Starting phenix.real_space_refine on Wed Sep 17 11:43:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk5_61544/09_2025/9jk5_61544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk5_61544/09_2025/9jk5_61544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jk5_61544/09_2025/9jk5_61544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk5_61544/09_2025/9jk5_61544.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk5_61544/09_2025/9jk5_61544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk5_61544/09_2025/9jk5_61544.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 64 5.16 5 C 5383 2.51 5 N 1424 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8359 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8279 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 997} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'NAG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.20, per 1000 atoms: 0.26 Number of scatterers: 8359 At special positions: 0 Unit cell: (79.68, 87.98, 160.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 1 15.00 O 1487 8.00 N 1424 7.00 C 5383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1401 " - " ASN A1202 " " NAG A1402 " - " ASN A1205 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 321.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 55.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 18 through 44 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.515A pdb=" N ALA A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 122 removed outlier: 3.735A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 117 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 139 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.494A pdb=" N ASN A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 302 removed outlier: 4.465A pdb=" N VAL A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 309 through 323 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 329 through 349 removed outlier: 3.799A pdb=" N GLN A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 575 through 581 removed outlier: 4.565A pdb=" N THR A 580 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 removed outlier: 3.675A pdb=" N GLY A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 616 removed outlier: 3.952A pdb=" N ARG A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.558A pdb=" N ALA A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 705 through 712 removed outlier: 3.618A pdb=" N VAL A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 743 Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.591A pdb=" N LEU A 762 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 858 through 866 Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 979 through 993 Processing helix chain 'A' and resid 1005 through 1007 No H-bonds generated for 'chain 'A' and resid 1005 through 1007' Processing helix chain 'A' and resid 1008 through 1015 removed outlier: 3.640A pdb=" N GLN A1014 " --> pdb=" O CYS A1010 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 Processing helix chain 'A' and resid 1074 through 1113 removed outlier: 3.569A pdb=" N LEU A1078 " --> pdb=" O SER A1074 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A1103 " --> pdb=" O CYS A1099 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1140 Proline residue: A1133 - end of helix removed outlier: 3.607A pdb=" N SER A1136 " --> pdb=" O TYR A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1201 removed outlier: 3.555A pdb=" N SER A1177 " --> pdb=" O LEU A1173 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU A1178 " --> pdb=" O LEU A1174 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N THR A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A1199 " --> pdb=" O CYS A1195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1251 removed outlier: 3.902A pdb=" N THR A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 3.682A pdb=" N THR A1265 " --> pdb=" O SER A1262 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A1266 " --> pdb=" O PRO A1263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1262 through 1266' Processing helix chain 'A' and resid 1268 through 1292 Proline residue: A1274 - end of helix removed outlier: 3.589A pdb=" N THR A1292 " --> pdb=" O LEU A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1352 removed outlier: 3.991A pdb=" N GLY A1313 " --> pdb=" O THR A1309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS A1314 " --> pdb=" O TRP A1310 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A1325 " --> pdb=" O VAL A1321 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A1326 " --> pdb=" O VAL A1322 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A1327 " --> pdb=" O THR A1323 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A1328 " --> pdb=" O ASN A1324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 170 Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190 removed outlier: 3.664A pdb=" N ARG A 241 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 878 through 880 removed outlier: 6.647A pdb=" N ILE A 879 " --> pdb=" O THR A 976 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE A 975 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR A 853 " --> pdb=" O PHE A 975 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 413 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE A 854 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS A 415 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 412 " --> pdb=" O CYS A 998 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU A1000 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N CYS A 414 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N SER A1002 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A 997 " --> pdb=" O ILE A1017 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A1019 " --> pdb=" O THR A 997 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS A 999 " --> pdb=" O ILE A1019 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A1021 " --> pdb=" O CYS A 999 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A1001 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER A1018 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE A1067 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A1020 " --> pdb=" O PHE A1067 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 557 removed outlier: 3.933A pdb=" N GLU A 554 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE A 434 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 556 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN A 830 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 431 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 435 " --> pdb=" O MET A 824 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N MET A 824 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS A 713 " --> pdb=" O GLN A 821 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 823 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP A 715 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLY A 825 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N TRP A 717 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 12.791A pdb=" N VAL A 827 " --> pdb=" O TRP A 717 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 552 through 557 removed outlier: 3.933A pdb=" N GLU A 554 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE A 434 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 556 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN A 830 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 431 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 435 " --> pdb=" O MET A 824 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N MET A 824 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN A 821 " --> pdb=" O PRO A 753 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE A 823 " --> pdb=" O TYR A 751 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR A 751 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY A 825 " --> pdb=" O PHE A 749 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 749 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 704 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 702 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A 752 " --> pdb=" O MET A 700 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 700 " --> pdb=" O LYS A 752 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER A 683 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS A 691 " --> pdb=" O GLN A 649 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN A 649 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N ILE A 767 " --> pdb=" O HIS A 652 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA A 654 " --> pdb=" O ILE A 767 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU A 769 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 656 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AA7, first strand: chain 'A' and resid 756 through 757 440 hydrogen bonds defined for protein. 1281 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: 1.54 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1449 1.32 - 1.45: 2114 1.45 - 1.57: 4892 1.57 - 1.69: 3 1.69 - 1.81: 87 Bond restraints: 8545 Sorted by residual: bond pdb=" C1 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CB PRO A 213 " pdb=" CG PRO A 213 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.52e+00 bond pdb=" C5 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG A1402 " pdb=" O5 NAG A1402 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C5 NAG A1402 " pdb=" O5 NAG A1402 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 ... (remaining 8540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11398 2.00 - 4.01: 173 4.01 - 6.01: 25 6.01 - 8.01: 3 8.01 - 10.01: 2 Bond angle restraints: 11601 Sorted by residual: angle pdb=" CA PRO A 213 " pdb=" N PRO A 213 " pdb=" CD PRO A 213 " ideal model delta sigma weight residual 112.00 101.99 10.01 1.40e+00 5.10e-01 5.12e+01 angle pdb=" N PRO A 213 " pdb=" CD PRO A 213 " pdb=" CG PRO A 213 " ideal model delta sigma weight residual 103.20 98.51 4.69 1.50e+00 4.44e-01 9.76e+00 angle pdb=" CA GLN A 830 " pdb=" CB GLN A 830 " pdb=" CG GLN A 830 " ideal model delta sigma weight residual 114.10 119.21 -5.11 2.00e+00 2.50e-01 6.52e+00 angle pdb=" C CYS A1131 " pdb=" N TYR A1132 " pdb=" CA TYR A1132 " ideal model delta sigma weight residual 121.80 115.59 6.21 2.44e+00 1.68e-01 6.47e+00 angle pdb=" C ASP A 133 " pdb=" N GLN A 134 " pdb=" CA GLN A 134 " ideal model delta sigma weight residual 120.28 116.91 3.37 1.34e+00 5.57e-01 6.33e+00 ... (remaining 11596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.19: 4577 23.19 - 46.37: 474 46.37 - 69.56: 98 69.56 - 92.75: 13 92.75 - 115.94: 3 Dihedral angle restraints: 5165 sinusoidal: 2108 harmonic: 3057 Sorted by residual: dihedral pdb=" C1 NAG A1401 " pdb=" C5 NAG A1401 " pdb=" O5 NAG A1401 " pdb=" C4 NAG A1401 " ideal model delta sinusoidal sigma weight residual -64.11 51.83 -115.94 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C1 NAG A1401 " pdb=" C5 NAG A1401 " pdb=" O5 NAG A1401 " pdb=" C6 NAG A1401 " ideal model delta sinusoidal sigma weight residual 171.16 -73.26 -115.58 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CA MET A1151 " pdb=" C MET A1151 " pdb=" N ALA A1152 " pdb=" CA ALA A1152 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1066 0.045 - 0.091: 238 0.091 - 0.136: 54 0.136 - 0.181: 3 0.181 - 0.227: 1 Chirality restraints: 1362 Sorted by residual: chirality pdb=" C1 NAG A1401 " pdb=" ND2 ASN A1202 " pdb=" C2 NAG A1401 " pdb=" O5 NAG A1401 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASP A 133 " pdb=" N ASP A 133 " pdb=" C ASP A 133 " pdb=" CB ASP A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1359 not shown) Planarity restraints: 1445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 212 " -0.071 5.00e-02 4.00e+02 1.01e-01 1.65e+01 pdb=" N PRO A 213 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 313 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C THR A 313 " -0.046 2.00e-02 2.50e+03 pdb=" O THR A 313 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 314 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1128 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C SER A1128 " -0.045 2.00e-02 2.50e+03 pdb=" O SER A1128 " 0.017 2.00e-02 2.50e+03 pdb=" N CYS A1129 " 0.015 2.00e-02 2.50e+03 ... (remaining 1442 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 728 2.74 - 3.28: 7765 3.28 - 3.82: 13533 3.82 - 4.36: 15180 4.36 - 4.90: 27767 Nonbonded interactions: 64973 Sorted by model distance: nonbonded pdb=" O HIS A 625 " pdb=" OH TYR A 745 " model vdw 2.202 3.040 nonbonded pdb=" O LEU A1135 " pdb=" OG SER A1138 " model vdw 2.206 3.040 nonbonded pdb=" N GLU A 207 " pdb=" OE1 GLU A 207 " model vdw 2.226 3.120 nonbonded pdb=" O THR A 267 " pdb=" ND2 ASN A 271 " model vdw 2.228 3.120 nonbonded pdb=" O ASP A 595 " pdb=" OG1 THR A 599 " model vdw 2.276 3.040 ... (remaining 64968 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 individual isotropic 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: 3.880 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.003 0.128 8547 Z= 0.147 Angle : 0.604 10.015 11607 Z= 0.315 Chirality : 0.039 0.227 1362 Planarity : 0.006 0.101 1443 Dihedral : 18.877 115.936 3169 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.95 % Allowed : 25.72 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.27), residues: 1034 helix: 2.00 (0.22), residues: 538 sheet: 0.12 (0.58), residues: 81 loop : -0.83 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1341 TYR 0.010 0.001 TYR A 312 PHE 0.038 0.001 PHE A 55 TRP 0.041 0.001 TRP A 875 HIS 0.006 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8545) covalent geometry : angle 0.60217 (11601) hydrogen bonds : bond 0.18328 ( 434) hydrogen bonds : angle 5.93519 ( 1281) link_NAG-ASN : bond 0.00316 ( 2) link_NAG-ASN : angle 1.88457 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 79 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 46 residues processed: 132 average time/residue: 0.4436 time to fit residues: 63.7071 Evaluate side-chains 123 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1296 SER Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1322 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 419 GLN A 963 GLN A1057 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.191588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124064 restraints weight = 9278.937| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.31 r_work: 0.3284 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8547 Z= 0.213 Angle : 0.692 9.759 11607 Z= 0.346 Chirality : 0.044 0.196 1362 Planarity : 0.006 0.073 1443 Dihedral : 12.094 92.111 1276 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 8.18 % Allowed : 21.68 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.27), residues: 1034 helix: 1.74 (0.22), residues: 544 sheet: -0.21 (0.58), residues: 88 loop : -0.91 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1341 TYR 0.017 0.002 TYR A 993 PHE 0.018 0.002 PHE A 386 TRP 0.019 0.002 TRP A 875 HIS 0.006 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 8545) covalent geometry : angle 0.69071 (11601) hydrogen bonds : bond 0.07745 ( 434) hydrogen bonds : angle 4.73704 ( 1281) link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 1.81351 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 76 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8204 (mmt) REVERT: A 578 HIS cc_start: 0.3036 (OUTLIER) cc_final: 0.2751 (t-90) REVERT: A 824 MET cc_start: 0.5344 (ppp) cc_final: 0.3360 (ttt) REVERT: A 832 GLN cc_start: 0.7305 (mm-40) cc_final: 0.7078 (mm-40) REVERT: A 856 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 967 ASN cc_start: 0.8535 (p0) cc_final: 0.8244 (p0) REVERT: A 1068 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6726 (ttm170) REVERT: A 1201 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6780 (ptt-90) REVERT: A 1248 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 1352 MET cc_start: 0.2320 (ttp) cc_final: 0.2037 (tmm) outliers start: 77 outliers final: 39 residues processed: 141 average time/residue: 0.4627 time to fit residues: 70.6837 Evaluate side-chains 115 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 71 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1010 CYS Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1201 ARG Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1320 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1057 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.198762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139821 restraints weight = 9163.059| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.60 r_work: 0.3462 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8547 Z= 0.115 Angle : 0.560 11.768 11607 Z= 0.278 Chirality : 0.038 0.139 1362 Planarity : 0.005 0.063 1443 Dihedral : 9.747 79.719 1243 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.63 % Allowed : 23.70 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.27), residues: 1034 helix: 2.23 (0.23), residues: 546 sheet: -0.28 (0.54), residues: 100 loop : -0.78 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 122 TYR 0.009 0.001 TYR A 312 PHE 0.011 0.001 PHE A 689 TRP 0.013 0.001 TRP A 310 HIS 0.008 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8545) covalent geometry : angle 0.55637 (11601) hydrogen bonds : bond 0.05203 ( 434) hydrogen bonds : angle 4.24193 ( 1281) link_NAG-ASN : bond 0.00185 ( 2) link_NAG-ASN : angle 2.69214 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 83 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8040 (mmt) REVERT: A 578 HIS cc_start: 0.3246 (OUTLIER) cc_final: 0.2936 (t-90) REVERT: A 824 MET cc_start: 0.5311 (ppp) cc_final: 0.3241 (ttt) outliers start: 53 outliers final: 20 residues processed: 127 average time/residue: 0.4930 time to fit residues: 67.3300 Evaluate side-chains 95 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1005 ASN A1057 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.193172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133146 restraints weight = 9282.809| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.56 r_work: 0.3329 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8547 Z= 0.178 Angle : 0.617 10.550 11607 Z= 0.310 Chirality : 0.040 0.149 1362 Planarity : 0.005 0.069 1443 Dihedral : 8.267 76.164 1221 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.84 % Allowed : 24.34 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.27), residues: 1034 helix: 2.01 (0.23), residues: 546 sheet: -0.13 (0.58), residues: 90 loop : -0.90 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1341 TYR 0.015 0.002 TYR A 993 PHE 0.029 0.002 PHE A 55 TRP 0.008 0.001 TRP A1269 HIS 0.010 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8545) covalent geometry : angle 0.61422 (11601) hydrogen bonds : bond 0.06734 ( 434) hydrogen bonds : angle 4.31484 ( 1281) link_NAG-ASN : bond 0.00280 ( 2) link_NAG-ASN : angle 2.80942 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 78 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8591 (t0) REVERT: A 280 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8225 (mmt) REVERT: A 578 HIS cc_start: 0.3273 (OUTLIER) cc_final: 0.2962 (t-90) REVERT: A 824 MET cc_start: 0.5139 (ppp) cc_final: 0.3140 (ttt) REVERT: A 830 GLN cc_start: 0.5842 (tp-100) cc_final: 0.5448 (tp-100) REVERT: A 1068 ARG cc_start: 0.7008 (ttm170) cc_final: 0.6644 (ttm170) REVERT: A 1185 ILE cc_start: 0.8380 (mt) cc_final: 0.8128 (mp) REVERT: A 1312 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6764 (tm) outliers start: 55 outliers final: 32 residues processed: 121 average time/residue: 0.4526 time to fit residues: 59.2506 Evaluate side-chains 111 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1322 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 50.0000 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN A 963 GLN A1005 ASN A1057 GLN A1330 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.193295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131816 restraints weight = 9223.249| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.95 r_work: 0.3338 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8547 Z= 0.164 Angle : 0.598 10.109 11607 Z= 0.303 Chirality : 0.040 0.149 1362 Planarity : 0.005 0.070 1443 Dihedral : 8.143 74.784 1220 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.70 % Allowed : 23.59 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.27), residues: 1034 helix: 1.99 (0.23), residues: 547 sheet: -0.15 (0.58), residues: 90 loop : -0.90 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1341 TYR 0.013 0.001 TYR A 993 PHE 0.030 0.002 PHE A 55 TRP 0.009 0.001 TRP A 67 HIS 0.009 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8545) covalent geometry : angle 0.59562 (11601) hydrogen bonds : bond 0.06493 ( 434) hydrogen bonds : angle 4.26971 ( 1281) link_NAG-ASN : bond 0.00109 ( 2) link_NAG-ASN : angle 2.25084 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 78 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8595 (t0) REVERT: A 280 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8195 (mmt) REVERT: A 578 HIS cc_start: 0.3151 (OUTLIER) cc_final: 0.2824 (t-90) REVERT: A 824 MET cc_start: 0.5181 (ppp) cc_final: 0.3303 (ttt) REVERT: A 1068 ARG cc_start: 0.6989 (ttm170) cc_final: 0.6623 (ttm170) REVERT: A 1312 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6685 (tm) outliers start: 63 outliers final: 37 residues processed: 131 average time/residue: 0.4638 time to fit residues: 65.5901 Evaluate side-chains 116 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1163 LYS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1322 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1005 ASN A1057 GLN A1330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.194977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127484 restraints weight = 9124.788| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.30 r_work: 0.3352 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8547 Z= 0.132 Angle : 0.565 9.188 11607 Z= 0.287 Chirality : 0.039 0.142 1362 Planarity : 0.005 0.067 1443 Dihedral : 7.914 74.946 1218 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.06 % Allowed : 24.34 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.27), residues: 1034 helix: 2.15 (0.23), residues: 547 sheet: -0.23 (0.53), residues: 101 loop : -0.82 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1341 TYR 0.012 0.001 TYR A 312 PHE 0.029 0.001 PHE A 55 TRP 0.012 0.001 TRP A 310 HIS 0.009 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8545) covalent geometry : angle 0.56325 (11601) hydrogen bonds : bond 0.05763 ( 434) hydrogen bonds : angle 4.15722 ( 1281) link_NAG-ASN : bond 0.00062 ( 2) link_NAG-ASN : angle 1.90707 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 80 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 578 HIS cc_start: 0.3304 (OUTLIER) cc_final: 0.2957 (t-90) REVERT: A 649 GLN cc_start: 0.1324 (OUTLIER) cc_final: 0.1008 (mm110) REVERT: A 824 MET cc_start: 0.5127 (ppp) cc_final: 0.3207 (ttt) REVERT: A 830 GLN cc_start: 0.5792 (tp-100) cc_final: 0.5282 (tp-100) REVERT: A 832 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6800 (mm110) REVERT: A 856 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7497 (mp) REVERT: A 1312 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6734 (tm) outliers start: 57 outliers final: 31 residues processed: 125 average time/residue: 0.4595 time to fit residues: 61.9634 Evaluate side-chains 110 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 50 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 399 HIS ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1057 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.194514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126936 restraints weight = 9209.612| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.32 r_work: 0.3352 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8547 Z= 0.142 Angle : 0.576 10.445 11607 Z= 0.291 Chirality : 0.039 0.181 1362 Planarity : 0.005 0.067 1443 Dihedral : 7.900 74.227 1218 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.27 % Allowed : 24.55 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.27), residues: 1034 helix: 2.08 (0.23), residues: 549 sheet: -0.26 (0.53), residues: 101 loop : -0.80 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1341 TYR 0.012 0.001 TYR A 312 PHE 0.029 0.002 PHE A 55 TRP 0.011 0.001 TRP A 310 HIS 0.009 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8545) covalent geometry : angle 0.57430 (11601) hydrogen bonds : bond 0.05926 ( 434) hydrogen bonds : angle 4.16391 ( 1281) link_NAG-ASN : bond 0.00032 ( 2) link_NAG-ASN : angle 1.84886 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 78 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7491 (tmt170) REVERT: A 60 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8627 (t0) REVERT: A 578 HIS cc_start: 0.3284 (OUTLIER) cc_final: 0.2927 (t-90) REVERT: A 649 GLN cc_start: 0.1407 (OUTLIER) cc_final: 0.1085 (mm110) REVERT: A 824 MET cc_start: 0.5052 (ppp) cc_final: 0.3187 (ttt) REVERT: A 830 GLN cc_start: 0.5801 (tp-100) cc_final: 0.5271 (tp-100) REVERT: A 832 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6889 (mm110) REVERT: A 856 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7542 (mp) REVERT: A 1312 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6851 (tm) outliers start: 59 outliers final: 39 residues processed: 126 average time/residue: 0.4977 time to fit residues: 67.6850 Evaluate side-chains 119 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 74 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1322 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1057 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.195327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134449 restraints weight = 9081.447| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.12 r_work: 0.3382 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8547 Z= 0.129 Angle : 0.561 10.221 11607 Z= 0.284 Chirality : 0.039 0.165 1362 Planarity : 0.005 0.066 1443 Dihedral : 7.777 73.907 1218 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.31 % Allowed : 25.50 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.27), residues: 1034 helix: 2.18 (0.23), residues: 549 sheet: -0.25 (0.54), residues: 101 loop : -0.74 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1341 TYR 0.012 0.001 TYR A 312 PHE 0.029 0.001 PHE A 55 TRP 0.012 0.001 TRP A 310 HIS 0.009 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8545) covalent geometry : angle 0.56010 (11601) hydrogen bonds : bond 0.05553 ( 434) hydrogen bonds : angle 4.09585 ( 1281) link_NAG-ASN : bond 0.00055 ( 2) link_NAG-ASN : angle 1.69342 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8590 (t0) REVERT: A 578 HIS cc_start: 0.3303 (OUTLIER) cc_final: 0.2918 (t-90) REVERT: A 649 GLN cc_start: 0.1409 (OUTLIER) cc_final: 0.1063 (mm110) REVERT: A 685 MET cc_start: 0.2385 (ttm) cc_final: 0.1894 (ttp) REVERT: A 824 MET cc_start: 0.5011 (ppp) cc_final: 0.3228 (ttt) REVERT: A 830 GLN cc_start: 0.5677 (tp-100) cc_final: 0.5300 (tp-100) REVERT: A 856 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7549 (mp) REVERT: A 1312 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6734 (tm) outliers start: 50 outliers final: 30 residues processed: 122 average time/residue: 0.4866 time to fit residues: 64.1656 Evaluate side-chains 113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1005 ASN A1057 GLN A1330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.193318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134272 restraints weight = 9167.046| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.42 r_work: 0.3320 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8547 Z= 0.172 Angle : 0.624 10.828 11607 Z= 0.315 Chirality : 0.042 0.287 1362 Planarity : 0.005 0.068 1443 Dihedral : 7.935 71.906 1213 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.74 % Allowed : 25.61 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.27), residues: 1034 helix: 2.00 (0.23), residues: 548 sheet: -0.31 (0.54), residues: 101 loop : -0.79 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1341 TYR 0.014 0.001 TYR A 993 PHE 0.031 0.002 PHE A 300 TRP 0.008 0.001 TRP A 310 HIS 0.008 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8545) covalent geometry : angle 0.62007 (11601) hydrogen bonds : bond 0.06520 ( 434) hydrogen bonds : angle 4.21090 ( 1281) link_NAG-ASN : bond 0.00331 ( 2) link_NAG-ASN : angle 3.23108 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 79 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7497 (tmt170) REVERT: A 60 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8601 (t0) REVERT: A 83 CYS cc_start: 0.7581 (m) cc_final: 0.7176 (t) REVERT: A 578 HIS cc_start: 0.3330 (OUTLIER) cc_final: 0.2924 (t-90) REVERT: A 649 GLN cc_start: 0.1462 (OUTLIER) cc_final: 0.1090 (mm110) REVERT: A 685 MET cc_start: 0.2481 (ttm) cc_final: 0.1938 (ttp) REVERT: A 754 MET cc_start: 0.3687 (mtt) cc_final: 0.3032 (mtm) REVERT: A 824 MET cc_start: 0.4963 (ppp) cc_final: 0.3255 (ttt) REVERT: A 856 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7552 (mp) REVERT: A 1068 ARG cc_start: 0.6996 (ttm170) cc_final: 0.6600 (ttm170) REVERT: A 1312 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6649 (tm) outliers start: 54 outliers final: 32 residues processed: 124 average time/residue: 0.5113 time to fit residues: 68.2454 Evaluate side-chains 113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1010 CYS Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 0.1980 chunk 48 optimal weight: 20.0000 chunk 96 optimal weight: 0.0070 chunk 77 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1057 GLN A1330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.198825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139896 restraints weight = 9075.361| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.59 r_work: 0.3434 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8547 Z= 0.113 Angle : 0.560 9.675 11607 Z= 0.283 Chirality : 0.038 0.187 1362 Planarity : 0.005 0.066 1443 Dihedral : 7.523 74.231 1213 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.55 % Allowed : 28.91 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.28), residues: 1034 helix: 2.33 (0.23), residues: 549 sheet: -0.21 (0.54), residues: 101 loop : -0.62 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1341 TYR 0.008 0.001 TYR A 312 PHE 0.039 0.001 PHE A 55 TRP 0.022 0.001 TRP A 875 HIS 0.009 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8545) covalent geometry : angle 0.55442 (11601) hydrogen bonds : bond 0.04619 ( 434) hydrogen bonds : angle 4.00223 ( 1281) link_NAG-ASN : bond 0.00500 ( 2) link_NAG-ASN : angle 3.60755 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 578 HIS cc_start: 0.3349 (OUTLIER) cc_final: 0.2958 (t-90) REVERT: A 649 GLN cc_start: 0.1500 (OUTLIER) cc_final: 0.1140 (mm110) REVERT: A 685 MET cc_start: 0.2295 (ttm) cc_final: 0.1788 (ttp) REVERT: A 754 MET cc_start: 0.3719 (mtt) cc_final: 0.3099 (mtm) REVERT: A 824 MET cc_start: 0.5005 (ppp) cc_final: 0.3399 (ttt) REVERT: A 830 GLN cc_start: 0.5116 (tp-100) cc_final: 0.4763 (tp-100) REVERT: A 1185 ILE cc_start: 0.8254 (mt) cc_final: 0.8017 (mp) REVERT: A 1312 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6570 (tm) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.5242 time to fit residues: 59.0753 Evaluate side-chains 95 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1010 CYS Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1145 HIS Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 0.0010 chunk 64 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 71 optimal weight: 0.0040 chunk 56 optimal weight: 7.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A 964 ASN A1057 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.197971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137580 restraints weight = 9200.200| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.89 r_work: 0.3425 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8547 Z= 0.116 Angle : 0.564 9.630 11607 Z= 0.286 Chirality : 0.039 0.162 1362 Planarity : 0.005 0.065 1443 Dihedral : 7.339 74.521 1211 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.44 % Allowed : 28.80 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.28), residues: 1034 helix: 2.35 (0.23), residues: 549 sheet: -0.22 (0.54), residues: 101 loop : -0.58 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1341 TYR 0.009 0.001 TYR A 312 PHE 0.038 0.001 PHE A 55 TRP 0.032 0.001 TRP A 875 HIS 0.011 0.001 HIS A1330 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8545) covalent geometry : angle 0.55698 (11601) hydrogen bonds : bond 0.04786 ( 434) hydrogen bonds : angle 3.93618 ( 1281) link_NAG-ASN : bond 0.00342 ( 2) link_NAG-ASN : angle 4.02415 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.45 seconds wall clock time: 63 minutes 0.13 seconds (3780.13 seconds total)