Starting phenix.real_space_refine on Tue Sep 24 06:58:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/09_2024/6mg8_9111.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/09_2024/6mg8_9111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/09_2024/6mg8_9111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/09_2024/6mg8_9111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/09_2024/6mg8_9111.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mg8_9111/09_2024/6mg8_9111.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 29 5.16 5 C 4653 2.51 5 N 1165 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7034 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 6922 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 266} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 940} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 881 Unresolved non-hydrogen angles: 1088 Unresolved non-hydrogen dihedrals: 717 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 32, 'PHE:plan': 7, 'GLU:plan': 33, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 483 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.77, per 1000 atoms: 0.68 Number of scatterers: 7034 At special positions: 0 Unit cell: (83.84, 110.04, 121.83, 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 29 16.00 O 1187 8.00 N 1165 7.00 C 4653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.04 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 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 60.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 59 through 84 removed outlier: 3.753A pdb=" N LEU A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.903A pdb=" N PHE A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.694A pdb=" N THR A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.548A pdb=" N HIS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 246 through 256 removed outlier: 4.093A pdb=" N GLU A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.740A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.642A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 395 removed outlier: 3.813A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 422 removed outlier: 3.609A pdb=" N LEU A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.674A pdb=" N GLY A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.949A pdb=" N ALA A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 removed outlier: 3.605A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 removed outlier: 3.552A pdb=" N VAL A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 530 removed outlier: 4.097A pdb=" N CYS A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 546 removed outlier: 3.562A pdb=" N SER A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 553 through 589 removed outlier: 4.338A pdb=" N PHE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 3.636A pdb=" N ASP A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 730 removed outlier: 3.726A pdb=" N PHE A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.648A pdb=" N ILE A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 removed outlier: 3.908A pdb=" N PHE A 776 " --> pdb=" O ARG A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 811 Processing helix chain 'A' and resid 830 through 851 removed outlier: 4.152A pdb=" N ASP A 836 " --> pdb=" O HIS A 832 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 874 Processing helix chain 'A' and resid 884 through 889 removed outlier: 4.125A pdb=" N THR A 889 " --> pdb=" O SER A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 969 through 989 removed outlier: 3.807A pdb=" N ILE A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.698A pdb=" N TRP A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1034 removed outlier: 4.448A pdb=" N SER A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG A1011 " --> pdb=" O TYR A1007 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A1019 " --> pdb=" O LEU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 3.505A pdb=" N GLY A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1093 removed outlier: 3.750A pdb=" N GLY A1077 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A1082 " --> pdb=" O ILE A1078 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1109 removed outlier: 4.257A pdb=" N ALA A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1123 Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'A' and resid 1131 through 1138 removed outlier: 3.618A pdb=" N VAL A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1155 Processing helix chain 'A' and resid 1155 through 1164 removed outlier: 3.864A pdb=" N VAL A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 352 Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.630A pdb=" N VAL A 176 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 178 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 181 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA5, first strand: chain 'A' and resid 959 through 964 389 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 2.13 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: 2223 1.34 - 1.46: 1789 1.46 - 1.58: 3161 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 7221 Sorted by residual: bond pdb=" C10 CLR A1401 " pdb=" C5 CLR A1401 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C10 CLR A1403 " pdb=" C5 CLR A1403 " ideal model delta sigma weight residual 1.519 1.404 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C10 CLR A1402 " pdb=" C5 CLR A1402 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C10 CLR A1404 " pdb=" C5 CLR A1404 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C4 CLR A1401 " pdb=" C5 CLR A1401 " ideal model delta sigma weight residual 1.506 1.397 0.109 2.00e-02 2.50e+03 3.00e+01 ... (remaining 7216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 9732 2.16 - 4.31: 173 4.31 - 6.47: 46 6.47 - 8.62: 5 8.62 - 10.78: 1 Bond angle restraints: 9957 Sorted by residual: angle pdb=" C HIS A 930 " pdb=" N ARG A 931 " pdb=" CA ARG A 931 " ideal model delta sigma weight residual 120.97 131.75 -10.78 2.84e+00 1.24e-01 1.44e+01 angle pdb=" C GLU A 108 " pdb=" N THR A 109 " pdb=" CA THR A 109 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.90e+00 angle pdb=" N GLY A 862 " pdb=" CA GLY A 862 " pdb=" C GLY A 862 " ideal model delta sigma weight residual 111.78 116.20 -4.42 1.69e+00 3.50e-01 6.83e+00 angle pdb=" C ASP A 895 " pdb=" N ALA A 896 " pdb=" CA ALA A 896 " ideal model delta sigma weight residual 122.15 115.01 7.14 2.83e+00 1.25e-01 6.37e+00 angle pdb=" N ASP A 895 " pdb=" CA ASP A 895 " pdb=" C ASP A 895 " ideal model delta sigma weight residual 110.80 116.17 -5.37 2.13e+00 2.20e-01 6.37e+00 ... (remaining 9952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 3945 16.65 - 33.29: 303 33.29 - 49.94: 74 49.94 - 66.58: 4 66.58 - 83.23: 5 Dihedral angle restraints: 4331 sinusoidal: 1463 harmonic: 2868 Sorted by residual: dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 313 " pdb=" CB CYS A 313 " ideal model delta sinusoidal sigma weight residual 93.00 168.74 -75.74 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CA VAL A 894 " pdb=" C VAL A 894 " pdb=" N ASP A 895 " pdb=" CA ASP A 895 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LYS A 191 " pdb=" C LYS A 191 " pdb=" N SER A 192 " pdb=" CA SER A 192 " ideal model delta harmonic sigma weight residual -180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1168 0.106 - 0.211: 26 0.211 - 0.317: 6 0.317 - 0.423: 3 0.423 - 0.529: 7 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C10 CLR A1401 " pdb=" C1 CLR A1401 " pdb=" C5 CLR A1401 " pdb=" C9 CLR A1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.32 -0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" C10 CLR A1404 " pdb=" C1 CLR A1404 " pdb=" C5 CLR A1404 " pdb=" C9 CLR A1404 " both_signs ideal model delta sigma weight residual False -2.85 -2.39 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" C10 CLR A1402 " pdb=" C1 CLR A1402 " pdb=" C5 CLR A1402 " pdb=" C9 CLR A1402 " both_signs ideal model delta sigma weight residual False -2.85 -2.39 -0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 1207 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1067 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A1068 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1068 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1068 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 931 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 932 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 932 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 932 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 354 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 355 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.019 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 148 2.71 - 3.25: 7542 3.25 - 3.80: 11010 3.80 - 4.35: 13506 4.35 - 4.90: 22463 Nonbonded interactions: 54669 Sorted by model distance: nonbonded pdb=" NH2 ARG A 280 " pdb=" O GLY A 315 " model vdw 2.157 3.120 nonbonded pdb=" O PRO A 856 " pdb=" OH TYR A 870 " model vdw 2.229 3.040 nonbonded pdb=" O TRP A1013 " pdb=" OG SER A1017 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR A 485 " pdb=" OE1 GLN A 562 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 806 " pdb=" NE ARG A 835 " model vdw 2.310 3.120 ... (remaining 54664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.090 Process input model: 19.990 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.006 0.117 7221 Z= 0.423 Angle : 0.747 10.778 9957 Z= 0.362 Chirality : 0.061 0.529 1210 Planarity : 0.004 0.040 1242 Dihedral : 12.860 83.230 2476 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.49 (0.23), residues: 981 helix: -1.83 (0.18), residues: 562 sheet: -4.46 (0.49), residues: 47 loop : -2.59 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 830 HIS 0.003 0.001 HIS A 175 PHE 0.015 0.001 PHE A 502 TYR 0.015 0.001 TYR A 999 ARG 0.002 0.000 ARG A 931 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.9230 (mp) cc_final: 0.8790 (tt) REVERT: A 358 MET cc_start: 0.9062 (tpt) cc_final: 0.8782 (tpp) REVERT: A 489 LEU cc_start: 0.8479 (tp) cc_final: 0.8277 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1258 time to fit residues: 22.4396 Evaluate side-chains 84 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.0270 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 163 GLN A 182 GLN A 228 GLN A 314 GLN A 506 HIS A 809 HIS A 875 GLN A 915 ASN A 926 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7221 Z= 0.208 Angle : 0.608 8.175 9957 Z= 0.302 Chirality : 0.041 0.148 1210 Planarity : 0.004 0.041 1242 Dihedral : 6.439 44.688 1302 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.40 % Allowed : 15.94 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.96 (0.26), residues: 981 helix: -0.54 (0.21), residues: 566 sheet: -3.88 (0.59), residues: 46 loop : -2.04 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 849 HIS 0.003 0.001 HIS A 275 PHE 0.020 0.002 PHE A 781 TYR 0.016 0.001 TYR A 870 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.814 Fit side-chains REVERT: A 204 GLN cc_start: 0.7927 (tt0) cc_final: 0.7680 (tt0) REVERT: A 208 TYR cc_start: 0.8482 (m-10) cc_final: 0.8271 (m-80) REVERT: A 248 LEU cc_start: 0.9152 (mp) cc_final: 0.8722 (tt) REVERT: A 358 MET cc_start: 0.8980 (tpt) cc_final: 0.8657 (tpp) REVERT: A 489 LEU cc_start: 0.8482 (tp) cc_final: 0.8251 (tp) REVERT: A 819 MET cc_start: 0.8324 (ttm) cc_final: 0.7992 (ttp) REVERT: A 1002 LEU cc_start: 0.9038 (mt) cc_final: 0.8692 (mt) REVERT: A 1091 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8509 (pt) outliers start: 8 outliers final: 4 residues processed: 111 average time/residue: 0.1364 time to fit residues: 23.2927 Evaluate side-chains 96 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1091 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 88 optimal weight: 0.0010 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.0670 overall best weight: 0.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7221 Z= 0.191 Angle : 0.605 10.317 9957 Z= 0.293 Chirality : 0.040 0.162 1210 Planarity : 0.004 0.042 1242 Dihedral : 6.176 54.096 1302 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.15 % Allowed : 16.46 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.15 (0.27), residues: 981 helix: 0.16 (0.22), residues: 568 sheet: -3.84 (0.57), residues: 46 loop : -1.73 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 830 HIS 0.002 0.001 HIS A 275 PHE 0.012 0.001 PHE A 569 TYR 0.019 0.001 TYR A 438 ARG 0.008 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.831 Fit side-chains REVERT: A 358 MET cc_start: 0.8946 (tpt) cc_final: 0.8628 (tpp) REVERT: A 411 THR cc_start: 0.8780 (p) cc_final: 0.8379 (p) REVERT: A 569 PHE cc_start: 0.8864 (m-80) cc_final: 0.8451 (m-10) REVERT: A 806 TYR cc_start: 0.8120 (m-80) cc_final: 0.7848 (m-80) REVERT: A 819 MET cc_start: 0.8316 (ttm) cc_final: 0.7966 (ttp) REVERT: A 1002 LEU cc_start: 0.9002 (mt) cc_final: 0.8640 (mt) REVERT: A 1056 MET cc_start: 0.9156 (mmm) cc_final: 0.8907 (mmm) REVERT: A 1091 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8569 (pt) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.1181 time to fit residues: 22.5038 Evaluate side-chains 104 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 25 optimal weight: 0.0270 chunk 78 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7221 Z= 0.186 Angle : 0.599 9.249 9957 Z= 0.290 Chirality : 0.040 0.203 1210 Planarity : 0.003 0.040 1242 Dihedral : 5.927 57.933 1302 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.85 % Allowed : 17.34 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.65 (0.28), residues: 981 helix: 0.57 (0.22), residues: 568 sheet: -3.55 (0.59), residues: 45 loop : -1.55 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 830 HIS 0.002 0.001 HIS A 275 PHE 0.022 0.001 PHE A 781 TYR 0.033 0.001 TYR A 999 ARG 0.003 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.789 Fit side-chains REVERT: A 358 MET cc_start: 0.8988 (tpt) cc_final: 0.8517 (tpp) REVERT: A 561 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8934 (mm) REVERT: A 569 PHE cc_start: 0.8825 (m-80) cc_final: 0.8442 (m-10) REVERT: A 806 TYR cc_start: 0.8041 (m-80) cc_final: 0.7790 (m-80) REVERT: A 1002 LEU cc_start: 0.9028 (mt) cc_final: 0.8680 (mt) REVERT: A 1056 MET cc_start: 0.9023 (mmm) cc_final: 0.8800 (mmm) REVERT: A 1091 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8603 (pt) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 0.1180 time to fit residues: 21.7279 Evaluate side-chains 115 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7221 Z= 0.234 Angle : 0.619 9.991 9957 Z= 0.299 Chirality : 0.041 0.198 1210 Planarity : 0.003 0.040 1242 Dihedral : 5.775 58.026 1302 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.20 % Allowed : 19.26 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.38 (0.28), residues: 981 helix: 0.81 (0.22), residues: 565 sheet: -3.57 (0.57), residues: 45 loop : -1.43 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 837 HIS 0.003 0.001 HIS A 344 PHE 0.011 0.001 PHE A1090 TYR 0.029 0.001 TYR A 999 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.738 Fit side-chains REVERT: A 556 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8448 (mm) REVERT: A 561 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8966 (mm) REVERT: A 1002 LEU cc_start: 0.9026 (mt) cc_final: 0.8654 (mt) REVERT: A 1056 MET cc_start: 0.8988 (mmm) cc_final: 0.8745 (mmm) REVERT: A 1088 LEU cc_start: 0.9494 (mm) cc_final: 0.9275 (mm) REVERT: A 1091 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8546 (pt) outliers start: 24 outliers final: 14 residues processed: 115 average time/residue: 0.1160 time to fit residues: 21.3148 Evaluate side-chains 111 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 55 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7221 Z= 0.263 Angle : 0.626 10.215 9957 Z= 0.304 Chirality : 0.042 0.191 1210 Planarity : 0.004 0.039 1242 Dihedral : 5.748 52.793 1302 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.20 % Allowed : 19.61 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.27 (0.28), residues: 981 helix: 0.92 (0.22), residues: 564 sheet: -3.69 (0.56), residues: 46 loop : -1.40 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 837 HIS 0.004 0.001 HIS A 344 PHE 0.024 0.002 PHE A 781 TYR 0.027 0.001 TYR A 999 ARG 0.001 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.786 Fit side-chains REVERT: A 358 MET cc_start: 0.9024 (tpt) cc_final: 0.8823 (tpt) REVERT: A 561 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8970 (mm) REVERT: A 819 MET cc_start: 0.8270 (ttm) cc_final: 0.7926 (ttp) REVERT: A 1002 LEU cc_start: 0.9057 (mt) cc_final: 0.8664 (mt) REVERT: A 1019 SER cc_start: 0.9501 (t) cc_final: 0.9218 (m) REVERT: A 1088 LEU cc_start: 0.9499 (mm) cc_final: 0.9280 (mm) REVERT: A 1091 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8637 (pt) outliers start: 24 outliers final: 18 residues processed: 112 average time/residue: 0.1185 time to fit residues: 21.1749 Evaluate side-chains 115 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7221 Z= 0.304 Angle : 0.650 11.471 9957 Z= 0.317 Chirality : 0.042 0.197 1210 Planarity : 0.004 0.039 1242 Dihedral : 5.835 52.840 1302 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.90 % Allowed : 20.84 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.25 (0.28), residues: 981 helix: 0.91 (0.22), residues: 567 sheet: -3.53 (0.62), residues: 46 loop : -1.36 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 837 HIS 0.005 0.001 HIS A 275 PHE 0.016 0.002 PHE A1131 TYR 0.025 0.001 TYR A 999 ARG 0.002 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.818 Fit side-chains REVERT: A 561 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8982 (mm) REVERT: A 1002 LEU cc_start: 0.9089 (mt) cc_final: 0.8699 (mt) REVERT: A 1019 SER cc_start: 0.9500 (t) cc_final: 0.9217 (m) REVERT: A 1056 MET cc_start: 0.9026 (mmm) cc_final: 0.8779 (mmm) REVERT: A 1088 LEU cc_start: 0.9506 (mm) cc_final: 0.9280 (mm) REVERT: A 1091 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8614 (pt) outliers start: 28 outliers final: 23 residues processed: 116 average time/residue: 0.1197 time to fit residues: 21.8783 Evaluate side-chains 115 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7221 Z= 0.311 Angle : 0.658 11.291 9957 Z= 0.320 Chirality : 0.043 0.197 1210 Planarity : 0.004 0.039 1242 Dihedral : 5.908 53.355 1302 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 5.25 % Allowed : 21.19 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.24 (0.28), residues: 981 helix: 0.95 (0.23), residues: 565 sheet: -3.50 (0.63), residues: 46 loop : -1.40 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 837 HIS 0.004 0.001 HIS A 275 PHE 0.025 0.002 PHE A 781 TYR 0.023 0.002 TYR A 999 ARG 0.002 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 0.828 Fit side-chains REVERT: A 489 LEU cc_start: 0.8382 (tp) cc_final: 0.8138 (tp) REVERT: A 561 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9028 (mm) REVERT: A 569 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8561 (m-10) REVERT: A 819 MET cc_start: 0.8467 (ttm) cc_final: 0.8173 (ttp) REVERT: A 1002 LEU cc_start: 0.9098 (mt) cc_final: 0.8736 (mt) REVERT: A 1019 SER cc_start: 0.9497 (t) cc_final: 0.9205 (m) REVERT: A 1056 MET cc_start: 0.9028 (mmm) cc_final: 0.8764 (mmm) REVERT: A 1088 LEU cc_start: 0.9508 (mm) cc_final: 0.9278 (mm) REVERT: A 1091 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8602 (pt) outliers start: 30 outliers final: 24 residues processed: 115 average time/residue: 0.1161 time to fit residues: 21.4495 Evaluate side-chains 113 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 90 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7221 Z= 0.245 Angle : 0.637 12.152 9957 Z= 0.308 Chirality : 0.042 0.190 1210 Planarity : 0.004 0.039 1242 Dihedral : 5.849 54.025 1302 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.08 % Allowed : 21.54 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.11 (0.28), residues: 981 helix: 1.03 (0.23), residues: 567 sheet: -3.36 (0.65), residues: 45 loop : -1.36 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 837 HIS 0.004 0.001 HIS A 275 PHE 0.015 0.001 PHE A1131 TYR 0.024 0.001 TYR A 999 ARG 0.001 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.834 Fit side-chains REVERT: A 489 LEU cc_start: 0.8367 (tp) cc_final: 0.8113 (tp) REVERT: A 556 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 561 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8963 (mm) REVERT: A 569 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8542 (m-10) REVERT: A 819 MET cc_start: 0.8432 (ttm) cc_final: 0.8133 (ttp) REVERT: A 1002 LEU cc_start: 0.9056 (mt) cc_final: 0.8693 (mt) REVERT: A 1019 SER cc_start: 0.9488 (t) cc_final: 0.9208 (m) REVERT: A 1049 MET cc_start: 0.8739 (ttp) cc_final: 0.8268 (ttm) REVERT: A 1056 MET cc_start: 0.8993 (mmm) cc_final: 0.8728 (mmm) REVERT: A 1088 LEU cc_start: 0.9499 (mm) cc_final: 0.9268 (mm) REVERT: A 1091 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8593 (pt) outliers start: 29 outliers final: 23 residues processed: 107 average time/residue: 0.1183 time to fit residues: 20.3516 Evaluate side-chains 112 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 0.0000 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7221 Z= 0.234 Angle : 0.636 12.519 9957 Z= 0.304 Chirality : 0.041 0.186 1210 Planarity : 0.004 0.039 1242 Dihedral : 5.794 54.280 1302 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.60 % Allowed : 21.19 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.04 (0.28), residues: 981 helix: 1.11 (0.23), residues: 567 sheet: -3.28 (0.66), residues: 45 loop : -1.37 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 837 HIS 0.003 0.001 HIS A 275 PHE 0.025 0.002 PHE A 781 TYR 0.024 0.001 TYR A 999 ARG 0.001 0.000 ARG A 835 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 0.802 Fit side-chains REVERT: A 146 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7651 (pp30) REVERT: A 325 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: A 358 MET cc_start: 0.8923 (ttt) cc_final: 0.8718 (ttt) REVERT: A 489 LEU cc_start: 0.8354 (tp) cc_final: 0.8116 (tp) REVERT: A 556 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8377 (mm) REVERT: A 561 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8956 (mm) REVERT: A 569 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8442 (m-10) REVERT: A 819 MET cc_start: 0.8426 (ttm) cc_final: 0.8129 (ttp) REVERT: A 1002 LEU cc_start: 0.9033 (mt) cc_final: 0.8655 (mt) REVERT: A 1016 LEU cc_start: 0.9227 (tp) cc_final: 0.8912 (tp) REVERT: A 1019 SER cc_start: 0.9503 (t) cc_final: 0.9229 (m) REVERT: A 1049 MET cc_start: 0.8741 (ttp) cc_final: 0.8265 (ttm) REVERT: A 1056 MET cc_start: 0.8912 (mmm) cc_final: 0.8666 (mmm) REVERT: A 1088 LEU cc_start: 0.9492 (mm) cc_final: 0.9259 (mm) REVERT: A 1091 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8596 (pt) outliers start: 32 outliers final: 23 residues processed: 115 average time/residue: 0.1143 time to fit residues: 21.0297 Evaluate side-chains 116 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.0170 chunk 77 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 9 optimal weight: 0.0060 chunk 14 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 overall best weight: 0.1234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099252 restraints weight = 14081.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100364 restraints weight = 6486.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.101530 restraints weight = 4498.832| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7221 Z= 0.148 Angle : 0.603 12.817 9957 Z= 0.285 Chirality : 0.040 0.175 1210 Planarity : 0.003 0.040 1242 Dihedral : 5.526 53.866 1302 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.50 % Allowed : 23.99 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.29 (0.29), residues: 981 helix: 1.32 (0.23), residues: 569 sheet: -3.00 (0.70), residues: 45 loop : -1.16 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1013 HIS 0.001 0.000 HIS A 361 PHE 0.015 0.001 PHE A1131 TYR 0.026 0.001 TYR A 999 ARG 0.001 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1608.96 seconds wall clock time: 29 minutes 31.49 seconds (1771.49 seconds total)