Starting phenix.real_space_refine on Wed May 14 01:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2y_50166/05_2025/9f2y_50166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2y_50166/05_2025/9f2y_50166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f2y_50166/05_2025/9f2y_50166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2y_50166/05_2025/9f2y_50166.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2y_50166/05_2025/9f2y_50166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2y_50166/05_2025/9f2y_50166.cif" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7070 2.51 5 N 1792 2.21 5 O 2094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10994 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 833 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "B" Number of atoms: 10094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1239, 10094 Classifications: {'peptide': 1239} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 1201} Chain breaks: 6 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.70, per 1000 atoms: 0.88 Number of scatterers: 10994 At special positions: 0 Unit cell: (115.7, 123.5, 125.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2094 8.00 N 1792 7.00 C 7070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 454 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 701 " - " ASN A 491 " " NAG A 702 " - " ASN A 441 " " NAG C 1 " - " ASN A 516 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 31.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.776A pdb=" N THR B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.589A pdb=" N ASN B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.535A pdb=" N THR B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.818A pdb=" N ILE B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 300 removed outlier: 3.577A pdb=" N GLU B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 334 through 347 Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 398 through 405 removed outlier: 3.607A pdb=" N PHE B 401 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLY B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 404 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.610A pdb=" N ASN B 470 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 Processing helix chain 'B' and resid 549 through 556 removed outlier: 3.611A pdb=" N TYR B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.826A pdb=" N LEU B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'B' and resid 599 through 601 No H-bonds generated for 'chain 'B' and resid 599 through 601' Processing helix chain 'B' and resid 602 through 619 Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 648 through 660 Processing helix chain 'B' and resid 689 through 721 Processing helix chain 'B' and resid 721 through 753 removed outlier: 3.523A pdb=" N ILE B 725 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 753 " --> pdb=" O TYR B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 766 through 800 removed outlier: 3.660A pdb=" N ASN B 783 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 825 removed outlier: 3.811A pdb=" N GLY B 804 " --> pdb=" O MET B 800 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 807 " --> pdb=" O TYR B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 845 Processing helix chain 'B' and resid 859 through 876 removed outlier: 4.219A pdb=" N THR B 876 " --> pdb=" O ASN B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 removed outlier: 3.566A pdb=" N LEU B1087 " --> pdb=" O GLU B1083 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.406A pdb=" N LYS A 428 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN A 450 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A 430 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 444 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 465 " --> pdb=" O MET A 444 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 467 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 448 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 469 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN A 450 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.406A pdb=" N LYS A 428 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN A 450 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A 430 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 444 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 465 " --> pdb=" O MET A 444 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 467 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 448 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 469 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN A 450 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N TYR A 488 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 467 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LYS A 490 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A 469 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE A 489 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 434 through 436 removed outlier: 5.773A pdb=" N VAL A 435 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 454 " --> pdb=" O ASP A 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 439 through 440 removed outlier: 6.280A pdb=" N PHE A 459 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 499 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 495 Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 148 removed outlier: 4.133A pdb=" N TYR B 21 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 20 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 35 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS B 34 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 44 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 155 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU B 47 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 152 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AA8, first strand: chain 'B' and resid 213 through 214 removed outlier: 4.524A pdb=" N VAL B 373 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AB1, first strand: chain 'B' and resid 455 through 458 Processing sheet with id=AB2, first strand: chain 'B' and resid 479 through 481 Processing sheet with id=AB3, first strand: chain 'B' and resid 567 through 569 removed outlier: 6.240A pdb=" N ALA B 567 " --> pdb=" O VAL B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.579A pdb=" N LEU B 881 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE B1072 " --> pdb=" O LEU B 881 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N TYR B 883 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N LYS B1070 " --> pdb=" O TYR B 883 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.579A pdb=" N LEU B 881 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE B1072 " --> pdb=" O LEU B 881 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N TYR B 883 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N LYS B1070 " --> pdb=" O TYR B 883 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE B1069 " --> pdb=" O ARG B 948 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG B 948 " --> pdb=" O ILE B1069 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR B1071 " --> pdb=" O TRP B 946 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TRP B 946 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 897 through 900 removed outlier: 3.766A pdb=" N LYS B 897 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASN B1052 " --> pdb=" O MET B 968 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N MET B 968 " --> pdb=" O ASN B1052 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE B 964 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP B1058 " --> pdb=" O TYR B 962 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR B 962 " --> pdb=" O ASP B1058 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR B 963 " --> pdb=" O LEU B 978 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 978 " --> pdb=" O THR B 963 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP B 974 " --> pdb=" O CYS B 967 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1122 through 1126 removed outlier: 6.539A pdb=" N MET B1134 " --> pdb=" O LEU B1261 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B1261 " --> pdb=" O MET B1134 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA B1259 " --> pdb=" O LEU B1136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B1264 " --> pdb=" O PHE B1249 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B1220 " --> pdb=" O GLN B1240 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1122 through 1126 removed outlier: 6.539A pdb=" N MET B1134 " --> pdb=" O LEU B1261 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B1261 " --> pdb=" O MET B1134 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA B1259 " --> pdb=" O LEU B1136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B1264 " --> pdb=" O PHE B1249 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B1220 " --> pdb=" O GLN B1240 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR B1181 " --> pdb=" O LYS B1163 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B1163 " --> pdb=" O TYR B1181 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1260 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: 4.72 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3450 1.34 - 1.46: 1862 1.46 - 1.57: 5855 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 11231 Sorted by residual: bond pdb=" C GLU B 47 " pdb=" N ARG B 48 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.31e-02 5.83e+03 1.14e+01 bond pdb=" N VAL B 857 " pdb=" CA VAL B 857 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.03e+01 bond pdb=" N ILE B 874 " pdb=" CA ILE B 874 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.25e-02 6.40e+03 7.62e+00 bond pdb=" N ILE B 878 " pdb=" CA ILE B 878 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.08e+00 bond pdb=" N ILE B 870 " pdb=" CA ILE B 870 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.14e-02 7.69e+03 6.89e+00 ... (remaining 11226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14797 2.04 - 4.08: 348 4.08 - 6.11: 41 6.11 - 8.15: 9 8.15 - 10.19: 2 Bond angle restraints: 15197 Sorted by residual: angle pdb=" N ILE B1084 " pdb=" CA ILE B1084 " pdb=" C ILE B1084 " ideal model delta sigma weight residual 111.58 106.29 5.29 1.06e+00 8.90e-01 2.49e+01 angle pdb=" CA ASP B1086 " pdb=" CB ASP B1086 " pdb=" CG ASP B1086 " ideal model delta sigma weight residual 112.60 117.02 -4.42 1.00e+00 1.00e+00 1.95e+01 angle pdb=" N LEU B1087 " pdb=" CA LEU B1087 " pdb=" C LEU B1087 " ideal model delta sigma weight residual 111.28 107.15 4.13 1.09e+00 8.42e-01 1.43e+01 angle pdb=" N GLU B 617 " pdb=" CA GLU B 617 " pdb=" CB GLU B 617 " ideal model delta sigma weight residual 110.16 115.65 -5.49 1.48e+00 4.57e-01 1.38e+01 angle pdb=" N GLN B 790 " pdb=" CA GLN B 790 " pdb=" CB GLN B 790 " ideal model delta sigma weight residual 110.22 115.90 -5.68 1.54e+00 4.22e-01 1.36e+01 ... (remaining 15192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 6274 22.15 - 44.30: 411 44.30 - 66.44: 58 66.44 - 88.59: 17 88.59 - 110.74: 4 Dihedral angle restraints: 6764 sinusoidal: 2811 harmonic: 3953 Sorted by residual: dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 177.97 110.74 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" CA GLN B 991 " pdb=" C GLN B 991 " pdb=" N GLU B 992 " pdb=" CA GLU B 992 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -61.25 108.87 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 6761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.013: 1687 1.013 - 2.026: 0 2.026 - 3.039: 0 3.039 - 4.052: 0 4.052 - 5.065: 1 Chirality restraints: 1688 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 441 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 2.66 -5.06 2.00e-01 2.50e+01 6.41e+02 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB ILE B 22 " pdb=" CA ILE B 22 " pdb=" CG1 ILE B 22 " pdb=" CG2 ILE B 22 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 1685 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.183 2.00e-02 2.50e+03 1.52e-01 2.87e+02 pdb=" C7 NAG A 701 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.133 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.247 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 441 " -0.040 2.00e-02 2.50e+03 9.57e-02 1.15e+02 pdb=" CG ASN A 441 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 441 " 0.097 2.00e-02 2.50e+03 pdb=" ND2 ASN A 441 " -0.146 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 702 " -0.099 2.00e-02 2.50e+03 8.26e-02 8.53e+01 pdb=" C7 NAG A 702 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG A 702 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG A 702 " 0.133 2.00e-02 2.50e+03 pdb=" O7 NAG A 702 " 0.013 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 219 2.67 - 3.23: 11283 3.23 - 3.78: 17188 3.78 - 4.34: 22869 4.34 - 4.90: 36668 Nonbonded interactions: 88227 Sorted by model distance: nonbonded pdb=" OG1 THR B 755 " pdb=" OE1 GLU B 758 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASN B 971 " pdb=" NE2 GLN B 988 " model vdw 2.139 3.120 nonbonded pdb=" O THR B 691 " pdb=" OG1 THR B 694 " model vdw 2.172 3.040 nonbonded pdb=" O ARG B1140 " pdb=" OG SER B1153 " model vdw 2.215 3.040 nonbonded pdb=" O ASN B 248 " pdb=" OH TYR B 543 " model vdw 2.216 3.040 ... (remaining 88222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 20.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 31.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 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 : 0.005 0.278 11237 Z= 0.259 Angle : 0.765 21.655 15214 Z= 0.428 Chirality : 0.134 5.065 1688 Planarity : 0.007 0.199 1941 Dihedral : 14.947 110.737 4213 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 0.16 % Allowed : 2.62 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1320 helix: 1.22 (0.27), residues: 369 sheet: 0.23 (0.43), residues: 140 loop : -1.33 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 974 HIS 0.005 0.001 HIS B 561 PHE 0.014 0.001 PHE B 652 TYR 0.021 0.002 TYR B 822 ARG 0.006 0.001 ARG B1192 Details of bonding type rmsd link_NAG-ASN : bond 0.17308 ( 3) link_NAG-ASN : angle 10.57647 ( 9) link_BETA1-4 : bond 0.00836 ( 2) link_BETA1-4 : angle 1.84552 ( 6) hydrogen bonds : bond 0.14633 ( 432) hydrogen bonds : angle 6.51497 ( 1260) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.18551 ( 2) covalent geometry : bond 0.00384 (11231) covalent geometry : angle 0.71996 (15197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8006 (mmtm) REVERT: A 448 ILE cc_start: 0.8950 (pt) cc_final: 0.8608 (mm) REVERT: A 470 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8610 (mp0) REVERT: A 500 TYR cc_start: 0.9050 (t80) cc_final: 0.8261 (t80) REVERT: A 501 ASN cc_start: 0.8612 (t0) cc_final: 0.8253 (t0) REVERT: A 511 ASN cc_start: 0.8063 (m-40) cc_final: 0.7802 (t0) REVERT: A 515 ILE cc_start: 0.9255 (mm) cc_final: 0.8975 (mm) REVERT: B 78 LEU cc_start: 0.8873 (tt) cc_final: 0.8494 (mt) REVERT: B 83 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7990 (mt-10) REVERT: B 96 GLU cc_start: 0.8096 (pp20) cc_final: 0.7622 (tp30) REVERT: B 106 MET cc_start: 0.8987 (mtm) cc_final: 0.8743 (mtm) REVERT: B 162 GLN cc_start: 0.8299 (tt0) cc_final: 0.7809 (tm-30) REVERT: B 212 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8666 (mtmm) REVERT: B 345 LEU cc_start: 0.8959 (mt) cc_final: 0.8700 (mt) REVERT: B 355 VAL cc_start: 0.8952 (t) cc_final: 0.8290 (t) REVERT: B 370 ASP cc_start: 0.8923 (m-30) cc_final: 0.8604 (m-30) REVERT: B 392 LEU cc_start: 0.8343 (tp) cc_final: 0.8095 (mt) REVERT: B 499 ILE cc_start: 0.9173 (mp) cc_final: 0.8491 (mt) REVERT: B 502 TYR cc_start: 0.8794 (m-10) cc_final: 0.8593 (m-80) REVERT: B 602 MET cc_start: 0.6453 (tpt) cc_final: 0.5825 (tpp) REVERT: B 651 ASP cc_start: 0.7327 (t0) cc_final: 0.6952 (t0) REVERT: B 714 VAL cc_start: 0.9615 (t) cc_final: 0.9390 (p) REVERT: B 741 GLU cc_start: 0.8438 (tp30) cc_final: 0.8139 (tp30) REVERT: B 1004 MET cc_start: 0.8445 (mpp) cc_final: 0.7999 (mpp) REVERT: B 1035 LEU cc_start: 0.8691 (tp) cc_final: 0.8368 (tp) REVERT: B 1044 LEU cc_start: 0.8370 (mm) cc_final: 0.7602 (tp) REVERT: B 1135 TYR cc_start: 0.7834 (p90) cc_final: 0.7586 (p90) REVERT: B 1165 TYR cc_start: 0.8061 (t80) cc_final: 0.7851 (t80) outliers start: 2 outliers final: 1 residues processed: 297 average time/residue: 0.2556 time to fit residues: 105.2436 Evaluate side-chains 178 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 0.0270 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 470 ASN B 501 GLN B 557 GLN B 697 ASN B 753 GLN B 778 ASN B 940 ASN B1032 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.109971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.093806 restraints weight = 42946.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.096140 restraints weight = 28032.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.097217 restraints weight = 20781.329| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11237 Z= 0.139 Angle : 0.682 20.722 15214 Z= 0.348 Chirality : 0.055 1.152 1688 Planarity : 0.004 0.056 1941 Dihedral : 7.518 69.989 1549 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.41 % Allowed : 4.43 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1320 helix: 1.42 (0.27), residues: 374 sheet: -0.35 (0.37), residues: 178 loop : -1.16 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 717 HIS 0.005 0.001 HIS B1048 PHE 0.022 0.001 PHE A 430 TYR 0.017 0.001 TYR B 869 ARG 0.006 0.001 ARG B 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 3) link_NAG-ASN : angle 8.46867 ( 9) link_BETA1-4 : bond 0.00793 ( 2) link_BETA1-4 : angle 2.92054 ( 6) hydrogen bonds : bond 0.04694 ( 432) hydrogen bonds : angle 5.24510 ( 1260) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.61933 ( 2) covalent geometry : bond 0.00294 (11231) covalent geometry : angle 0.64789 (15197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 223 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 TYR cc_start: 0.8996 (t80) cc_final: 0.8444 (t80) REVERT: B 50 THR cc_start: 0.8512 (p) cc_final: 0.7514 (t) REVERT: B 78 LEU cc_start: 0.8976 (tt) cc_final: 0.8746 (mt) REVERT: B 212 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8655 (mtmm) REVERT: B 351 GLU cc_start: 0.6913 (pp20) cc_final: 0.6435 (pp20) REVERT: B 362 ASN cc_start: 0.8234 (p0) cc_final: 0.8020 (p0) REVERT: B 383 ASN cc_start: 0.7463 (m110) cc_final: 0.7165 (t0) REVERT: B 602 MET cc_start: 0.6161 (tpt) cc_final: 0.5486 (tpp) REVERT: B 697 ASN cc_start: 0.5857 (OUTLIER) cc_final: 0.5479 (m-40) REVERT: B 714 VAL cc_start: 0.9501 (t) cc_final: 0.9203 (p) REVERT: B 750 GLN cc_start: 0.8609 (mm110) cc_final: 0.8402 (mm-40) REVERT: B 1004 MET cc_start: 0.8712 (mpp) cc_final: 0.8427 (mpp) REVERT: B 1011 ILE cc_start: 0.8783 (tt) cc_final: 0.8453 (pt) outliers start: 5 outliers final: 1 residues processed: 226 average time/residue: 0.2124 time to fit residues: 70.2862 Evaluate side-chains 160 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 230 HIS B 238 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.104015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087183 restraints weight = 43861.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.088679 restraints weight = 29286.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.090655 restraints weight = 22750.840| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11237 Z= 0.258 Angle : 0.769 20.610 15214 Z= 0.404 Chirality : 0.056 1.092 1688 Planarity : 0.005 0.063 1941 Dihedral : 6.838 57.269 1549 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.16 % Allowed : 5.82 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1320 helix: 1.00 (0.26), residues: 370 sheet: -0.52 (0.35), residues: 195 loop : -1.36 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 43 HIS 0.007 0.002 HIS B 561 PHE 0.028 0.002 PHE B 652 TYR 0.028 0.002 TYR B 754 ARG 0.004 0.001 ARG B1034 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 3) link_NAG-ASN : angle 8.02079 ( 9) link_BETA1-4 : bond 0.00591 ( 2) link_BETA1-4 : angle 3.22245 ( 6) hydrogen bonds : bond 0.05034 ( 432) hydrogen bonds : angle 5.51325 ( 1260) SS BOND : bond 0.00269 ( 1) SS BOND : angle 0.65485 ( 2) covalent geometry : bond 0.00559 (11231) covalent geometry : angle 0.74143 (15197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASN cc_start: 0.6206 (t0) cc_final: 0.5866 (t0) REVERT: A 482 VAL cc_start: 0.8698 (m) cc_final: 0.8074 (m) REVERT: A 500 TYR cc_start: 0.8826 (t80) cc_final: 0.8262 (t80) REVERT: A 520 LEU cc_start: 0.9037 (mt) cc_final: 0.8815 (mt) REVERT: B 212 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8702 (mtmm) REVERT: B 292 ASP cc_start: 0.8667 (t0) cc_final: 0.8406 (t0) REVERT: B 602 MET cc_start: 0.5990 (tpt) cc_final: 0.5513 (mmm) REVERT: B 648 TYR cc_start: 0.7167 (t80) cc_final: 0.6918 (m-80) REVERT: B 763 ASN cc_start: 0.8115 (p0) cc_final: 0.7727 (p0) REVERT: B 795 TYR cc_start: 0.7659 (t80) cc_final: 0.7273 (t80) REVERT: B 1011 ILE cc_start: 0.9120 (tt) cc_final: 0.8786 (pt) REVERT: B 1044 LEU cc_start: 0.8271 (mm) cc_final: 0.7565 (tp) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.2274 time to fit residues: 64.6253 Evaluate side-chains 142 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 739 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.104929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088121 restraints weight = 42981.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089697 restraints weight = 29197.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091108 restraints weight = 22456.067| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11237 Z= 0.160 Angle : 0.649 18.381 15214 Z= 0.344 Chirality : 0.051 0.850 1688 Planarity : 0.004 0.061 1941 Dihedral : 6.281 58.052 1549 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1320 helix: 1.28 (0.27), residues: 370 sheet: -0.47 (0.34), residues: 202 loop : -1.37 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 974 HIS 0.005 0.001 HIS B 223 PHE 0.017 0.001 PHE B 652 TYR 0.016 0.002 TYR B 894 ARG 0.006 0.001 ARG B 827 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 3) link_NAG-ASN : angle 7.15654 ( 9) link_BETA1-4 : bond 0.00307 ( 2) link_BETA1-4 : angle 2.73095 ( 6) hydrogen bonds : bond 0.04304 ( 432) hydrogen bonds : angle 5.16804 ( 1260) SS BOND : bond 0.00386 ( 1) SS BOND : angle 0.93631 ( 2) covalent geometry : bond 0.00351 (11231) covalent geometry : angle 0.62274 (15197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.1653 (mpp) cc_final: 0.1419 (mpp) REVERT: A 448 ILE cc_start: 0.8427 (mm) cc_final: 0.7946 (mp) REVERT: A 482 VAL cc_start: 0.8624 (m) cc_final: 0.7840 (m) REVERT: A 500 TYR cc_start: 0.8942 (t80) cc_final: 0.8577 (t80) REVERT: A 515 ILE cc_start: 0.9391 (mp) cc_final: 0.8438 (mp) REVERT: B 78 LEU cc_start: 0.8874 (tp) cc_final: 0.8514 (tp) REVERT: B 212 LYS cc_start: 0.8965 (mmtm) cc_final: 0.8709 (mtmm) REVERT: B 292 ASP cc_start: 0.8685 (t0) cc_final: 0.8394 (t0) REVERT: B 351 GLU cc_start: 0.7006 (pp20) cc_final: 0.6354 (pp20) REVERT: B 362 ASN cc_start: 0.8561 (p0) cc_final: 0.8279 (p0) REVERT: B 383 ASN cc_start: 0.7838 (m-40) cc_final: 0.7357 (t0) REVERT: B 388 ASP cc_start: 0.8167 (t0) cc_final: 0.7865 (t0) REVERT: B 602 MET cc_start: 0.6110 (tpt) cc_final: 0.5678 (mmm) REVERT: B 648 TYR cc_start: 0.7262 (t80) cc_final: 0.6939 (m-80) REVERT: B 763 ASN cc_start: 0.8089 (p0) cc_final: 0.7723 (p0) REVERT: B 775 GLU cc_start: 0.8773 (mp0) cc_final: 0.8558 (tp30) REVERT: B 781 MET cc_start: 0.8915 (mmm) cc_final: 0.8671 (mmm) REVERT: B 1004 MET cc_start: 0.9026 (mpp) cc_final: 0.8623 (mmt) REVERT: B 1011 ILE cc_start: 0.9127 (tt) cc_final: 0.8819 (pt) REVERT: B 1044 LEU cc_start: 0.8300 (mm) cc_final: 0.7589 (tp) REVERT: B 1113 MET cc_start: 0.8067 (tpt) cc_final: 0.6417 (tpt) REVERT: B 1193 LEU cc_start: 0.7629 (mm) cc_final: 0.7406 (mm) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2015 time to fit residues: 58.9122 Evaluate side-chains 145 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 4 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 739 GLN B1147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.102210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.085388 restraints weight = 42945.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087738 restraints weight = 29607.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.088545 restraints weight = 22310.780| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11237 Z= 0.192 Angle : 0.669 17.688 15214 Z= 0.356 Chirality : 0.051 0.808 1688 Planarity : 0.004 0.065 1941 Dihedral : 5.888 57.780 1549 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1320 helix: 1.06 (0.27), residues: 367 sheet: -0.15 (0.38), residues: 173 loop : -1.35 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 43 HIS 0.006 0.001 HIS B 223 PHE 0.018 0.002 PHE B1284 TYR 0.023 0.002 TYR B 684 ARG 0.006 0.001 ARG B 827 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 3) link_NAG-ASN : angle 6.93775 ( 9) link_BETA1-4 : bond 0.00114 ( 2) link_BETA1-4 : angle 2.57527 ( 6) hydrogen bonds : bond 0.04287 ( 432) hydrogen bonds : angle 5.11917 ( 1260) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.57735 ( 2) covalent geometry : bond 0.00420 (11231) covalent geometry : angle 0.64565 (15197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 HIS cc_start: 0.8161 (t70) cc_final: 0.7743 (t-90) REVERT: A 482 VAL cc_start: 0.8677 (m) cc_final: 0.7950 (m) REVERT: A 500 TYR cc_start: 0.8843 (t80) cc_final: 0.8180 (t80) REVERT: B 78 LEU cc_start: 0.8943 (tp) cc_final: 0.8688 (tp) REVERT: B 212 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8664 (mtmm) REVERT: B 292 ASP cc_start: 0.8700 (t0) cc_final: 0.8426 (t0) REVERT: B 332 SER cc_start: 0.8634 (m) cc_final: 0.8351 (t) REVERT: B 362 ASN cc_start: 0.8683 (p0) cc_final: 0.8449 (p0) REVERT: B 388 ASP cc_start: 0.8204 (t0) cc_final: 0.7750 (t0) REVERT: B 602 MET cc_start: 0.6242 (tpt) cc_final: 0.6007 (mmm) REVERT: B 648 TYR cc_start: 0.7448 (t80) cc_final: 0.7020 (m-80) REVERT: B 763 ASN cc_start: 0.8166 (p0) cc_final: 0.7792 (p0) REVERT: B 775 GLU cc_start: 0.8793 (mp0) cc_final: 0.8502 (tp30) REVERT: B 968 MET cc_start: 0.8370 (tmm) cc_final: 0.7931 (tmm) REVERT: B 1004 MET cc_start: 0.9149 (mpp) cc_final: 0.8805 (mmt) REVERT: B 1011 ILE cc_start: 0.9207 (tt) cc_final: 0.8899 (pt) REVERT: B 1044 LEU cc_start: 0.8353 (mm) cc_final: 0.7661 (tp) REVERT: B 1113 MET cc_start: 0.8070 (tpt) cc_final: 0.7285 (tpp) REVERT: B 1193 LEU cc_start: 0.7731 (mm) cc_final: 0.7499 (mm) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2119 time to fit residues: 58.0958 Evaluate side-chains 146 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.0570 chunk 1 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.104494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088127 restraints weight = 43533.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089800 restraints weight = 29099.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.091862 restraints weight = 21848.666| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11237 Z= 0.131 Angle : 0.616 16.624 15214 Z= 0.327 Chirality : 0.049 0.706 1688 Planarity : 0.004 0.065 1941 Dihedral : 5.695 54.191 1549 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1320 helix: 1.29 (0.27), residues: 368 sheet: -0.30 (0.39), residues: 158 loop : -1.22 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 974 HIS 0.004 0.001 HIS B 561 PHE 0.015 0.001 PHE B 866 TYR 0.019 0.001 TYR B 754 ARG 0.010 0.000 ARG B 893 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 3) link_NAG-ASN : angle 6.48235 ( 9) link_BETA1-4 : bond 0.00271 ( 2) link_BETA1-4 : angle 2.04012 ( 6) hydrogen bonds : bond 0.03871 ( 432) hydrogen bonds : angle 5.02433 ( 1260) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.70701 ( 2) covalent geometry : bond 0.00289 (11231) covalent geometry : angle 0.59473 (15197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 HIS cc_start: 0.8171 (t70) cc_final: 0.7702 (t-90) REVERT: A 482 VAL cc_start: 0.8658 (m) cc_final: 0.8448 (m) REVERT: A 500 TYR cc_start: 0.8771 (t80) cc_final: 0.8097 (t80) REVERT: B 78 LEU cc_start: 0.8906 (tp) cc_final: 0.8648 (tp) REVERT: B 212 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8636 (mtmm) REVERT: B 292 ASP cc_start: 0.8629 (t0) cc_final: 0.8370 (t0) REVERT: B 332 SER cc_start: 0.8678 (m) cc_final: 0.8389 (t) REVERT: B 388 ASP cc_start: 0.8150 (t0) cc_final: 0.7708 (t0) REVERT: B 602 MET cc_start: 0.6191 (tpt) cc_final: 0.5781 (tpp) REVERT: B 648 TYR cc_start: 0.7463 (t80) cc_final: 0.7094 (m-80) REVERT: B 665 LEU cc_start: 0.9154 (mm) cc_final: 0.8859 (mt) REVERT: B 763 ASN cc_start: 0.8084 (p0) cc_final: 0.7745 (p0) REVERT: B 821 LYS cc_start: 0.6333 (mptt) cc_final: 0.5936 (mmmm) REVERT: B 968 MET cc_start: 0.8331 (tmm) cc_final: 0.8086 (tmm) REVERT: B 1004 MET cc_start: 0.9136 (mpp) cc_final: 0.8701 (mmt) REVERT: B 1011 ILE cc_start: 0.9155 (tt) cc_final: 0.8878 (pt) REVERT: B 1044 LEU cc_start: 0.8242 (mm) cc_final: 0.7572 (tp) REVERT: B 1113 MET cc_start: 0.7782 (tpp) cc_final: 0.7478 (tpp) REVERT: B 1193 LEU cc_start: 0.7778 (mm) cc_final: 0.7561 (mm) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2485 time to fit residues: 69.9005 Evaluate side-chains 143 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 113 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 693 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.084370 restraints weight = 43773.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086219 restraints weight = 30675.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.087850 restraints weight = 22668.363| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11237 Z= 0.216 Angle : 0.688 17.088 15214 Z= 0.367 Chirality : 0.050 0.728 1688 Planarity : 0.004 0.069 1941 Dihedral : 5.809 50.981 1549 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1320 helix: 1.01 (0.27), residues: 368 sheet: -0.32 (0.38), residues: 173 loop : -1.35 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 43 HIS 0.005 0.001 HIS B 223 PHE 0.017 0.002 PHE B 537 TYR 0.020 0.002 TYR B 822 ARG 0.003 0.001 ARG B1065 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 3) link_NAG-ASN : angle 6.61212 ( 9) link_BETA1-4 : bond 0.00287 ( 2) link_BETA1-4 : angle 2.00683 ( 6) hydrogen bonds : bond 0.04470 ( 432) hydrogen bonds : angle 5.32431 ( 1260) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.36781 ( 2) covalent geometry : bond 0.00473 (11231) covalent geometry : angle 0.66836 (15197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 HIS cc_start: 0.8273 (t70) cc_final: 0.7905 (t-90) REVERT: A 482 VAL cc_start: 0.8815 (m) cc_final: 0.8174 (m) REVERT: A 500 TYR cc_start: 0.8739 (t80) cc_final: 0.8023 (t80) REVERT: B 292 ASP cc_start: 0.8739 (t0) cc_final: 0.8455 (t0) REVERT: B 332 SER cc_start: 0.8701 (m) cc_final: 0.8457 (t) REVERT: B 351 GLU cc_start: 0.7220 (pp20) cc_final: 0.6491 (pp20) REVERT: B 388 ASP cc_start: 0.8240 (t0) cc_final: 0.7711 (t0) REVERT: B 602 MET cc_start: 0.6256 (tpt) cc_final: 0.5880 (tpp) REVERT: B 648 TYR cc_start: 0.7586 (t80) cc_final: 0.7127 (m-80) REVERT: B 665 LEU cc_start: 0.9194 (mm) cc_final: 0.8895 (mt) REVERT: B 763 ASN cc_start: 0.8160 (p0) cc_final: 0.7804 (p0) REVERT: B 775 GLU cc_start: 0.8903 (mp0) cc_final: 0.8496 (mp0) REVERT: B 821 LYS cc_start: 0.6706 (mptt) cc_final: 0.6172 (mmmm) REVERT: B 1004 MET cc_start: 0.9096 (mpp) cc_final: 0.8767 (mmt) REVERT: B 1011 ILE cc_start: 0.9275 (tt) cc_final: 0.8981 (pt) REVERT: B 1044 LEU cc_start: 0.8339 (mm) cc_final: 0.7693 (tp) REVERT: B 1130 ILE cc_start: 0.8190 (mp) cc_final: 0.7974 (mp) REVERT: B 1135 TYR cc_start: 0.7447 (p90) cc_final: 0.6229 (p90) REVERT: B 1193 LEU cc_start: 0.7737 (mm) cc_final: 0.7531 (mm) REVERT: B 1283 GLU cc_start: 0.8355 (tp30) cc_final: 0.8149 (tm-30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2335 time to fit residues: 60.5766 Evaluate side-chains 133 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 765 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086362 restraints weight = 43336.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087624 restraints weight = 31267.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089868 restraints weight = 23002.317| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11237 Z= 0.147 Angle : 0.631 15.961 15214 Z= 0.333 Chirality : 0.049 0.684 1688 Planarity : 0.004 0.069 1941 Dihedral : 5.697 52.633 1549 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1320 helix: 1.08 (0.27), residues: 368 sheet: -0.38 (0.38), residues: 168 loop : -1.24 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 974 HIS 0.004 0.001 HIS B 223 PHE 0.015 0.001 PHE B 851 TYR 0.017 0.001 TYR B 754 ARG 0.002 0.000 ARG B 827 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 3) link_NAG-ASN : angle 6.16507 ( 9) link_BETA1-4 : bond 0.00353 ( 2) link_BETA1-4 : angle 1.68167 ( 6) hydrogen bonds : bond 0.03989 ( 432) hydrogen bonds : angle 5.17786 ( 1260) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.59256 ( 2) covalent geometry : bond 0.00326 (11231) covalent geometry : angle 0.61239 (15197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 HIS cc_start: 0.8224 (t70) cc_final: 0.7896 (t-90) REVERT: A 481 ASP cc_start: 0.7663 (m-30) cc_final: 0.6871 (t0) REVERT: A 482 VAL cc_start: 0.8685 (m) cc_final: 0.8014 (m) REVERT: A 500 TYR cc_start: 0.8728 (t80) cc_final: 0.8071 (t80) REVERT: B 292 ASP cc_start: 0.8673 (t0) cc_final: 0.8432 (t0) REVERT: B 313 MET cc_start: 0.6389 (mmp) cc_final: 0.6176 (mmp) REVERT: B 351 GLU cc_start: 0.7167 (pp20) cc_final: 0.6530 (pp20) REVERT: B 388 ASP cc_start: 0.8137 (t0) cc_final: 0.7659 (t0) REVERT: B 602 MET cc_start: 0.6203 (tpt) cc_final: 0.5849 (tpp) REVERT: B 648 TYR cc_start: 0.7601 (t80) cc_final: 0.7171 (m-80) REVERT: B 665 LEU cc_start: 0.9205 (mm) cc_final: 0.8889 (mt) REVERT: B 763 ASN cc_start: 0.8194 (p0) cc_final: 0.7803 (p0) REVERT: B 775 GLU cc_start: 0.8856 (mp0) cc_final: 0.8439 (mp0) REVERT: B 821 LYS cc_start: 0.6753 (mptt) cc_final: 0.6241 (mmmm) REVERT: B 1004 MET cc_start: 0.9100 (mpp) cc_final: 0.8687 (mmt) REVERT: B 1011 ILE cc_start: 0.9184 (tt) cc_final: 0.8935 (pt) REVERT: B 1044 LEU cc_start: 0.8252 (mm) cc_final: 0.7637 (tp) REVERT: B 1113 MET cc_start: 0.7809 (tpp) cc_final: 0.7104 (tpp) REVERT: B 1114 LEU cc_start: 0.9333 (tp) cc_final: 0.9091 (tp) REVERT: B 1135 TYR cc_start: 0.7786 (p90) cc_final: 0.7035 (p90) REVERT: B 1193 LEU cc_start: 0.7679 (mm) cc_final: 0.7333 (mm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2239 time to fit residues: 59.8921 Evaluate side-chains 135 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 4 optimal weight: 0.0980 chunk 115 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.103783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087313 restraints weight = 43446.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089083 restraints weight = 28990.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090603 restraints weight = 21728.951| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11237 Z= 0.122 Angle : 0.627 15.338 15214 Z= 0.328 Chirality : 0.048 0.611 1688 Planarity : 0.004 0.071 1941 Dihedral : 5.432 52.884 1549 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1320 helix: 1.12 (0.27), residues: 371 sheet: -0.30 (0.39), residues: 168 loop : -1.15 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 974 HIS 0.004 0.001 HIS B 223 PHE 0.017 0.001 PHE B 851 TYR 0.019 0.001 TYR B 754 ARG 0.002 0.000 ARG B 827 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 3) link_NAG-ASN : angle 5.91064 ( 9) link_BETA1-4 : bond 0.00491 ( 2) link_BETA1-4 : angle 1.60061 ( 6) hydrogen bonds : bond 0.03787 ( 432) hydrogen bonds : angle 5.08632 ( 1260) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.50332 ( 2) covalent geometry : bond 0.00265 (11231) covalent geometry : angle 0.60967 (15197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 HIS cc_start: 0.8336 (t70) cc_final: 0.7977 (t-90) REVERT: A 481 ASP cc_start: 0.7637 (m-30) cc_final: 0.6924 (t0) REVERT: A 482 VAL cc_start: 0.8700 (m) cc_final: 0.7838 (m) REVERT: B 292 ASP cc_start: 0.8745 (t0) cc_final: 0.8492 (t0) REVERT: B 344 MET cc_start: 0.8668 (tpp) cc_final: 0.8425 (tpp) REVERT: B 351 GLU cc_start: 0.7105 (pp20) cc_final: 0.6473 (pp20) REVERT: B 362 ASN cc_start: 0.8682 (p0) cc_final: 0.8440 (p0) REVERT: B 388 ASP cc_start: 0.8107 (t0) cc_final: 0.7644 (t0) REVERT: B 602 MET cc_start: 0.6522 (tpt) cc_final: 0.6164 (tpp) REVERT: B 603 PHE cc_start: 0.8436 (m-80) cc_final: 0.8093 (m-80) REVERT: B 648 TYR cc_start: 0.7600 (t80) cc_final: 0.7222 (m-80) REVERT: B 665 LEU cc_start: 0.9200 (mm) cc_final: 0.8877 (mt) REVERT: B 763 ASN cc_start: 0.8092 (p0) cc_final: 0.7625 (p0) REVERT: B 775 GLU cc_start: 0.8863 (mp0) cc_final: 0.8501 (tp30) REVERT: B 821 LYS cc_start: 0.6585 (mptt) cc_final: 0.6165 (mmmm) REVERT: B 1011 ILE cc_start: 0.9200 (tt) cc_final: 0.8963 (pt) REVERT: B 1044 LEU cc_start: 0.8250 (mm) cc_final: 0.7620 (tp) REVERT: B 1135 TYR cc_start: 0.7940 (p90) cc_final: 0.6863 (p90) REVERT: B 1193 LEU cc_start: 0.7670 (mm) cc_final: 0.7401 (mm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2085 time to fit residues: 55.9639 Evaluate side-chains 142 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 125 optimal weight: 0.2980 chunk 58 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088074 restraints weight = 42839.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089760 restraints weight = 30620.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.090815 restraints weight = 22516.525| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11237 Z= 0.119 Angle : 0.614 14.778 15214 Z= 0.323 Chirality : 0.047 0.570 1688 Planarity : 0.004 0.071 1941 Dihedral : 5.279 53.286 1549 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1320 helix: 1.22 (0.27), residues: 370 sheet: -0.15 (0.39), residues: 168 loop : -1.12 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 974 HIS 0.004 0.001 HIS B 561 PHE 0.017 0.001 PHE B 851 TYR 0.019 0.001 TYR B 754 ARG 0.006 0.000 ARG B1034 Details of bonding type rmsd link_NAG-ASN : bond 0.00747 ( 3) link_NAG-ASN : angle 5.66690 ( 9) link_BETA1-4 : bond 0.00347 ( 2) link_BETA1-4 : angle 1.54737 ( 6) hydrogen bonds : bond 0.03725 ( 432) hydrogen bonds : angle 5.00567 ( 1260) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.44656 ( 2) covalent geometry : bond 0.00261 (11231) covalent geometry : angle 0.59823 (15197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 HIS cc_start: 0.8364 (t-90) cc_final: 0.7930 (t-90) REVERT: A 481 ASP cc_start: 0.7579 (m-30) cc_final: 0.6933 (t0) REVERT: A 501 ASN cc_start: 0.7702 (t0) cc_final: 0.7423 (t0) REVERT: B 292 ASP cc_start: 0.8726 (t0) cc_final: 0.8485 (t0) REVERT: B 344 MET cc_start: 0.8706 (tpp) cc_final: 0.8492 (tpp) REVERT: B 351 GLU cc_start: 0.7059 (pp20) cc_final: 0.6469 (pp20) REVERT: B 362 ASN cc_start: 0.8428 (p0) cc_final: 0.7886 (p0) REVERT: B 388 ASP cc_start: 0.8061 (t0) cc_final: 0.7615 (t0) REVERT: B 602 MET cc_start: 0.6643 (tpt) cc_final: 0.6251 (tpp) REVERT: B 603 PHE cc_start: 0.8398 (m-80) cc_final: 0.8053 (m-80) REVERT: B 648 TYR cc_start: 0.7657 (t80) cc_final: 0.7286 (m-80) REVERT: B 665 LEU cc_start: 0.9192 (mm) cc_final: 0.8835 (mt) REVERT: B 775 GLU cc_start: 0.8870 (mp0) cc_final: 0.8515 (tp30) REVERT: B 821 LYS cc_start: 0.6602 (mptt) cc_final: 0.6191 (mmmm) REVERT: B 1004 MET cc_start: 0.9205 (mmt) cc_final: 0.8627 (mmt) REVERT: B 1011 ILE cc_start: 0.9248 (tt) cc_final: 0.8978 (pt) REVERT: B 1044 LEU cc_start: 0.8256 (mm) cc_final: 0.7589 (tp) REVERT: B 1113 MET cc_start: 0.7681 (tpp) cc_final: 0.6370 (tpp) REVERT: B 1114 LEU cc_start: 0.9174 (tp) cc_final: 0.8964 (tp) REVERT: B 1134 MET cc_start: 0.7872 (mmp) cc_final: 0.7668 (mmm) REVERT: B 1135 TYR cc_start: 0.7816 (p90) cc_final: 0.6630 (p90) REVERT: B 1193 LEU cc_start: 0.7621 (mm) cc_final: 0.7330 (mm) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2372 time to fit residues: 63.9667 Evaluate side-chains 141 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.101189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.084704 restraints weight = 43435.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.086358 restraints weight = 30451.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.088203 restraints weight = 22626.848| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11237 Z= 0.203 Angle : 0.688 15.450 15214 Z= 0.365 Chirality : 0.049 0.627 1688 Planarity : 0.004 0.071 1941 Dihedral : 5.614 51.235 1549 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1320 helix: 1.01 (0.27), residues: 369 sheet: -0.14 (0.42), residues: 157 loop : -1.29 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 717 HIS 0.004 0.001 HIS B 223 PHE 0.019 0.002 PHE B 95 TYR 0.020 0.002 TYR B 754 ARG 0.005 0.001 ARG B 231 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 3) link_NAG-ASN : angle 5.89600 ( 9) link_BETA1-4 : bond 0.00367 ( 2) link_BETA1-4 : angle 1.62973 ( 6) hydrogen bonds : bond 0.04270 ( 432) hydrogen bonds : angle 5.25871 ( 1260) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.35613 ( 2) covalent geometry : bond 0.00447 (11231) covalent geometry : angle 0.67204 (15197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4334.06 seconds wall clock time: 77 minutes 10.72 seconds (4630.72 seconds total)