Starting phenix.real_space_refine on Sat Sep 12 01:45:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6fn1_4281/09_2026/6fn1_4281.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fn1_4281/09_2026/6fn1_4281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fn1_4281/09_2026/6fn1_4281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fn1_4281/09_2026/6fn1_4281.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6fn1_4281/09_2026/6fn1_4281.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6fn1_4281/09_2026/6fn1_4281.cif" model { file = "/net/cci-nas-00/data/ceres_data/6fn1_4281/09_2026/6fn1_4281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fn1_4281/09_2026/6fn1_4281.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 8174 2.51 5 N 2128 2.21 5 O 2383 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 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12739 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9186 Classifications: {'peptide': 1182} Link IDs: {'CIS': 4, 'PTRANS': 27, 'TRANS': 1150} 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: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 120 Unusual residues: {'NAG': 3, 'ZQU': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.99, per 1000 atoms: 0.23 Number of scatterers: 12739 At special positions: 0 Unit cell: (96.6, 93.24, 206.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 F 4 9.00 O 2383 8.00 N 2128 7.00 C 8174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A1203 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG ACYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG BCYS B 200 " distance=2.05 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 ACYS C 204 " distance=2.04 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG BCYS C 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 93 " " NAG A1303 " - " ASN A 98 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 686.1 milliseconds 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3002 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 50.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 43 through 62 removed outlier: 3.847A pdb=" N ARG A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 48 " --> pdb=" O TRP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 removed outlier: 3.839A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 removed outlier: 4.359A pdb=" N LEU A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 156 removed outlier: 3.655A pdb=" N TYR A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.651A pdb=" N ASP A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 186 removed outlier: 4.168A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 210 removed outlier: 4.134A pdb=" N PHE A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 237 removed outlier: 3.622A pdb=" N THR A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 222 - end of helix removed outlier: 4.030A pdb=" N SER A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 268 through 321 removed outlier: 4.096A pdb=" N GLU A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 347 removed outlier: 3.845A pdb=" N GLY A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 370 removed outlier: 4.165A pdb=" N ILE A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 440 removed outlier: 3.962A pdb=" N THR A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 508 through 514 removed outlier: 3.603A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 Processing helix chain 'A' and resid 563 through 576 removed outlier: 4.246A pdb=" N VAL A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 618 removed outlier: 3.827A pdb=" N LYS A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 629 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.776A pdb=" N ILE A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 738 removed outlier: 3.623A pdb=" N PHE A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Proline residue: A 725 - end of helix removed outlier: 3.649A pdb=" N SER A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 798 removed outlier: 3.756A pdb=" N THR A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 804 removed outlier: 3.721A pdb=" N PHE A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 820 Processing helix chain 'A' and resid 824 through 853 removed outlier: 3.818A pdb=" N THR A 828 " --> pdb=" O VAL A 824 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ARG A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 879 removed outlier: 3.588A pdb=" N THR A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Proline residue: A 865 - end of helix removed outlier: 3.741A pdb=" N ALA A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 902 removed outlier: 3.655A pdb=" N ALA A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 909 Processing helix chain 'A' and resid 911 through 965 Proline residue: A 926 - end of helix removed outlier: 3.896A pdb=" N HIS A 935 " --> pdb=" O MET A 931 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 994 Processing helix chain 'A' and resid 997 through 1011 Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 4.060A pdb=" N GLN A1080 " --> pdb=" O SER A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1104 through 1111 Processing helix chain 'A' and resid 1125 through 1132 Processing helix chain 'A' and resid 1140 through 1151 removed outlier: 3.560A pdb=" N ILE A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A1145 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 4.367A pdb=" N ARG A1191 " --> pdb=" O ARG A1187 " (cutoff:3.500A) 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 1273 removed outlier: 4.174A pdb=" N GLN A1273 " --> pdb=" O MET A1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.526A pdb=" N SER C 91 " --> pdb=" O PHE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing sheet with id=AA1, first strand: chain 'A' and resid 409 through 416 removed outlier: 6.955A pdb=" N LYS A 410 " --> pdb=" O HIS A 397 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS A 397 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 412 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 396 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP A 447 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 472 removed outlier: 6.252A pdb=" N GLY A 470 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ASP A 554 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 472 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 551 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE A 584 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 553 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU A 607 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP A 601 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1059 removed outlier: 6.728A pdb=" N GLN A1053 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A1040 " --> pdb=" O GLN A1053 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU A1055 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL A1039 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ALA A1090 " --> pdb=" O VAL A1039 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1113 through 1115 removed outlier: 6.225A pdb=" N GLY A1113 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASP A1199 " --> pdb=" O GLY A1113 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL A1115 " --> pdb=" O ASP A1199 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A1196 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A1229 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A1198 " --> pdb=" O ILE A1229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.712A pdb=" N SER B 68 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 54 removed outlier: 5.196A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 124 removed outlier: 5.865A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 removed outlier: 6.295A pdb=" N HIS B 204 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER B 209 " --> pdb=" O HIS B 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 4.926A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 111 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 4.926A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 133 Processing sheet with id=AB4, first strand: chain 'C' and resid 129 through 133 Processing sheet with id=AB5, first strand: chain 'C' and resid 160 through 163 738 hydrogen bonds defined for protein. 2107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 2067 1.31 - 1.45: 3723 1.45 - 1.59: 7139 1.59 - 1.74: 0 1.74 - 1.88: 85 Bond restraints: 13014 Sorted by residual: bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C7 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.514 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.514 -0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 13009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 17452 4.49 - 8.99: 175 8.99 - 13.48: 15 13.48 - 17.97: 2 17.97 - 22.47: 1 Bond angle restraints: 17645 Sorted by residual: angle pdb=" C SER A 237 " pdb=" N PHE A 238 " pdb=" CA PHE A 238 " ideal model delta sigma weight residual 121.70 135.87 -14.17 1.80e+00 3.09e-01 6.20e+01 angle pdb=" C ASN A 370 " pdb=" N LYS A 371 " pdb=" CA LYS A 371 " ideal model delta sigma weight residual 121.70 133.65 -11.95 1.80e+00 3.09e-01 4.41e+01 angle pdb=" CA LEU A 723 " pdb=" CB LEU A 723 " pdb=" CG LEU A 723 " ideal model delta sigma weight residual 116.30 138.77 -22.47 3.50e+00 8.16e-02 4.12e+01 angle pdb=" C SER B 94 " pdb=" N GLN B 95 " pdb=" CA GLN B 95 " ideal model delta sigma weight residual 121.70 132.11 -10.41 1.80e+00 3.09e-01 3.34e+01 angle pdb=" N VAL B 56 " pdb=" CA VAL B 56 " pdb=" C VAL B 56 " ideal model delta sigma weight residual 109.34 120.19 -10.85 2.08e+00 2.31e-01 2.72e+01 ... (remaining 17640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 7216 17.40 - 34.80: 436 34.80 - 52.20: 77 52.20 - 69.60: 15 69.60 - 87.00: 5 Dihedral angle restraints: 7749 sinusoidal: 3063 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 180.00 109.15 70.85 0 5.00e+00 4.00e-02 2.01e+02 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 -133.84 -46.16 0 5.00e+00 4.00e-02 8.52e+01 dihedral pdb=" CA ASN A 93 " pdb=" C ASN A 93 " pdb=" N ARG A 94 " pdb=" CA ARG A 94 " ideal model delta harmonic sigma weight residual -180.00 -135.22 -44.78 0 5.00e+00 4.00e-02 8.02e+01 ... (remaining 7746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 2013 0.289 - 0.578: 4 0.578 - 0.867: 0 0.867 - 1.156: 0 1.156 - 1.445: 1 Chirality restraints: 2018 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 98 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -0.95 -1.45 2.00e-01 2.50e+01 5.22e+01 chirality pdb=" CB ILE C 20 " pdb=" CA ILE C 20 " pdb=" CG1 ILE C 20 " pdb=" CG2 ILE C 20 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CB ILE A 91 " pdb=" CA ILE A 91 " pdb=" CG1 ILE A 91 " pdb=" CG2 ILE A 91 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2015 not shown) Planarity restraints: 2227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " 0.164 2.00e-02 2.50e+03 2.82e-01 9.92e+02 pdb=" CG ASN A 98 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.087 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " -0.497 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 7 " 0.029 2.00e-02 2.50e+03 5.84e-02 3.42e+01 pdb=" C SER B 7 " -0.101 2.00e-02 2.50e+03 pdb=" O SER B 7 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO B 8 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 7 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO B 8 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " 0.063 5.00e-02 4.00e+02 ... (remaining 2224 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 284 2.67 - 3.23: 12235 3.23 - 3.79: 19656 3.79 - 4.34: 25728 4.34 - 4.90: 43223 Nonbonded interactions: 101126 Sorted by model distance: nonbonded pdb=" O ASP A1162 " pdb=" OG1 THR A1166 " model vdw 2.115 3.040 nonbonded pdb=" OG SER A1125 " pdb=" OE1 GLU A1128 " model vdw 2.145 3.040 nonbonded pdb=" OE2 GLU A 525 " pdb=" NH1 ARG A 526 " model vdw 2.166 3.120 nonbonded pdb=" O LEU A 588 " pdb=" NH1 ARG A 592 " model vdw 2.213 3.120 nonbonded pdb=" NH1 ARG B 59 " pdb=" OD1 ASP B 65 " model vdw 2.228 3.120 ... (remaining 101121 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.009 0.134 13024 Z= 0.395 Angle : 1.272 44.932 17667 Z= 0.638 Chirality : 0.074 1.445 2018 Planarity : 0.008 0.126 2225 Dihedral : 11.742 86.996 4723 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.36 % Favored : 93.39 % Rotamer: Outliers : 0.58 % Allowed : 6.51 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.16), residues: 1621 helix: -2.87 (0.13), residues: 764 sheet: -1.63 (0.28), residues: 279 loop : -2.48 (0.22), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 587 TYR 0.063 0.004 TYR A 952 PHE 0.061 0.004 PHE A 958 TRP 0.055 0.004 TRP C 112 HIS 0.028 0.003 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00912 / 0.39 (13014) covalent geometry : angle 1.19748 / 0.62 (17645) SS BOND : bond 0.01334 / 0.83 ( 8) SS BOND : angle 3.21515 / 2.07 ( 16) hydrogen bonds : bond 0.14280 / 9.44 ( 710) hydrogen bonds : angle 9.23018 / 6.53 ( 2107) link_NAG-ASN : bond 0.02730 / 1.84 ( 2) link_NAG-ASN : angle 22.81709 / 18.06 ( 6) *********************** 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 228 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7629 (t160) cc_final: 0.7392 (t0) REVERT: A 94 ARG cc_start: 0.6522 (ptp90) cc_final: 0.5847 (mmm-85) REVERT: A 395 ASN cc_start: 0.7940 (t0) cc_final: 0.7706 (t0) REVERT: A 465 LEU cc_start: 0.7324 (tp) cc_final: 0.7083 (tp) REVERT: A 507 ASN cc_start: 0.7674 (t0) cc_final: 0.7408 (t0) REVERT: A 706 GLU cc_start: 0.7431 (pm20) cc_final: 0.7114 (pm20) REVERT: A 842 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5590 (mm) REVERT: A 869 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 886 LYS cc_start: 0.7175 (mttt) cc_final: 0.6847 (tptt) REVERT: A 931 MET cc_start: 0.7897 (mmp) cc_final: 0.7313 (mmm) REVERT: A 1118 GLU cc_start: 0.7633 (pp20) cc_final: 0.7103 (pm20) REVERT: A 1211 LYS cc_start: 0.7280 (pptt) cc_final: 0.6933 (pttm) REVERT: A 1218 ASP cc_start: 0.7453 (m-30) cc_final: 0.6988 (m-30) REVERT: B 153 LYS cc_start: 0.7734 (tptt) cc_final: 0.7350 (tptp) REVERT: C 67 LYS cc_start: 0.7953 (pttm) cc_final: 0.7472 (tmmt) REVERT: C 83 PHE cc_start: 0.7259 (t80) cc_final: 0.7056 (t80) REVERT: C 85 SER cc_start: 0.8280 (m) cc_final: 0.7867 (p) REVERT: C 200 GLN cc_start: 0.7894 (mt0) cc_final: 0.7613 (mt0) REVERT: C 216 ASP cc_start: 0.7644 (m-30) cc_final: 0.7428 (t70) REVERT: C 219 ILE cc_start: 0.6801 (pp) cc_final: 0.6538 (mp) outliers start: 6 outliers final: 1 residues processed: 228 average time/residue: 0.1217 time to fit residues: 39.3202 Evaluate side-chains 138 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 869 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 90 ASN A 142 GLN A 152 HIS A 420 GLN A 569 GLN A 586 HIS ** A 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 838 ASN A 935 HIS A 965 HIS ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 HIS B 18 GLN B 130 GLN C 180 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.149117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119147 restraints weight = 28162.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121373 restraints weight = 35214.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122928 restraints weight = 17152.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123153 restraints weight = 11868.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123637 restraints weight = 10597.100| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13024 Z= 0.179 Angle : 0.771 9.991 17667 Z= 0.403 Chirality : 0.047 0.237 2018 Planarity : 0.006 0.105 2225 Dihedral : 6.968 72.485 1831 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.44 % Favored : 94.38 % Rotamer: Outliers : 3.14 % Allowed : 11.92 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.19), residues: 1621 helix: -0.95 (0.17), residues: 779 sheet: -1.22 (0.29), residues: 274 loop : -2.10 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 194 TYR 0.017 0.002 TYR C 32 PHE 0.023 0.002 PHE C 50 TRP 0.025 0.002 TRP C 112 HIS 0.006 0.001 HIS A1194 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (13014) covalent geometry : angle 0.76603 / 0.40 (17645) SS BOND : bond 0.00882 / 0.49 ( 8) SS BOND : angle 1.78805 / 1.11 ( 16) hydrogen bonds : bond 0.05404 / 3.55 ( 710) hydrogen bonds : angle 6.12288 / 4.31 ( 2107) link_NAG-ASN : bond 0.00408 / 0.29 ( 2) link_NAG-ASN : angle 4.19723 / 2.85 ( 6) *********************** 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 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.488 Fit side-chains REVERT: A 73 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: A 94 ARG cc_start: 0.6515 (ptp90) cc_final: 0.5812 (mmm-85) REVERT: A 137 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7139 (mp) REVERT: A 391 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6961 (tp) REVERT: A 393 PHE cc_start: 0.8094 (m-10) cc_final: 0.7729 (m-10) REVERT: A 783 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8809 (tt) REVERT: A 869 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 890 GLU cc_start: 0.7757 (pt0) cc_final: 0.7256 (tm-30) REVERT: A 909 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7630 (pp) REVERT: A 931 MET cc_start: 0.6876 (mmp) cc_final: 0.6641 (mmm) REVERT: A 1251 LYS cc_start: 0.5581 (tptp) cc_final: 0.5323 (ttmt) REVERT: B 24 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7382 (mtp85) REVERT: B 196 ASN cc_start: 0.6391 (OUTLIER) cc_final: 0.6121 (t0) REVERT: C 85 SER cc_start: 0.7868 (m) cc_final: 0.7631 (p) REVERT: C 188 SER cc_start: 0.9220 (t) cc_final: 0.8918 (t) outliers start: 41 outliers final: 18 residues processed: 189 average time/residue: 0.1056 time to fit residues: 29.7113 Evaluate side-chains 146 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 190 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 113 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 105 ASN ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS A 611 HIS ** A1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118786 restraints weight = 24967.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120524 restraints weight = 28985.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121863 restraints weight = 17139.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122267 restraints weight = 11047.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122796 restraints weight = 10217.452| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13024 Z= 0.160 Angle : 0.708 10.122 17667 Z= 0.368 Chirality : 0.045 0.238 2018 Planarity : 0.005 0.101 2225 Dihedral : 6.460 69.659 1831 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.73 % Allowed : 12.50 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.20), residues: 1621 helix: -0.18 (0.18), residues: 791 sheet: -0.87 (0.30), residues: 279 loop : -1.92 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 194 TYR 0.016 0.002 TYR C 33 PHE 0.033 0.002 PHE A 769 TRP 0.020 0.001 TRP C 112 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (13014) covalent geometry : angle 0.70321 / 0.37 (17645) SS BOND : bond 0.00682 / 0.40 ( 8) SS BOND : angle 1.45153 / 0.91 ( 16) hydrogen bonds : bond 0.04737 / 3.10 ( 710) hydrogen bonds : angle 5.46815 / 3.85 ( 2107) link_NAG-ASN : bond 0.00222 / 0.15 ( 2) link_NAG-ASN : angle 3.75169 / 2.67 ( 6) *********************** 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 187 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.6471 (ptp90) cc_final: 0.5843 (mmm-85) REVERT: A 110 MET cc_start: 0.7558 (mmm) cc_final: 0.7308 (tpp) REVERT: A 137 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7098 (mp) REVERT: A 507 ASN cc_start: 0.8116 (t0) cc_final: 0.7860 (t0) REVERT: A 783 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8768 (tt) REVERT: A 890 GLU cc_start: 0.7856 (pt0) cc_final: 0.7310 (tm-30) REVERT: A 909 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7532 (pp) REVERT: A 931 MET cc_start: 0.6888 (mmp) cc_final: 0.6654 (mmm) REVERT: A 1008 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 24 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7462 (mtt90) REVERT: B 37 TYR cc_start: 0.7927 (m-80) cc_final: 0.6604 (m-80) REVERT: B 196 ASN cc_start: 0.6509 (OUTLIER) cc_final: 0.6209 (t0) REVERT: C 85 SER cc_start: 0.7661 (m) cc_final: 0.7366 (p) REVERT: C 188 SER cc_start: 0.9154 (t) cc_final: 0.8846 (t) outliers start: 50 outliers final: 25 residues processed: 181 average time/residue: 0.1035 time to fit residues: 28.4310 Evaluate side-chains 152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 126 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN B 95 GLN C 200 GLN C 208 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.145657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115320 restraints weight = 31306.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118365 restraints weight = 39486.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120087 restraints weight = 15755.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120298 restraints weight = 11386.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120791 restraints weight = 10088.084| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13024 Z= 0.211 Angle : 0.747 10.455 17667 Z= 0.385 Chirality : 0.047 0.275 2018 Planarity : 0.005 0.097 2225 Dihedral : 6.355 68.197 1829 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 4.02 % Allowed : 13.08 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.20), residues: 1621 helix: 0.05 (0.18), residues: 791 sheet: -0.66 (0.31), residues: 279 loop : -1.73 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1046 TYR 0.016 0.002 TYR C 33 PHE 0.032 0.002 PHE C 50 TRP 0.027 0.002 TRP B 102 HIS 0.006 0.001 HIS A 935 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (13014) covalent geometry : angle 0.74330 / 0.38 (17645) SS BOND : bond 0.00741 / 0.44 ( 8) SS BOND : angle 1.57518 / 1.02 ( 16) hydrogen bonds : bond 0.05073 / 3.33 ( 710) hydrogen bonds : angle 5.39837 / 3.81 ( 2107) link_NAG-ASN : bond 0.00134 / 0.10 ( 2) link_NAG-ASN : angle 3.58249 / 2.63 ( 6) *********************** 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 187 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.7592 (mmm) cc_final: 0.7160 (tpt) REVERT: A 467 GLU cc_start: 0.7756 (mp0) cc_final: 0.7478 (tt0) REVERT: A 507 ASN cc_start: 0.8168 (t0) cc_final: 0.7879 (t0) REVERT: A 511 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6661 (p90) REVERT: A 783 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8768 (tt) REVERT: A 883 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7694 (mm) REVERT: A 1008 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 1211 LYS cc_start: 0.8038 (pptt) cc_final: 0.7569 (pttm) REVERT: B 95 GLN cc_start: 0.8193 (pt0) cc_final: 0.7885 (pt0) REVERT: B 102 TRP cc_start: 0.9438 (OUTLIER) cc_final: 0.8154 (m100) REVERT: B 196 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.6312 (t0) REVERT: C 85 SER cc_start: 0.7646 (m) cc_final: 0.7337 (p) REVERT: C 188 SER cc_start: 0.9211 (t) cc_final: 0.8899 (t) outliers start: 54 outliers final: 30 residues processed: 179 average time/residue: 0.1037 time to fit residues: 27.6904 Evaluate side-chains 148 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain C residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 118 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 130 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN C 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118861 restraints weight = 35286.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122801 restraints weight = 42014.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123747 restraints weight = 15584.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124455 restraints weight = 11608.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124845 restraints weight = 9857.299| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13024 Z= 0.141 Angle : 0.679 9.851 17667 Z= 0.349 Chirality : 0.044 0.197 2018 Planarity : 0.005 0.097 2225 Dihedral : 6.111 67.253 1829 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.65 % Allowed : 14.04 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1621 helix: 0.41 (0.18), residues: 788 sheet: -0.46 (0.32), residues: 278 loop : -1.59 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.018 0.001 TYR A1132 PHE 0.017 0.001 PHE A 792 TRP 0.018 0.001 TRP B 102 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (13014) covalent geometry : angle 0.67523 / 0.35 (17645) SS BOND : bond 0.00611 / 0.36 ( 8) SS BOND : angle 1.41229 / 0.89 ( 16) hydrogen bonds : bond 0.04459 / 2.92 ( 710) hydrogen bonds : angle 5.08910 / 3.57 ( 2107) link_NAG-ASN : bond 0.00194 / 0.14 ( 2) link_NAG-ASN : angle 3.23200 / 2.32 ( 6) *********************** 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 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8288 (t70) cc_final: 0.8070 (t0) REVERT: A 110 MET cc_start: 0.7865 (mmm) cc_final: 0.7211 (tpt) REVERT: A 137 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6938 (mp) REVERT: A 507 ASN cc_start: 0.8146 (t0) cc_final: 0.7877 (t0) REVERT: A 511 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6736 (p90) REVERT: A 883 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7711 (mm) REVERT: A 1269 MET cc_start: -0.0032 (OUTLIER) cc_final: -0.0763 (mpp) REVERT: C 85 SER cc_start: 0.7496 (m) cc_final: 0.7152 (p) REVERT: C 188 SER cc_start: 0.9112 (t) cc_final: 0.8790 (t) outliers start: 49 outliers final: 28 residues processed: 171 average time/residue: 0.1086 time to fit residues: 27.6778 Evaluate side-chains 153 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 141 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 44 optimal weight: 0.0370 chunk 86 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.150037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120449 restraints weight = 38612.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123918 restraints weight = 48867.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125797 restraints weight = 16918.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126554 restraints weight = 11671.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126901 restraints weight = 9444.204| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13024 Z= 0.136 Angle : 0.668 15.560 17667 Z= 0.342 Chirality : 0.043 0.195 2018 Planarity : 0.005 0.095 2225 Dihedral : 5.971 66.665 1829 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.00 % Allowed : 15.42 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1621 helix: 0.63 (0.19), residues: 789 sheet: -0.31 (0.33), residues: 274 loop : -1.57 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.013 0.001 TYR C 33 PHE 0.024 0.001 PHE C 88 TRP 0.019 0.001 TRP B 102 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (13014) covalent geometry : angle 0.66537 / 0.34 (17645) SS BOND : bond 0.00655 / 0.40 ( 8) SS BOND : angle 1.45298 / 0.96 ( 16) hydrogen bonds : bond 0.04285 / 2.81 ( 710) hydrogen bonds : angle 4.93307 / 3.46 ( 2107) link_NAG-ASN : bond 0.00097 / 0.07 ( 2) link_NAG-ASN : angle 2.86116 / 2.08 ( 6) *********************** 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 168 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8251 (t70) cc_final: 0.8041 (t0) REVERT: A 94 ARG cc_start: 0.6500 (ptp90) cc_final: 0.6156 (mmm-85) REVERT: A 110 MET cc_start: 0.7839 (mmm) cc_final: 0.7156 (tpt) REVERT: A 137 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7018 (mp) REVERT: A 507 ASN cc_start: 0.8158 (t0) cc_final: 0.7857 (t0) REVERT: A 511 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6792 (p90) REVERT: A 883 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7688 (mm) REVERT: A 1269 MET cc_start: 0.0069 (OUTLIER) cc_final: -0.0725 (mpp) REVERT: B 95 GLN cc_start: 0.7494 (pt0) cc_final: 0.7182 (pp30) REVERT: B 102 TRP cc_start: 0.9326 (OUTLIER) cc_final: 0.8060 (m100) REVERT: C 85 SER cc_start: 0.7354 (m) cc_final: 0.7020 (p) REVERT: C 188 SER cc_start: 0.9110 (t) cc_final: 0.8783 (t) outliers start: 40 outliers final: 29 residues processed: 163 average time/residue: 0.0974 time to fit residues: 24.4973 Evaluate side-chains 152 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1164 TYR Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 62 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118948 restraints weight = 35017.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121465 restraints weight = 44676.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123686 restraints weight = 17857.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124064 restraints weight = 11827.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124537 restraints weight = 10251.921| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13024 Z= 0.152 Angle : 0.685 16.918 17667 Z= 0.349 Chirality : 0.044 0.205 2018 Planarity : 0.004 0.094 2225 Dihedral : 5.940 65.768 1829 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.65 % Allowed : 15.35 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1621 helix: 0.69 (0.18), residues: 790 sheet: -0.26 (0.33), residues: 274 loop : -1.52 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 114 TYR 0.014 0.001 TYR C 33 PHE 0.022 0.002 PHE C 50 TRP 0.022 0.001 TRP B 102 HIS 0.003 0.001 HIS A 965 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (13014) covalent geometry : angle 0.68195 / 0.35 (17645) SS BOND : bond 0.00670 / 0.41 ( 8) SS BOND : angle 1.46685 / 0.96 ( 16) hydrogen bonds : bond 0.04384 / 2.87 ( 710) hydrogen bonds : angle 4.89111 / 3.44 ( 2107) link_NAG-ASN : bond 0.00099 / 0.07 ( 2) link_NAG-ASN : angle 2.65744 / 1.98 ( 6) *********************** 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 167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.6363 (ptp90) cc_final: 0.6120 (mmm-85) REVERT: A 110 MET cc_start: 0.7887 (mmm) cc_final: 0.7239 (tpt) REVERT: A 137 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7015 (mp) REVERT: A 507 ASN cc_start: 0.8150 (t0) cc_final: 0.7859 (t0) REVERT: A 511 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6935 (p90) REVERT: A 883 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7717 (mm) REVERT: A 1029 MET cc_start: 0.5137 (tmm) cc_final: 0.4843 (tmm) REVERT: A 1118 GLU cc_start: 0.7112 (pm20) cc_final: 0.6630 (pm20) REVERT: A 1269 MET cc_start: -0.0045 (OUTLIER) cc_final: -0.0829 (mpp) REVERT: B 102 TRP cc_start: 0.9375 (OUTLIER) cc_final: 0.8095 (m100) REVERT: C 103 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8995 (p90) REVERT: C 188 SER cc_start: 0.9122 (t) cc_final: 0.8795 (t) outliers start: 49 outliers final: 37 residues processed: 158 average time/residue: 0.1007 time to fit residues: 24.2499 Evaluate side-chains 153 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1164 TYR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 0.0070 chunk 141 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.150084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120181 restraints weight = 33587.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122306 restraints weight = 41874.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124008 restraints weight = 19872.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124335 restraints weight = 12839.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124850 restraints weight = 11344.614| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13024 Z= 0.152 Angle : 0.679 16.988 17667 Z= 0.347 Chirality : 0.044 0.208 2018 Planarity : 0.004 0.093 2225 Dihedral : 5.897 65.223 1829 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.65 % Allowed : 15.86 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1621 helix: 0.78 (0.18), residues: 790 sheet: -0.15 (0.33), residues: 268 loop : -1.53 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 114 TYR 0.015 0.001 TYR C 33 PHE 0.021 0.002 PHE C 50 TRP 0.023 0.001 TRP B 102 HIS 0.003 0.001 HIS A 935 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (13014) covalent geometry : angle 0.67617 / 0.35 (17645) SS BOND : bond 0.00659 / 0.40 ( 8) SS BOND : angle 1.47120 / 0.96 ( 16) hydrogen bonds : bond 0.04355 / 2.86 ( 710) hydrogen bonds : angle 4.85824 / 3.41 ( 2107) link_NAG-ASN : bond 0.00171 / 0.12 ( 2) link_NAG-ASN : angle 2.47822 / 1.85 ( 6) *********************** 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 169 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7840 (mmm) cc_final: 0.7157 (tpt) REVERT: A 137 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7007 (mp) REVERT: A 167 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8168 (p) REVERT: A 507 ASN cc_start: 0.8139 (t0) cc_final: 0.7861 (t0) REVERT: A 511 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7130 (p90) REVERT: A 869 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8265 (mp) REVERT: A 883 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7711 (mm) REVERT: A 1008 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8642 (mp) REVERT: A 1029 MET cc_start: 0.4887 (tmm) cc_final: 0.4675 (tmm) REVERT: A 1118 GLU cc_start: 0.7101 (pm20) cc_final: 0.6581 (pm20) REVERT: A 1269 MET cc_start: -0.0096 (OUTLIER) cc_final: -0.0921 (mpp) REVERT: B 102 TRP cc_start: 0.9396 (OUTLIER) cc_final: 0.8141 (m100) outliers start: 49 outliers final: 36 residues processed: 160 average time/residue: 0.0992 time to fit residues: 24.3806 Evaluate side-chains 156 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1164 TYR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 0.0870 chunk 105 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.151694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121963 restraints weight = 32349.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124156 restraints weight = 40935.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126338 restraints weight = 18911.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126392 restraints weight = 12133.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126893 restraints weight = 10939.063| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13024 Z= 0.133 Angle : 0.658 15.143 17667 Z= 0.337 Chirality : 0.043 0.202 2018 Planarity : 0.004 0.093 2225 Dihedral : 5.791 64.425 1829 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.29 % Allowed : 16.15 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1621 helix: 0.95 (0.19), residues: 783 sheet: -0.12 (0.32), residues: 274 loop : -1.41 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 161 TYR 0.014 0.001 TYR C 33 PHE 0.016 0.001 PHE C 50 TRP 0.019 0.001 TRP B 102 HIS 0.002 0.001 HIS A 935 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13014) covalent geometry : angle 0.65573 / 0.34 (17645) SS BOND : bond 0.00624 / 0.37 ( 8) SS BOND : angle 1.35314 / 0.88 ( 16) hydrogen bonds : bond 0.04187 / 2.74 ( 710) hydrogen bonds : angle 4.77008 / 3.35 ( 2107) link_NAG-ASN : bond 0.00145 / 0.10 ( 2) link_NAG-ASN : angle 2.34941 / 1.74 ( 6) *********************** 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 163 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7828 (mmm) cc_final: 0.7160 (tpt) REVERT: A 449 MET cc_start: 0.7552 (tmm) cc_final: 0.7257 (tmm) REVERT: A 507 ASN cc_start: 0.8112 (t0) cc_final: 0.7884 (t0) REVERT: A 511 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7131 (p90) REVERT: A 883 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7691 (mm) REVERT: A 996 ASP cc_start: 0.7361 (t70) cc_final: 0.7112 (p0) REVERT: A 1008 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8625 (mp) REVERT: A 1118 GLU cc_start: 0.7064 (pm20) cc_final: 0.6520 (pm20) REVERT: A 1269 MET cc_start: -0.0058 (OUTLIER) cc_final: -0.0912 (mpp) REVERT: B 102 TRP cc_start: 0.9355 (OUTLIER) cc_final: 0.8089 (m100) outliers start: 44 outliers final: 33 residues processed: 155 average time/residue: 0.0956 time to fit residues: 22.6943 Evaluate side-chains 149 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 107 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 121 optimal weight: 0.1980 chunk 152 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** 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 = 0.3962 r_free = 0.3962 target = 0.152995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124638 restraints weight = 39405.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128137 restraints weight = 48723.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129990 restraints weight = 16707.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130386 restraints weight = 11918.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.130824 restraints weight = 9619.214| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13024 Z= 0.130 Angle : 0.663 13.625 17667 Z= 0.343 Chirality : 0.043 0.198 2018 Planarity : 0.004 0.090 2225 Dihedral : 5.715 63.649 1829 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.00 % Allowed : 16.74 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1621 helix: 1.05 (0.19), residues: 783 sheet: 0.05 (0.33), residues: 261 loop : -1.41 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 161 TYR 0.013 0.001 TYR C 33 PHE 0.016 0.001 PHE B 92 TRP 0.020 0.001 TRP B 102 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (13014) covalent geometry : angle 0.66160 / 0.34 (17645) SS BOND : bond 0.00579 / 0.34 ( 8) SS BOND : angle 1.20722 / 0.75 ( 16) hydrogen bonds : bond 0.04089 / 2.68 ( 710) hydrogen bonds : angle 4.73025 / 3.32 ( 2107) link_NAG-ASN : bond 0.00217 / 0.15 ( 2) link_NAG-ASN : angle 2.16453 / 1.55 ( 6) ********************** 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 155 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7588 (tmm) cc_final: 0.7273 (tmm) REVERT: A 507 ASN cc_start: 0.8051 (t0) cc_final: 0.7791 (t0) REVERT: A 511 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7079 (p90) REVERT: A 869 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 883 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7671 (mm) REVERT: A 952 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7420 (t80) REVERT: A 956 PHE cc_start: 0.7702 (m-10) cc_final: 0.7454 (m-80) REVERT: A 1008 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 1118 GLU cc_start: 0.7010 (pm20) cc_final: 0.6460 (pm20) REVERT: A 1269 MET cc_start: -0.0125 (OUTLIER) cc_final: -0.0922 (mpp) REVERT: B 102 TRP cc_start: 0.9319 (OUTLIER) cc_final: 0.8088 (m100) outliers start: 40 outliers final: 31 residues processed: 146 average time/residue: 0.1039 time to fit residues: 23.3526 Evaluate side-chains 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 769 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 952 TYR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1126 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1269 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 85 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 156 optimal weight: 0.0970 chunk 131 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** 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 = 0.3963 r_free = 0.3963 target = 0.153104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123204 restraints weight = 34366.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126211 restraints weight = 39358.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127633 restraints weight = 17011.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127928 restraints weight = 12006.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128439 restraints weight = 10563.109| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13024 Z= 0.128 Angle : 0.650 12.901 17667 Z= 0.335 Chirality : 0.043 0.197 2018 Planarity : 0.004 0.090 2225 Dihedral : 5.647 62.272 1829 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.07 % Allowed : 16.59 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.32 % Twisted Proline : 1.96 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1621 helix: 1.14 (0.19), residues: 783 sheet: 0.12 (0.32), residues: 268 loop : -1.43 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 161 TYR 0.012 0.001 TYR C 32 PHE 0.016 0.001 PHE B 92 TRP 0.020 0.001 TRP B 102 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (13014) covalent geometry : angle 0.64749 / 0.33 (17645) SS BOND : bond 0.00573 / 0.34 ( 8) SS BOND : angle 1.68291 / 1.07 ( 16) hydrogen bonds : bond 0.04028 / 2.63 ( 710) hydrogen bonds : angle 4.67758 / 3.29 ( 2107) link_NAG-ASN : bond 0.00183 / 0.13 ( 2) link_NAG-ASN : angle 2.12500 / 1.54 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.04 seconds wall clock time: 36 minutes 59.81 seconds (2219.81 seconds total)