Starting phenix.real_space_refine on Tue Jun 10 02:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f2y_50166/06_2025/9f2y_50166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f2y_50166/06_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_50166/06_2025/9f2y_50166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f2y_50166/06_2025/9f2y_50166.map" model { file = "/net/cci-nas-00/data/ceres_data/9f2y_50166/06_2025/9f2y_50166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f2y_50166/06_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-5710/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: 10.27, per 1000 atoms: 0.93 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: 2.92 Conformation dependent library (CDL) restraints added in 1.6 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: 1.51 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: 4.64 Time building geometry restraints manager: 3.44 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: 159.060 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: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.120 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.280 ------------------------------------------------------------------------------- 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 : 1.280 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: 0.2527 time to fit residues: 104.3749 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 : 1.406 ------------------------------------------------------------------------------- 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 = 28032.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.097216 restraints weight = 20781.932| |-----------------------------------------------------------------------------| 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 : 1.563 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: 0.8998 (t80) cc_final: 0.8447 (t80) REVERT: B 50 THR cc_start: 0.8515 (p) cc_final: 0.7517 (t) REVERT: B 78 LEU cc_start: 0.8976 (tt) cc_final: 0.8745 (mt) REVERT: B 96 GLU cc_start: 0.7803 (pp20) cc_final: 0.7602 (tp30) REVERT: B 212 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8656 (mtmm) REVERT: B 351 GLU cc_start: 0.6912 (pp20) cc_final: 0.6434 (pp20) REVERT: B 362 ASN cc_start: 0.8235 (p0) cc_final: 0.8020 (p0) REVERT: B 383 ASN cc_start: 0.7467 (m110) cc_final: 0.7168 (t0) REVERT: B 602 MET cc_start: 0.6168 (tpt) cc_final: 0.5491 (tpp) REVERT: B 697 ASN cc_start: 0.5853 (OUTLIER) cc_final: 0.5476 (m-40) REVERT: B 714 VAL cc_start: 0.9502 (t) cc_final: 0.9204 (p) REVERT: B 750 GLN cc_start: 0.8610 (mm110) cc_final: 0.8402 (mm-40) REVERT: B 1004 MET cc_start: 0.8712 (mpp) cc_final: 0.8425 (mpp) REVERT: B 1011 ILE cc_start: 0.8786 (tt) cc_final: 0.8455 (pt) outliers start: 5 outliers final: 1 residues processed: 226 average time/residue: 0.2154 time to fit residues: 71.1126 Evaluate side-chains 161 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.106904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.090067 restraints weight = 43780.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091928 restraints weight = 29143.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.093618 restraints weight = 21790.962| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 11237 Z= 0.202 Angle : 0.689 19.517 15214 Z= 0.359 Chirality : 0.054 1.091 1688 Planarity : 0.004 0.059 1941 Dihedral : 6.714 56.362 1549 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.31 % 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: -0.52 (0.22), residues: 1320 helix: 1.38 (0.27), residues: 371 sheet: -0.42 (0.34), residues: 202 loop : -1.26 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1282 HIS 0.006 0.001 HIS B 561 PHE 0.028 0.002 PHE B 603 TYR 0.016 0.002 TYR B 824 ARG 0.004 0.000 ARG B1034 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 3) link_NAG-ASN : angle 7.69699 ( 9) link_BETA1-4 : bond 0.00304 ( 2) link_BETA1-4 : angle 2.95972 ( 6) hydrogen bonds : bond 0.04574 ( 432) hydrogen bonds : angle 5.28630 ( 1260) SS BOND : bond 0.00175 ( 1) SS BOND : angle 1.19708 ( 2) covalent geometry : bond 0.00442 (11231) covalent geometry : angle 0.66068 (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 205 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 1.212 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: symmetry clash REVERT: A 446 ASN cc_start: 0.6678 (t0) cc_final: 0.6399 (t0) REVERT: A 500 TYR cc_start: 0.8915 (t80) cc_final: 0.8525 (t80) REVERT: B 212 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8686 (mtmm) REVERT: B 292 ASP cc_start: 0.8625 (t0) cc_final: 0.8336 (t0) REVERT: B 351 GLU cc_start: 0.7064 (pp20) cc_final: 0.6517 (pp20) REVERT: B 602 MET cc_start: 0.6037 (tpt) cc_final: 0.5496 (mmm) REVERT: B 732 MET cc_start: 0.8742 (mmt) cc_final: 0.8522 (mmm) REVERT: B 775 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8596 (mm-30) REVERT: B 795 TYR cc_start: 0.7606 (t80) cc_final: 0.7286 (t80) REVERT: B 1011 ILE cc_start: 0.9001 (tt) cc_final: 0.8677 (pt) REVERT: B 1044 LEU cc_start: 0.8248 (mm) cc_final: 0.7505 (tp) outliers start: 2 outliers final: 1 residues processed: 205 average time/residue: 0.2307 time to fit residues: 67.8669 Evaluate side-chains 148 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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: 0.9980 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 238 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 739 GLN ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.105760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088955 restraints weight = 43234.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.090697 restraints weight = 29385.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092476 restraints weight = 22765.659| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11237 Z= 0.163 Angle : 0.643 17.920 15214 Z= 0.338 Chirality : 0.051 0.839 1688 Planarity : 0.004 0.061 1941 Dihedral : 6.044 59.623 1549 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % 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: -0.47 (0.22), residues: 1320 helix: 1.37 (0.27), residues: 371 sheet: -0.35 (0.36), residues: 190 loop : -1.20 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 974 HIS 0.004 0.001 HIS B 223 PHE 0.024 0.001 PHE B 652 TYR 0.017 0.002 TYR B 824 ARG 0.004 0.000 ARG B 893 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 3) link_NAG-ASN : angle 7.02989 ( 9) link_BETA1-4 : bond 0.00491 ( 2) link_BETA1-4 : angle 2.71407 ( 6) hydrogen bonds : bond 0.04230 ( 432) hydrogen bonds : angle 5.12037 ( 1260) SS BOND : bond 0.00365 ( 1) SS BOND : angle 0.86585 ( 2) covalent geometry : bond 0.00356 (11231) covalent geometry : angle 0.61734 (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 201 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.350 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 500 TYR cc_start: 0.8863 (t80) cc_final: 0.8650 (t80) REVERT: A 515 ILE cc_start: 0.9359 (mp) cc_final: 0.8396 (mp) REVERT: B 78 LEU cc_start: 0.8854 (tp) cc_final: 0.8585 (tp) REVERT: B 212 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8685 (mtmm) REVERT: B 292 ASP cc_start: 0.8657 (t0) cc_final: 0.8351 (t0) REVERT: B 351 GLU cc_start: 0.7103 (pp20) cc_final: 0.6562 (pp20) REVERT: B 362 ASN cc_start: 0.8582 (p0) cc_final: 0.8274 (p0) REVERT: B 388 ASP cc_start: 0.8057 (t0) cc_final: 0.7784 (t0) REVERT: B 602 MET cc_start: 0.6074 (tpt) cc_final: 0.5641 (mmm) REVERT: B 707 ASP cc_start: 0.9263 (m-30) cc_final: 0.9063 (m-30) REVERT: B 800 MET cc_start: 0.8343 (mtt) cc_final: 0.7968 (mtt) REVERT: B 1004 MET cc_start: 0.9030 (mpp) cc_final: 0.8588 (mmt) REVERT: B 1011 ILE cc_start: 0.9084 (tt) cc_final: 0.8783 (pt) REVERT: B 1044 LEU cc_start: 0.8206 (mm) cc_final: 0.7501 (tp) REVERT: B 1113 MET cc_start: 0.8268 (tpt) cc_final: 0.6342 (tpt) REVERT: B 1135 TYR cc_start: 0.7632 (p90) cc_final: 0.6675 (p90) REVERT: B 1193 LEU cc_start: 0.7770 (mm) cc_final: 0.7568 (mm) outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.2490 time to fit residues: 73.4859 Evaluate side-chains 137 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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: 5.9990 chunk 131 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 739 GLN B 988 GLN B1147 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.104961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.088199 restraints weight = 42903.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090133 restraints weight = 28331.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092115 restraints weight = 20974.012| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11237 Z= 0.157 Angle : 0.635 17.256 15214 Z= 0.339 Chirality : 0.050 0.769 1688 Planarity : 0.004 0.063 1941 Dihedral : 5.760 56.948 1549 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % 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: -0.48 (0.22), residues: 1320 helix: 1.32 (0.27), residues: 367 sheet: -0.27 (0.36), residues: 193 loop : -1.19 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 974 HIS 0.005 0.001 HIS B 223 PHE 0.014 0.001 PHE B 537 TYR 0.046 0.002 TYR B 710 ARG 0.002 0.000 ARG B1140 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 3) link_NAG-ASN : angle 6.76024 ( 9) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 2.37313 ( 6) hydrogen bonds : bond 0.04133 ( 432) hydrogen bonds : angle 4.97560 ( 1260) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.63214 ( 2) covalent geometry : bond 0.00346 (11231) covalent geometry : angle 0.61203 (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 193 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.334 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: 0.8032 (t70) cc_final: 0.7582 (t-90) REVERT: A 500 TYR cc_start: 0.8888 (t80) cc_final: 0.8014 (t80) REVERT: A 521 GLU cc_start: 0.7038 (pp20) cc_final: 0.6539 (tm-30) REVERT: B 78 LEU cc_start: 0.8866 (tp) cc_final: 0.8642 (tp) REVERT: B 212 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8665 (mtmm) REVERT: B 292 ASP cc_start: 0.8703 (t0) cc_final: 0.8427 (t0) REVERT: B 351 GLU cc_start: 0.7171 (pp20) cc_final: 0.6620 (pp20) REVERT: B 362 ASN cc_start: 0.8435 (p0) cc_final: 0.7915 (p0) REVERT: B 388 ASP cc_start: 0.8214 (t0) cc_final: 0.7849 (t0) REVERT: B 602 MET cc_start: 0.6056 (tpt) cc_final: 0.5832 (mmm) REVERT: B 707 ASP cc_start: 0.9243 (m-30) cc_final: 0.9030 (m-30) REVERT: B 763 ASN cc_start: 0.8099 (p0) cc_final: 0.7712 (p0) REVERT: B 775 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8689 (mm-30) REVERT: B 800 MET cc_start: 0.8354 (mtt) cc_final: 0.8102 (mtt) REVERT: B 1004 MET cc_start: 0.9072 (mpp) cc_final: 0.8700 (mmt) REVERT: B 1011 ILE cc_start: 0.9114 (tt) cc_final: 0.8798 (pt) REVERT: B 1044 LEU cc_start: 0.8227 (mm) cc_final: 0.7562 (tp) REVERT: B 1114 LEU cc_start: 0.9376 (tp) cc_final: 0.9139 (tp) REVERT: B 1116 LEU cc_start: 0.8849 (mp) cc_final: 0.8259 (mp) REVERT: B 1193 LEU cc_start: 0.7579 (mm) cc_final: 0.7310 (mm) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.2612 time to fit residues: 74.8880 Evaluate side-chains 135 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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: 6.9990 chunk 121 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.104656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.087819 restraints weight = 43300.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089596 restraints weight = 28668.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.091506 restraints weight = 21785.663| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4522 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= 0.151 Angle : 0.644 16.483 15214 Z= 0.342 Chirality : 0.049 0.709 1688 Planarity : 0.004 0.065 1941 Dihedral : 5.682 52.759 1549 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % 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: -0.53 (0.22), residues: 1320 helix: 1.08 (0.27), residues: 371 sheet: -0.06 (0.38), residues: 163 loop : -1.17 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 706 HIS 0.004 0.001 HIS B 223 PHE 0.015 0.001 PHE B1284 TYR 0.025 0.002 TYR B 710 ARG 0.008 0.000 ARG B 893 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 3) link_NAG-ASN : angle 6.44108 ( 9) link_BETA1-4 : bond 0.00346 ( 2) link_BETA1-4 : angle 2.15413 ( 6) hydrogen bonds : bond 0.04204 ( 432) hydrogen bonds : angle 5.05960 ( 1260) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.55607 ( 2) covalent geometry : bond 0.00333 (11231) covalent geometry : angle 0.62309 (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 197 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 1.435 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 466 HIS cc_start: 0.8225 (t70) cc_final: 0.7754 (t-90) REVERT: A 500 TYR cc_start: 0.8848 (t80) cc_final: 0.8584 (t80) REVERT: B 78 LEU cc_start: 0.8901 (tp) cc_final: 0.8696 (tp) REVERT: B 212 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8650 (mtmm) REVERT: B 292 ASP cc_start: 0.8662 (t0) cc_final: 0.8392 (t0) REVERT: B 351 GLU cc_start: 0.7124 (pp20) cc_final: 0.6607 (pp20) REVERT: B 383 ASN cc_start: 0.7802 (m-40) cc_final: 0.7324 (t0) REVERT: B 388 ASP cc_start: 0.8187 (t0) cc_final: 0.7767 (t0) REVERT: B 602 MET cc_start: 0.6167 (tpt) cc_final: 0.5923 (mmm) REVERT: B 763 ASN cc_start: 0.8067 (p0) cc_final: 0.7813 (p0) REVERT: B 790 GLN cc_start: 0.8835 (mt0) cc_final: 0.8564 (mm-40) REVERT: B 800 MET cc_start: 0.8459 (mtt) cc_final: 0.8214 (mtt) REVERT: B 862 LEU cc_start: 0.8832 (tp) cc_final: 0.8591 (tt) REVERT: B 968 MET cc_start: 0.8390 (tmm) cc_final: 0.7958 (tmm) REVERT: B 1004 MET cc_start: 0.9118 (mpp) cc_final: 0.8665 (mmt) REVERT: B 1011 ILE cc_start: 0.9130 (tt) cc_final: 0.8839 (pt) REVERT: B 1044 LEU cc_start: 0.8254 (mm) cc_final: 0.7561 (tp) REVERT: B 1113 MET cc_start: 0.7759 (tpp) cc_final: 0.7495 (tpp) REVERT: B 1252 PHE cc_start: 0.7974 (p90) cc_final: 0.7734 (p90) outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.2807 time to fit residues: 80.4754 Evaluate side-chains 142 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 50 optimal weight: 0.0770 chunk 117 optimal weight: 4.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- 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 230 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 418 ASN B 514 ASN ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN B1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.096780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080606 restraints weight = 42816.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081493 restraints weight = 29746.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082849 restraints weight = 25087.359| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 11237 Z= 0.388 Angle : 0.886 19.215 15214 Z= 0.475 Chirality : 0.056 0.898 1688 Planarity : 0.005 0.068 1941 Dihedral : 6.722 50.321 1549 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.25 % Allowed : 3.77 % Favored : 95.98 % 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: -1.37 (0.21), residues: 1320 helix: 0.25 (0.25), residues: 366 sheet: -0.49 (0.39), residues: 167 loop : -1.64 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 43 HIS 0.006 0.002 HIS A 449 PHE 0.027 0.003 PHE B 537 TYR 0.036 0.003 TYR B 312 ARG 0.010 0.001 ARG B1065 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 3) link_NAG-ASN : angle 7.42638 ( 9) link_BETA1-4 : bond 0.00900 ( 2) link_BETA1-4 : angle 2.17258 ( 6) hydrogen bonds : bond 0.05714 ( 432) hydrogen bonds : angle 5.88217 ( 1260) SS BOND : bond 0.00277 ( 1) SS BOND : angle 0.23903 ( 2) covalent geometry : bond 0.00850 (11231) covalent geometry : angle 0.86688 (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 171 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 1.201 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: A 466 HIS cc_start: 0.8323 (t70) cc_final: 0.7938 (t-90) REVERT: A 500 TYR cc_start: 0.8731 (t80) cc_final: 0.8132 (t80) REVERT: B 292 ASP cc_start: 0.8726 (t0) cc_final: 0.8439 (t0) REVERT: B 332 SER cc_start: 0.8470 (m) cc_final: 0.8168 (t) REVERT: B 362 ASN cc_start: 0.8800 (p0) cc_final: 0.8539 (p0) REVERT: B 388 ASP cc_start: 0.8330 (t0) cc_final: 0.7713 (t0) REVERT: B 418 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7664 (p0) REVERT: B 420 THR cc_start: 0.9117 (p) cc_final: 0.8774 (p) REVERT: B 460 TRP cc_start: 0.8445 (m100) cc_final: 0.7632 (m100) REVERT: B 602 MET cc_start: 0.6269 (tpt) cc_final: 0.5868 (tpp) REVERT: B 684 TYR cc_start: 0.5508 (m-80) cc_final: 0.5081 (m-10) REVERT: B 763 ASN cc_start: 0.8198 (p0) cc_final: 0.7958 (p0) REVERT: B 821 LYS cc_start: 0.6954 (mptt) cc_final: 0.6344 (mmmm) REVERT: B 968 MET cc_start: 0.8416 (tmm) cc_final: 0.8211 (tmm) REVERT: B 1004 MET cc_start: 0.9290 (mpp) cc_final: 0.9056 (mmt) REVERT: B 1044 LEU cc_start: 0.8366 (mm) cc_final: 0.7774 (tp) REVERT: B 1193 LEU cc_start: 0.7575 (mm) cc_final: 0.7285 (mm) outliers start: 3 outliers final: 1 residues processed: 171 average time/residue: 0.2217 time to fit residues: 55.5146 Evaluate side-chains 130 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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: 0.4980 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 418 ASN B 473 ASN ** B1240 GLN ** 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 = 0.3851 r_free = 0.3851 target = 0.104232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088019 restraints weight = 42846.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089118 restraints weight = 27868.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.090415 restraints weight = 22429.861| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11237 Z= 0.136 Angle : 0.675 16.456 15214 Z= 0.355 Chirality : 0.052 0.807 1688 Planarity : 0.004 0.074 1941 Dihedral : 5.777 52.340 1549 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.08 % Allowed : 1.15 % 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: -0.81 (0.22), residues: 1320 helix: 0.89 (0.26), residues: 362 sheet: -0.31 (0.38), residues: 168 loop : -1.33 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 974 HIS 0.004 0.001 HIS B 561 PHE 0.013 0.001 PHE B 95 TYR 0.032 0.002 TYR B 754 ARG 0.009 0.001 ARG B 827 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 3) link_NAG-ASN : angle 6.50300 ( 9) link_BETA1-4 : bond 0.00173 ( 2) link_BETA1-4 : angle 1.56784 ( 6) hydrogen bonds : bond 0.04275 ( 432) hydrogen bonds : angle 5.25958 ( 1260) SS BOND : bond 0.00323 ( 1) SS BOND : angle 0.80264 ( 2) covalent geometry : bond 0.00299 (11231) covalent geometry : angle 0.65601 (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 188 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.210 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: 0.8374 (t70) cc_final: 0.8147 (t-90) REVERT: A 481 ASP cc_start: 0.7651 (m-30) cc_final: 0.7003 (t0) REVERT: B 292 ASP cc_start: 0.8692 (t0) cc_final: 0.8408 (t0) REVERT: B 313 MET cc_start: 0.5818 (mmp) cc_final: 0.5223 (mmp) REVERT: B 351 GLU cc_start: 0.7133 (pp20) cc_final: 0.6733 (pp20) REVERT: B 388 ASP cc_start: 0.8146 (t0) cc_final: 0.7651 (t0) REVERT: B 418 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7463 (p0) REVERT: B 420 THR cc_start: 0.9109 (p) cc_final: 0.8771 (p) REVERT: B 741 GLU cc_start: 0.8511 (pm20) cc_final: 0.8092 (pm20) REVERT: B 763 ASN cc_start: 0.8143 (p0) cc_final: 0.7865 (p0) REVERT: B 821 LYS cc_start: 0.6608 (mptt) cc_final: 0.6167 (mmmm) REVERT: B 985 TRP cc_start: 0.8926 (t-100) cc_final: 0.8664 (t60) REVERT: B 1004 MET cc_start: 0.9120 (mpp) cc_final: 0.8856 (mmt) REVERT: B 1011 ILE cc_start: 0.9139 (tt) cc_final: 0.8916 (pt) REVERT: B 1044 LEU cc_start: 0.8247 (mm) cc_final: 0.7646 (tp) REVERT: B 1113 MET cc_start: 0.7774 (tpp) cc_final: 0.7570 (tpp) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.2965 time to fit residues: 83.6787 Evaluate side-chains 126 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 6.9990 chunk 115 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 418 ASN B 473 ASN B 693 GLN ** B1240 GLN ** 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 = 0.3784 r_free = 0.3784 target = 0.100468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083688 restraints weight = 44479.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084807 restraints weight = 31185.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086671 restraints weight = 25036.459| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11237 Z= 0.240 Angle : 0.723 16.207 15214 Z= 0.387 Chirality : 0.051 0.733 1688 Planarity : 0.004 0.072 1941 Dihedral : 6.009 51.689 1549 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.08 % Allowed : 0.74 % Favored : 99.18 % 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: -0.99 (0.22), residues: 1320 helix: 0.79 (0.26), residues: 365 sheet: -0.39 (0.39), residues: 164 loop : -1.47 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 43 HIS 0.004 0.001 HIS B 223 PHE 0.019 0.002 PHE B 537 TYR 0.033 0.002 TYR B 754 ARG 0.005 0.001 ARG B1065 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 3) link_NAG-ASN : angle 6.23265 ( 9) link_BETA1-4 : bond 0.00363 ( 2) link_BETA1-4 : angle 1.72315 ( 6) hydrogen bonds : bond 0.04818 ( 432) hydrogen bonds : angle 5.44268 ( 1260) SS BOND : bond 0.01004 ( 1) SS BOND : angle 0.84392 ( 2) covalent geometry : bond 0.00534 (11231) covalent geometry : angle 0.70614 (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 173 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.213 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: A 427 MET cc_start: 0.2317 (mtm) cc_final: 0.1739 (mtt) REVERT: A 466 HIS cc_start: 0.8403 (t70) cc_final: 0.8198 (t-90) REVERT: A 481 ASP cc_start: 0.7661 (m-30) cc_final: 0.6975 (t0) REVERT: B 184 GLN cc_start: 0.8905 (mm110) cc_final: 0.8637 (mm110) REVERT: B 292 ASP cc_start: 0.8766 (t0) cc_final: 0.8438 (t0) REVERT: B 313 MET cc_start: 0.6468 (mmp) cc_final: 0.6174 (mmp) REVERT: B 351 GLU cc_start: 0.7402 (pp20) cc_final: 0.6643 (pp20) REVERT: B 388 ASP cc_start: 0.8197 (t0) cc_final: 0.7619 (t0) REVERT: B 418 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7562 (p0) REVERT: B 420 THR cc_start: 0.9060 (p) cc_final: 0.8738 (p) REVERT: B 737 GLU cc_start: 0.8265 (pp20) cc_final: 0.8047 (pp20) REVERT: B 763 ASN cc_start: 0.8247 (p0) cc_final: 0.7993 (p0) REVERT: B 821 LYS cc_start: 0.6905 (mptt) cc_final: 0.6354 (mmmm) REVERT: B 1004 MET cc_start: 0.9158 (mpp) cc_final: 0.8852 (mmt) REVERT: B 1011 ILE cc_start: 0.9239 (tt) cc_final: 0.8965 (pt) REVERT: B 1113 MET cc_start: 0.7901 (tpp) cc_final: 0.7308 (tpt) REVERT: B 1135 TYR cc_start: 0.7610 (p90) cc_final: 0.6494 (p90) REVERT: B 1193 LEU cc_start: 0.7576 (mm) cc_final: 0.7317 (mm) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.2093 time to fit residues: 53.9531 Evaluate side-chains 126 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 125 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B1240 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 = 0.3840 r_free = 0.3840 target = 0.103520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.086838 restraints weight = 43159.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.088414 restraints weight = 29408.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090027 restraints weight = 21862.332| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11237 Z= 0.129 Angle : 0.654 14.864 15214 Z= 0.344 Chirality : 0.050 0.640 1688 Planarity : 0.004 0.075 1941 Dihedral : 5.602 52.898 1549 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % 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: -0.76 (0.22), residues: 1320 helix: 0.92 (0.27), residues: 370 sheet: -0.17 (0.39), residues: 168 loop : -1.34 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 985 HIS 0.004 0.001 HIS B 561 PHE 0.015 0.001 PHE B 537 TYR 0.030 0.001 TYR B 754 ARG 0.004 0.000 ARG B 231 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 3) link_NAG-ASN : angle 5.70772 ( 9) link_BETA1-4 : bond 0.00313 ( 2) link_BETA1-4 : angle 1.51181 ( 6) hydrogen bonds : bond 0.04163 ( 432) hydrogen bonds : angle 5.16385 ( 1260) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.05452 ( 2) covalent geometry : bond 0.00286 (11231) covalent geometry : angle 0.63825 (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 174 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.2654 (mtm) cc_final: 0.1873 (mtm) REVERT: A 481 ASP cc_start: 0.7525 (m-30) cc_final: 0.6841 (t0) REVERT: A 492 CYS cc_start: 0.7611 (m) cc_final: 0.6817 (m) REVERT: A 500 TYR cc_start: 0.8797 (t80) cc_final: 0.8527 (t80) REVERT: B 152 VAL cc_start: 0.8282 (t) cc_final: 0.7754 (m) REVERT: B 292 ASP cc_start: 0.8702 (t0) cc_final: 0.8431 (t0) REVERT: B 313 MET cc_start: 0.6059 (mmp) cc_final: 0.5747 (mmp) REVERT: B 351 GLU cc_start: 0.7249 (pp20) cc_final: 0.6600 (pp20) REVERT: B 362 ASN cc_start: 0.8687 (p0) cc_final: 0.8470 (p0) REVERT: B 388 ASP cc_start: 0.8038 (t0) cc_final: 0.7557 (t0) REVERT: B 418 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7437 (p0) REVERT: B 420 THR cc_start: 0.9088 (p) cc_final: 0.8773 (p) REVERT: B 732 MET cc_start: 0.8294 (tpp) cc_final: 0.7873 (tpp) REVERT: B 763 ASN cc_start: 0.8207 (p0) cc_final: 0.7911 (p0) REVERT: B 821 LYS cc_start: 0.6756 (mptt) cc_final: 0.6296 (mmmm) REVERT: B 1004 MET cc_start: 0.9126 (mpp) cc_final: 0.8783 (mmt) REVERT: B 1011 ILE cc_start: 0.9208 (tt) cc_final: 0.8966 (pt) REVERT: B 1124 ASP cc_start: 0.8524 (t70) cc_final: 0.8315 (t0) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2300 time to fit residues: 61.2544 Evaluate side-chains 131 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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: 2.9990 chunk 96 optimal weight: 0.0370 chunk 47 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 765 ASN B1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.104861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.087738 restraints weight = 43247.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089051 restraints weight = 31135.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090666 restraints weight = 23575.330| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11237 Z= 0.116 Angle : 0.621 13.772 15214 Z= 0.326 Chirality : 0.048 0.544 1688 Planarity : 0.004 0.073 1941 Dihedral : 5.251 53.275 1549 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.08 % Allowed : 0.16 % Favored : 99.75 % 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: -0.57 (0.22), residues: 1320 helix: 1.09 (0.27), residues: 370 sheet: -0.05 (0.39), residues: 173 loop : -1.23 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 706 HIS 0.004 0.001 HIS B 561 PHE 0.012 0.001 PHE B 537 TYR 0.025 0.001 TYR B 754 ARG 0.003 0.000 ARG B 231 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 3) link_NAG-ASN : angle 5.24831 ( 9) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.52218 ( 6) hydrogen bonds : bond 0.03884 ( 432) hydrogen bonds : angle 4.98581 ( 1260) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.15647 ( 2) covalent geometry : bond 0.00250 (11231) covalent geometry : angle 0.60779 (15197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4765.44 seconds wall clock time: 85 minutes 30.17 seconds (5130.17 seconds total)