5301 (mm) REVERT: A 615 MET cc_start: 0.6956 (mmm) cc_final: 0.5848 (tpt) REVERT: A 877 MET cc_start: 0.8901 (tmt) cc_final: 0.8240 (tmt) REVERT: A 948 MET cc_start: 0.7715 (ttm) cc_final: 0.7486 (ttm) REVERT: B 219 GLU cc_start: 0.7030 (pm20) cc_final: 0.6108 (pm20) outliers start: 37 outliers final: 23 residues processed: 122 average time/residue: 0.1106 time to fit residues: 20.5926 Evaluate side-chains 109 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 102 optimal weight: 0.0010 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 153 optimal weight: 6.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A1194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.109551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086293 restraints weight = 47200.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088300 restraints weight = 74755.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.089741 restraints weight = 28379.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089937 restraints weight = 21342.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090364 restraints weight = 16524.129| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13277 Z= 0.122 Angle : 0.617 15.567 18038 Z= 0.303 Chirality : 0.043 0.527 2072 Planarity : 0.004 0.071 2227 Dihedral : 6.330 56.604 1919 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.84 % Allowed : 16.05 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1621 helix: 0.79 (0.19), residues: 776 sheet: -1.10 (0.32), residues: 259 loop : -1.71 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 82 TYR 0.021 0.001 TYR A 927 PHE 0.014 0.001 PHE B 92 TRP 0.009 0.001 TRP C 47 HIS 0.002 0.000 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (13270) covalent geometry : angle 0.59590 / 0.30 (18021) SS BOND : bond 0.00927 / 0.48 ( 4) SS BOND : angle 1.41481 / 0.58 ( 8) hydrogen bonds : bond 0.04933 / 3.21 ( 627) hydrogen bonds : angle 4.45181 / 3.21 ( 1814) link_NAG-ASN : bond 0.02457 / 1.74 ( 3) link_NAG-ASN : angle 7.11932 / 5.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 THR cc_start: 0.7519 (m) cc_final: 0.7307 (t) REVERT: A 478 LEU cc_start: 0.7404 (tp) cc_final: 0.6977 (tp) REVERT: A 614 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5252 (mm) REVERT: A 615 MET cc_start: 0.6790 (mmm) cc_final: 0.5712 (tpt) REVERT: A 877 MET cc_start: 0.8821 (tmt) cc_final: 0.8127 (tmt) REVERT: A 948 MET cc_start: 0.7625 (ttm) cc_final: 0.7362 (ttm) REVERT: B 219 GLU cc_start: 0.6833 (pm20) cc_final: 0.6138 (pm20) outliers start: 37 outliers final: 25 residues processed: 130 average time/residue: 0.0961 time to fit residues: 19.3552 Evaluate side-chains 112 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.109199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089674 restraints weight = 56526.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090705 restraints weight = 90425.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092666 restraints weight = 31277.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.092885 restraints weight = 18427.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093013 restraints weight = 14014.845| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13277 Z= 0.148 Angle : 0.886 59.189 18038 Z= 0.465 Chirality : 0.043 0.306 2072 Planarity : 0.004 0.071 2227 Dihedral : 6.316 56.829 1919 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.70 % Allowed : 16.85 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.21), residues: 1621 helix: 0.81 (0.19), residues: 776 sheet: -1.05 (0.32), residues: 261 loop : -1.68 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 82 TYR 0.021 0.001 TYR A 927 PHE 0.034 0.001 PHE A 266 TRP 0.009 0.001 TRP C 47 HIS 0.007 0.001 HIS A1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (13270) covalent geometry : angle 0.84910 / 0.46 (18021) SS BOND : bond 0.00895 / 0.45 ( 4) SS BOND : angle 4.11109 / 2.54 ( 8) hydrogen bonds : bond 0.04963 / 3.24 ( 627) hydrogen bonds : angle 4.45741 / 3.21 ( 1814) link_NAG-ASN : bond 0.02567 / 1.82 ( 3) link_NAG-ASN : angle 10.74389 / 8.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LEU cc_start: 0.7395 (tp) cc_final: 0.6984 (tp) REVERT: A 614 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5286 (mm) REVERT: A 615 MET cc_start: 0.6557 (mmm) cc_final: 0.5494 (tpt) REVERT: A 877 MET cc_start: 0.8888 (tmt) cc_final: 0.8080 (tmt) REVERT: A 948 MET cc_start: 0.7593 (ttm) cc_final: 0.7337 (ttm) REVERT: B 219 GLU cc_start: 0.6678 (pm20) cc_final: 0.6027 (pm20) outliers start: 35 outliers final: 28 residues processed: 118 average time/residue: 0.0904 time to fit residues: 16.7049 Evaluate side-chains 113 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 142 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 720 ASN A 924 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.109745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085320 restraints weight = 33909.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086271 restraints weight = 55113.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087410 restraints weight = 33476.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087551 restraints weight = 21246.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087909 restraints weight = 20488.065| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13277 Z= 0.133 Angle : 0.648 13.531 18038 Z= 0.316 Chirality : 0.049 0.982 2072 Planarity : 0.004 0.071 2227 Dihedral : 6.175 56.483 1919 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 3.21 % Allowed : 16.63 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1621 helix: 0.85 (0.19), residues: 775 sheet: -0.78 (0.33), residues: 249 loop : -1.56 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 94 TYR 0.021 0.001 TYR A 927 PHE 0.034 0.001 PHE A 334 TRP 0.008 0.001 TRP C 47 HIS 0.004 0.000 HIS A1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (13270) covalent geometry : angle 0.62322 / 0.31 (18021) SS BOND : bond 0.00863 / 0.44 ( 4) SS BOND : angle 1.70620 / 0.82 ( 8) hydrogen bonds : bond 0.04844 / 3.17 ( 627) hydrogen bonds : angle 4.38717 / 3.16 ( 1814) link_NAG-ASN : bond 0.02617 / 1.84 ( 3) link_NAG-ASN : angle 7.78048 / 4.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6908 (mmp) cc_final: 0.6544 (mpp) REVERT: A 351 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8488 (tp) REVERT: A 478 LEU cc_start: 0.7448 (tp) cc_final: 0.7011 (tp) REVERT: A 614 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5251 (mm) REVERT: A 615 MET cc_start: 0.6678 (mmm) cc_final: 0.5671 (tpt) REVERT: A 877 MET cc_start: 0.8932 (tmt) cc_final: 0.8068 (tmt) REVERT: A 948 MET cc_start: 0.7665 (ttm) cc_final: 0.7434 (ttm) REVERT: B 219 GLU cc_start: 0.6825 (pm20) cc_final: 0.6175 (pm20) outliers start: 41 outliers final: 30 residues processed: 121 average time/residue: 0.0988 time to fit residues: 18.3503 Evaluate side-chains 114 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 838 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.106608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086430 restraints weight = 50451.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087345 restraints weight = 88817.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088182 restraints weight = 31970.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088690 restraints weight = 22707.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.088941 restraints weight = 17038.092| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13277 Z= 0.202 Angle : 0.709 15.591 18038 Z= 0.351 Chirality : 0.048 0.703 2072 Planarity : 0.005 0.076 2227 Dihedral : 6.586 59.038 1919 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.84 % Allowed : 17.14 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1621 helix: 0.56 (0.18), residues: 780 sheet: -0.85 (0.34), residues: 249 loop : -1.56 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 82 TYR 0.022 0.002 TYR A 952 PHE 0.049 0.002 PHE A 334 TRP 0.011 0.001 TRP B 102 HIS 0.006 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (13270) covalent geometry : angle 0.68296 / 0.35 (18021) SS BOND : bond 0.01055 / 0.54 ( 4) SS BOND : angle 2.16440 / 1.10 ( 8) hydrogen bonds : bond 0.05682 / 3.72 ( 627) hydrogen bonds : angle 4.69117 / 3.37 ( 1814) link_NAG-ASN : bond 0.01953 / 1.21 ( 3) link_NAG-ASN : angle 8.25711 / 5.36 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6946 (mmp) cc_final: 0.6454 (mpp) REVERT: A 351 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 615 MET cc_start: 0.6286 (mmm) cc_final: 0.5411 (tpt) REVERT: A 877 MET cc_start: 0.9050 (tmt) cc_final: 0.8145 (tmt) REVERT: A 948 MET cc_start: 0.7593 (ttm) cc_final: 0.7354 (ttm) REVERT: B 219 GLU cc_start: 0.6709 (pm20) cc_final: 0.5957 (pm20) outliers start: 36 outliers final: 27 residues processed: 120 average time/residue: 0.0981 time to fit residues: 18.0956 Evaluate side-chains 112 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.107606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085191 restraints weight = 47660.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.087098 restraints weight = 78089.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.087607 restraints weight = 29363.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088402 restraints weight = 22030.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.088549 restraints weight = 17007.039| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13277 Z= 0.161 Angle : 0.666 15.280 18038 Z= 0.329 Chirality : 0.046 0.578 2072 Planarity : 0.004 0.071 2227 Dihedral : 6.442 59.571 1919 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.63 % Allowed : 17.65 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1621 helix: 0.66 (0.19), residues: 778 sheet: -0.79 (0.34), residues: 249 loop : -1.47 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.022 0.002 TYR A 927 PHE 0.021 0.001 PHE A 266 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (13270) covalent geometry : angle 0.64128 / 0.32 (18021) SS BOND : bond 0.00958 / 0.49 ( 4) SS BOND : angle 1.87310 / 0.91 ( 8) hydrogen bonds : bond 0.05351 / 3.49 ( 627) hydrogen bonds : angle 4.58993 / 3.30 ( 1814) link_NAG-ASN : bond 0.02275 / 1.47 ( 3) link_NAG-ASN : angle 7.93992 / 5.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6941 (mmp) cc_final: 0.6503 (mpp) REVERT: A 351 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 615 MET cc_start: 0.6343 (mmm) cc_final: 0.5259 (tpt) REVERT: A 877 MET cc_start: 0.9019 (tmt) cc_final: 0.8065 (tmt) REVERT: A 948 MET cc_start: 0.7514 (ttm) cc_final: 0.7245 (ttm) REVERT: B 219 GLU cc_start: 0.6822 (pm20) cc_final: 0.6191 (pm20) outliers start: 33 outliers final: 26 residues processed: 114 average time/residue: 0.0978 time to fit residues: 17.4870 Evaluate side-chains 107 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 83 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 36 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 838 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.109021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090488 restraints weight = 55514.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091474 restraints weight = 90396.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.092189 restraints weight = 32277.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092556 restraints weight = 23788.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092867 restraints weight = 16746.302| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13277 Z= 0.132 Angle : 0.650 15.474 18038 Z= 0.317 Chirality : 0.045 0.541 2072 Planarity : 0.004 0.072 2227 Dihedral : 6.196 57.881 1919 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.48 % Allowed : 18.31 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1621 helix: 0.82 (0.19), residues: 778 sheet: -0.70 (0.34), residues: 249 loop : -1.41 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.022 0.001 TYR A 927 PHE 0.022 0.001 PHE A 334 TRP 0.009 0.001 TRP B 169 HIS 0.007 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (13270) covalent geometry : angle 0.62526 / 0.31 (18021) SS BOND : bond 0.00886 / 0.45 ( 4) SS BOND : angle 1.68412 / 0.78 ( 8) hydrogen bonds : bond 0.05005 / 3.25 ( 627) hydrogen bonds : angle 4.42009 / 3.19 ( 1814) link_NAG-ASN : bond 0.01983 / 1.27 ( 3) link_NAG-ASN : angle 7.90467 / 5.08 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8528 (tp) REVERT: A 478 LEU cc_start: 0.7392 (tp) cc_final: 0.7111 (tp) REVERT: A 615 MET cc_start: 0.6181 (mmm) cc_final: 0.5074 (tpt) REVERT: A 877 MET cc_start: 0.9003 (tmt) cc_final: 0.8104 (tmt) REVERT: A 948 MET cc_start: 0.7524 (ttm) cc_final: 0.7261 (ttm) REVERT: B 219 GLU cc_start: 0.6580 (pm20) cc_final: 0.6203 (mp0) outliers start: 31 outliers final: 26 residues processed: 112 average time/residue: 0.0929 time to fit residues: 16.1451 Evaluate side-chains 111 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 83 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 63 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 ASN A 838 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.109044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086899 restraints weight = 41991.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088954 restraints weight = 73477.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089041 restraints weight = 29183.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089372 restraints weight = 25484.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089582 restraints weight = 19813.124| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13277 Z= 0.147 Angle : 0.889 59.192 18038 Z= 0.465 Chirality : 0.045 0.431 2072 Planarity : 0.004 0.071 2227 Dihedral : 6.126 57.913 1918 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.41 % Allowed : 18.31 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1621 helix: 0.84 (0.19), residues: 780 sheet: -0.69 (0.34), residues: 249 loop : -1.40 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 82 TYR 0.022 0.001 TYR A 927 PHE 0.020 0.001 PHE A 334 TRP 0.008 0.001 TRP C 47 HIS 0.015 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (13270) covalent geometry : angle 0.85305 / 0.46 (18021) SS BOND : bond 0.00896 / 0.46 ( 4) SS BOND : angle 1.68555 / 0.77 ( 8) hydrogen bonds : bond 0.05002 / 3.26 ( 627) hydrogen bonds : angle 4.42620 / 3.20 ( 1814) link_NAG-ASN : bond 0.04377 / 3.05 ( 3) link_NAG-ASN : angle 11.17238 / 7.90 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2360.00 seconds wall clock time: 41 minutes 34.30 seconds (2494.30 seconds total)