Starting phenix.real_space_refine on Thu Jul 31 15:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qee_4536/07_2025/6qee_4536.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qee_4536/07_2025/6qee_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6qee_4536/07_2025/6qee_4536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qee_4536/07_2025/6qee_4536.map" model { file = "/net/cci-nas-00/data/ceres_data/6qee_4536/07_2025/6qee_4536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qee_4536/07_2025/6qee_4536.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 18 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.88, per 1000 atoms: 0.84 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: 3.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.78 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: 5.59 Time building geometry restraints manager: 4.09 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: 7361 17.84 - 35.69: 723 35.69 - 53.53: 160 53.53 - 71.37: 39 71.37 - 89.21: 14 Dihedral angle restraints: 8297 sinusoidal: 3611 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 8294 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: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.070 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 15.211 89.214 5283 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.003 TRP B 102 HIS 0.007 0.002 HIS A 611 PHE 0.029 0.003 PHE A 731 TYR 0.025 0.003 TYR A 952 ARG 0.018 0.001 ARG A 94 Details of bonding type rmsd link_NAG-ASN : bond 0.28846 ( 3) link_NAG-ASN : angle 18.70038 ( 9) hydrogen bonds : bond 0.18961 ( 627) hydrogen bonds : angle 7.49199 ( 1814) SS BOND : bond 0.02549 ( 4) SS BOND : angle 2.83952 ( 8) covalent geometry : bond 0.01107 (13270) covalent geometry : angle 1.25448 (18021) *********************** 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 : 1.378 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: 0.6716 (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: 0.7824 (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: 0.2538 time to fit residues: 58.2608 Evaluate side-chains 97 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 136 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A1152 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.108260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086331 restraints weight = 49442.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.088073 restraints weight = 83905.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089303 restraints weight = 29022.304| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1759 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= 0.156 Angle : 0.677 8.027 18038 Z= 0.347 Chirality : 0.043 0.216 2072 Planarity : 0.005 0.078 2227 Dihedral : 9.178 58.998 2392 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.97 % Allowed : 12.04 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1621 helix: -0.66 (0.17), residues: 779 sheet: -1.65 (0.33), residues: 242 loop : -2.31 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 102 HIS 0.003 0.001 HIS A 611 PHE 0.021 0.001 PHE A 398 TYR 0.024 0.002 TYR A 927 ARG 0.009 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00766 ( 3) link_NAG-ASN : angle 4.95530 ( 9) hydrogen bonds : bond 0.06128 ( 627) hydrogen bonds : angle 5.22675 ( 1814) SS BOND : bond 0.01345 ( 4) SS BOND : angle 1.50525 ( 8) covalent geometry : bond 0.00330 (13270) covalent geometry : angle 0.66786 (18021) *********************** 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 134 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 LEU cc_start: 0.1051 (OUTLIER) cc_final: 0.0835 (pt) REVERT: A 615 MET cc_start: 0.6936 (mmm) cc_final: 0.5809 (tpt) REVERT: A 715 PHE cc_start: 0.8154 (t80) cc_final: 0.7510 (t80) REVERT: A 861 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8839 (mp) REVERT: A 877 MET cc_start: 0.8265 (tmm) cc_final: 0.7760 (tmt) REVERT: A 948 MET cc_start: 0.7813 (ttm) cc_final: 0.7506 (ttm) REVERT: A 1089 MET cc_start: 0.5426 (mpp) cc_final: 0.5214 (mpp) REVERT: B 219 GLU cc_start: 0.7108 (pm20) cc_final: 0.6193 (pm20) outliers start: 25 outliers final: 13 residues processed: 127 average time/residue: 0.2491 time to fit residues: 47.4443 Evaluate side-chains 102 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1041 PHE Chi-restraints excluded: chain A residue 1228 VAL 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 72 VAL 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 145 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.0170 chunk 39 optimal weight: 10.0000 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 720 ASN A1154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.108711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085532 restraints weight = 47491.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.087355 restraints weight = 81281.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088576 restraints weight = 29149.110| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2234 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= 0.140 Angle : 0.622 7.726 18038 Z= 0.315 Chirality : 0.042 0.264 2072 Planarity : 0.004 0.080 2227 Dihedral : 8.465 59.981 2389 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.82 % Allowed : 13.49 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1621 helix: 0.24 (0.19), residues: 778 sheet: -1.38 (0.32), residues: 245 loop : -2.06 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS A 611 PHE 0.014 0.001 PHE B 92 TYR 0.020 0.002 TYR A 927 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00926 ( 3) link_NAG-ASN : angle 3.91242 ( 9) hydrogen bonds : bond 0.05503 ( 627) hydrogen bonds : angle 4.77891 ( 1814) SS BOND : bond 0.01180 ( 4) SS BOND : angle 1.52513 ( 8) covalent geometry : bond 0.00299 (13270) covalent geometry : angle 0.61535 (18021) *********************** 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 120 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 GLU cc_start: 0.6035 (tp30) cc_final: 0.5823 (tp30) REVERT: A 615 MET cc_start: 0.6986 (mmm) cc_final: 0.5736 (tpt) REVERT: A 715 PHE cc_start: 0.8141 (t80) cc_final: 0.7526 (t80) REVERT: A 948 MET cc_start: 0.7663 (ttm) cc_final: 0.7346 (ttm) REVERT: B 219 GLU cc_start: 0.7095 (pm20) cc_final: 0.5879 (pm20) REVERT: C 202 ILE cc_start: 0.8096 (tp) cc_final: 0.7877 (mp) outliers start: 23 outliers final: 14 residues processed: 115 average time/residue: 0.2391 time to fit residues: 41.9085 Evaluate side-chains 103 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 399 SER 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 509 TYR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL 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 13 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 118 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN C 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.109277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084440 restraints weight = 40554.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.084357 restraints weight = 66269.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.086046 restraints weight = 40461.741| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13277 Z= 0.128 Angle : 0.584 7.513 18038 Z= 0.296 Chirality : 0.041 0.278 2072 Planarity : 0.004 0.073 2227 Dihedral : 7.959 57.566 2387 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.77 % Allowed : 14.08 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1621 helix: 0.66 (0.19), residues: 776 sheet: -1.35 (0.31), residues: 257 loop : -1.74 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.002 0.001 HIS A 611 PHE 0.014 0.001 PHE B 92 TYR 0.020 0.001 TYR A 927 ARG 0.004 0.000 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 3) link_NAG-ASN : angle 3.53344 ( 9) hydrogen bonds : bond 0.05089 ( 627) hydrogen bonds : angle 4.52483 ( 1814) SS BOND : bond 0.01058 ( 4) SS BOND : angle 1.47923 ( 8) covalent geometry : bond 0.00269 (13270) covalent geometry : angle 0.57823 (18021) *********************** 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 133 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 467 GLU cc_start: 0.6179 (tp30) cc_final: 0.5971 (tp30) REVERT: A 614 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.5254 (mm) REVERT: A 615 MET cc_start: 0.7103 (mmm) cc_final: 0.6008 (tpt) REVERT: A 948 MET cc_start: 0.7605 (ttm) cc_final: 0.7329 (ttm) REVERT: A 1191 ARG cc_start: 0.7438 (mtt90) cc_final: 0.7150 (tpp80) REVERT: B 219 GLU cc_start: 0.7092 (pm20) cc_final: 0.6244 (pm20) outliers start: 36 outliers final: 21 residues processed: 127 average time/residue: 0.2377 time to fit residues: 45.6501 Evaluate side-chains 110 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 509 TYR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 737 VAL 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 1041 PHE Chi-restraints excluded: chain A residue 1081 LEU 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 C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 97 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 95 optimal weight: 30.0000 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1181 GLN A1194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.109113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088937 restraints weight = 50255.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.089885 restraints weight = 85095.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091638 restraints weight = 30512.204| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2724 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= 0.136 Angle : 0.625 16.507 18038 Z= 0.309 Chirality : 0.043 0.535 2072 Planarity : 0.004 0.074 2227 Dihedral : 7.843 56.533 2387 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.55 % Allowed : 15.24 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1621 helix: 0.77 (0.19), residues: 778 sheet: -1.18 (0.32), residues: 257 loop : -1.60 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.002 0.000 HIS A 611 PHE 0.015 0.001 PHE B 92 TYR 0.020 0.001 TYR A 927 ARG 0.011 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.01771 ( 3) link_NAG-ASN : angle 7.40074 ( 9) hydrogen bonds : bond 0.05049 ( 627) hydrogen bonds : angle 4.47466 ( 1814) SS BOND : bond 0.00948 ( 4) SS BOND : angle 1.93690 ( 8) covalent geometry : bond 0.00292 (13270) covalent geometry : angle 0.60176 (18021) *********************** 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 126 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7544 (m-30) cc_final: 0.7337 (m-30) REVERT: A 110 MET cc_start: 0.8426 (mmm) cc_final: 0.8095 (tpp) REVERT: A 351 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 434 THR cc_start: 0.7536 (m) cc_final: 0.7282 (t) REVERT: A 614 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5313 (mm) REVERT: A 615 MET cc_start: 0.6626 (mmm) cc_final: 0.5493 (tpt) REVERT: A 948 MET cc_start: 0.7541 (ttm) cc_final: 0.7311 (ttm) REVERT: A 1112 LEU cc_start: 0.6531 (tp) cc_final: 0.6278 (tp) REVERT: B 219 GLU cc_start: 0.6628 (pm20) cc_final: 0.5910 (pm20) outliers start: 33 outliers final: 23 residues processed: 119 average time/residue: 0.2374 time to fit residues: 43.4605 Evaluate side-chains 110 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 509 TYR 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 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 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 132 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 92 optimal weight: 0.0970 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 60 optimal weight: 0.0000 chunk 71 optimal weight: 0.9980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN A1181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.109602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086299 restraints weight = 44633.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088569 restraints weight = 71466.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089051 restraints weight = 26338.471| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 13277 Z= 0.135 Angle : 0.853 59.198 18038 Z= 0.453 Chirality : 0.042 0.308 2072 Planarity : 0.004 0.072 2227 Dihedral : 7.822 56.595 2387 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.33 % Allowed : 16.27 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1621 helix: 0.83 (0.19), residues: 778 sheet: -1.12 (0.32), residues: 259 loop : -1.54 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.002 0.000 HIS B 39 PHE 0.016 0.001 PHE B 92 TYR 0.020 0.001 TYR A 927 ARG 0.007 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.02636 ( 3) link_NAG-ASN : angle 9.70676 ( 9) hydrogen bonds : bond 0.05015 ( 627) hydrogen bonds : angle 4.44713 ( 1814) SS BOND : bond 0.00897 ( 4) SS BOND : angle 1.71278 ( 8) covalent geometry : bond 0.00275 (13270) covalent geometry : angle 0.82412 (18021) *********************** 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 121 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7566 (m-30) cc_final: 0.7343 (m-30) REVERT: A 110 MET cc_start: 0.8436 (mmm) cc_final: 0.8059 (tpp) REVERT: A 351 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 434 THR cc_start: 0.7642 (m) cc_final: 0.7402 (t) REVERT: A 614 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5289 (mm) REVERT: A 615 MET cc_start: 0.6789 (mmm) cc_final: 0.5679 (tpt) REVERT: A 948 MET cc_start: 0.7529 (ttm) cc_final: 0.7274 (ttm) REVERT: B 219 GLU cc_start: 0.6822 (pm20) cc_final: 0.6081 (pm20) outliers start: 30 outliers final: 25 residues processed: 115 average time/residue: 0.2444 time to fit residues: 42.8001 Evaluate side-chains 113 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 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 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 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 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 144 optimal weight: 0.0060 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 112 optimal weight: 0.0370 overall best weight: 0.9076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A1181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.109467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086514 restraints weight = 49780.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088717 restraints weight = 80019.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089575 restraints weight = 27573.295| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13277 Z= 0.134 Angle : 0.616 14.109 18038 Z= 0.310 Chirality : 0.048 1.096 2072 Planarity : 0.004 0.072 2227 Dihedral : 7.712 59.447 2387 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 2.92 % Allowed : 16.12 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1621 helix: 0.90 (0.19), residues: 778 sheet: -1.03 (0.32), residues: 260 loop : -1.42 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.002 0.000 HIS A 611 PHE 0.019 0.001 PHE A 266 TYR 0.021 0.001 TYR A 927 ARG 0.007 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.01969 ( 3) link_NAG-ASN : angle 4.91437 ( 9) hydrogen bonds : bond 0.04932 ( 627) hydrogen bonds : angle 4.38388 ( 1814) SS BOND : bond 0.00898 ( 4) SS BOND : angle 1.78633 ( 8) covalent geometry : bond 0.00279 (13270) covalent geometry : angle 0.60567 (18021) *********************** 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 127 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7633 (m-30) cc_final: 0.7416 (m-30) REVERT: A 351 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8503 (tp) REVERT: A 434 THR cc_start: 0.7647 (m) cc_final: 0.7393 (t) REVERT: A 614 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5316 (mm) REVERT: A 615 MET cc_start: 0.6828 (mmm) cc_final: 0.5852 (tpt) REVERT: A 948 MET cc_start: 0.7660 (ttm) cc_final: 0.7413 (ttm) REVERT: B 219 GLU cc_start: 0.6772 (pm20) cc_final: 0.6030 (pm20) outliers start: 38 outliers final: 26 residues processed: 121 average time/residue: 0.2489 time to fit residues: 45.9338 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 : 1.618 ------------------------------------------------------------------------------- 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 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 507 ASN 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 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 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 C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 71 optimal weight: 0.0870 chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.110321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089365 restraints weight = 47803.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090913 restraints weight = 82871.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.091569 restraints weight = 30385.614| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- 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 = 0.26 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13277 Z= 0.124 Angle : 0.627 17.528 18038 Z= 0.308 Chirality : 0.044 0.710 2072 Planarity : 0.004 0.071 2227 Dihedral : 7.455 55.865 2387 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 2.33 % Allowed : 17.43 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1621 helix: 1.03 (0.19), residues: 781 sheet: -0.92 (0.33), residues: 259 loop : -1.42 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.003 0.000 HIS A1154 PHE 0.016 0.001 PHE A 266 TYR 0.021 0.001 TYR A 927 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.02570 ( 3) link_NAG-ASN : angle 8.36183 ( 9) hydrogen bonds : bond 0.04717 ( 627) hydrogen bonds : angle 4.26937 ( 1814) SS BOND : bond 0.00908 ( 4) SS BOND : angle 1.65270 ( 8) covalent geometry : bond 0.00255 (13270) covalent geometry : angle 0.59790 (18021) *********************** 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 116 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6925 (mmp) cc_final: 0.6541 (mpp) REVERT: A 104 MET cc_start: 0.5883 (mtp) cc_final: 0.5215 (tpt) REVERT: A 351 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8457 (tp) REVERT: A 434 THR cc_start: 0.7554 (m) cc_final: 0.7312 (t) REVERT: A 614 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5328 (mm) REVERT: A 615 MET cc_start: 0.6461 (mmm) cc_final: 0.5504 (tpt) REVERT: A 948 MET cc_start: 0.7650 (ttm) cc_final: 0.7407 (ttm) REVERT: B 219 GLU cc_start: 0.6500 (pm20) cc_final: 0.6056 (mp0) outliers start: 30 outliers final: 24 residues processed: 113 average time/residue: 0.2164 time to fit residues: 38.3119 Evaluate side-chains 109 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 313 PHE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 377 PHE 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 498 GLU Chi-restraints excluded: chain A residue 507 ASN 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 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 C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 41 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.0970 chunk 161 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.109457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.084589 restraints weight = 38734.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084625 restraints weight = 64264.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.086218 restraints weight = 39684.830| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13277 Z= 0.133 Angle : 0.625 16.992 18038 Z= 0.310 Chirality : 0.043 0.504 2072 Planarity : 0.004 0.072 2227 Dihedral : 7.265 54.582 2387 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.97 % Allowed : 17.94 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1621 helix: 1.03 (0.19), residues: 784 sheet: -0.92 (0.33), residues: 260 loop : -1.38 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.004 0.001 HIS A 611 PHE 0.053 0.001 PHE A 334 TYR 0.021 0.001 TYR A 927 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 3) link_NAG-ASN : angle 7.15815 ( 9) hydrogen bonds : bond 0.04870 ( 627) hydrogen bonds : angle 4.28349 ( 1814) SS BOND : bond 0.00899 ( 4) SS BOND : angle 1.71562 ( 8) covalent geometry : bond 0.00289 (13270) covalent geometry : angle 0.60301 (18021) *********************** 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 115 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.7031 (mmp) cc_final: 0.6659 (mpp) REVERT: A 104 MET cc_start: 0.6039 (mtp) cc_final: 0.5262 (tpt) REVERT: A 156 ASN cc_start: 0.8213 (t0) cc_final: 0.7894 (t0) REVERT: A 203 PHE cc_start: 0.7998 (m-10) cc_final: 0.7767 (m-80) REVERT: A 351 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8471 (tp) REVERT: A 434 THR cc_start: 0.7730 (m) cc_final: 0.7453 (t) REVERT: A 615 MET cc_start: 0.6671 (mmm) cc_final: 0.5573 (tpt) REVERT: B 219 GLU cc_start: 0.6882 (pm20) cc_final: 0.6356 (mp0) outliers start: 25 outliers final: 21 residues processed: 112 average time/residue: 0.2443 time to fit residues: 42.7738 Evaluate side-chains 104 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 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 498 GLU 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 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 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 152 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 147 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 112 optimal weight: 0.0770 chunk 81 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.111217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.088041 restraints weight = 47375.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.089828 restraints weight = 77579.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091694 restraints weight = 29467.330| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13277 Z= 0.115 Angle : 0.608 15.926 18038 Z= 0.300 Chirality : 0.042 0.476 2072 Planarity : 0.004 0.070 2227 Dihedral : 7.026 54.686 2387 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.97 % Allowed : 17.94 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1621 helix: 1.13 (0.19), residues: 784 sheet: -0.82 (0.33), residues: 259 loop : -1.33 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.006 0.000 HIS A 611 PHE 0.023 0.001 PHE A 334 TYR 0.022 0.001 TYR A 509 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 3) link_NAG-ASN : angle 6.55956 ( 9) hydrogen bonds : bond 0.04556 ( 627) hydrogen bonds : angle 4.16427 ( 1814) SS BOND : bond 0.00801 ( 4) SS BOND : angle 1.52984 ( 8) covalent geometry : bond 0.00232 (13270) covalent geometry : angle 0.58986 (18021) ********************** 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 113 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6896 (mmp) cc_final: 0.6525 (mpp) REVERT: A 104 MET cc_start: 0.5610 (mtp) cc_final: 0.4972 (tpt) REVERT: A 156 ASN cc_start: 0.8156 (t0) cc_final: 0.7792 (t0) REVERT: A 434 THR cc_start: 0.7560 (m) cc_final: 0.7284 (t) REVERT: A 615 MET cc_start: 0.6488 (mmm) cc_final: 0.5314 (tpt) REVERT: B 219 GLU cc_start: 0.6591 (pm20) cc_final: 0.6260 (mp0) outliers start: 25 outliers final: 23 residues processed: 111 average time/residue: 0.2280 time to fit residues: 39.5036 Evaluate side-chains 106 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 313 PHE Chi-restraints excluded: chain A residue 377 PHE 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 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 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 C residue 18 VAL Chi-restraints excluded: chain C residue 72 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 148 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086618 restraints weight = 37955.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.088964 restraints weight = 54411.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.089059 restraints weight = 25701.235| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13277 Z= 0.120 Angle : 0.613 14.347 18038 Z= 0.303 Chirality : 0.042 0.432 2072 Planarity : 0.004 0.071 2227 Dihedral : 6.951 54.426 2387 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 17.94 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1621 helix: 1.18 (0.19), residues: 782 sheet: -0.78 (0.33), residues: 259 loop : -1.29 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.008 0.001 HIS A 611 PHE 0.026 0.001 PHE A 78 TYR 0.023 0.001 TYR A 927 ARG 0.006 0.000 ARG B 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 3) link_NAG-ASN : angle 5.76297 ( 9) hydrogen bonds : bond 0.04589 ( 627) hydrogen bonds : angle 4.18486 ( 1814) SS BOND : bond 0.00825 ( 4) SS BOND : angle 1.58547 ( 8) covalent geometry : bond 0.00252 (13270) covalent geometry : angle 0.59918 (18021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4848.55 seconds wall clock time: 84 minutes 38.31 seconds (5078.31 seconds total)