Starting phenix.real_space_refine on Sun Jun 8 00:17:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjc_62366/06_2025/9kjc_62366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjc_62366/06_2025/9kjc_62366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kjc_62366/06_2025/9kjc_62366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjc_62366/06_2025/9kjc_62366.map" model { file = "/net/cci-nas-00/data/ceres_data/9kjc_62366/06_2025/9kjc_62366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjc_62366/06_2025/9kjc_62366.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 5789 2.51 5 N 1521 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9015 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 8981 Classifications: {'peptide': 1168} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 1138} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'BLD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.63 Number of scatterers: 9015 At special positions: 0 Unit cell: (78.66, 106.875, 138.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1668 8.00 N 1521 7.00 C 5789 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 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 63.9% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 34 through 71 Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 75 through 130 Processing helix chain 'A' and resid 139 through 160 removed outlier: 3.617A pdb=" N PHE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 removed outlier: 3.539A pdb=" N GLY A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 233 removed outlier: 3.794A pdb=" N LEU A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Proline residue: A 196 - end of helix removed outlier: 4.407A pdb=" N GLN A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 242 through 297 removed outlier: 3.560A pdb=" N ASN A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 343 removed outlier: 4.510A pdb=" N ILE A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 456 through 462 removed outlier: 3.684A pdb=" N ASN A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.910A pdb=" N ALA A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.607A pdb=" N THR A 487 " --> pdb=" O HIS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 521 removed outlier: 3.762A pdb=" N ALA A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 548 removed outlier: 4.248A pdb=" N VAL A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 removed outlier: 4.197A pdb=" N SER A 592 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 593 " --> pdb=" O ALA A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 593' Processing helix chain 'A' and resid 595 through 605 removed outlier: 3.742A pdb=" N VAL A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 683 through 715 removed outlier: 3.791A pdb=" N SER A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 689 " --> pdb=" O PRO A 685 " (cutoff:3.500A) Proline residue: A 702 - end of helix Processing helix chain 'A' and resid 719 through 773 removed outlier: 3.539A pdb=" N MET A 723 " --> pdb=" O ASP A 719 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 724 " --> pdb=" O TYR A 720 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.894A pdb=" N PHE A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 829 removed outlier: 4.016A pdb=" N ALA A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS A 801 " --> pdb=" O ALA A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 853 removed outlier: 3.811A pdb=" N LEU A 835 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) Proline residue: A 841 - end of helix Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 865 through 878 removed outlier: 3.841A pdb=" N SER A 869 " --> pdb=" O HIS A 865 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 884 removed outlier: 3.952A pdb=" N ALA A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 941 removed outlier: 3.778A pdb=" N SER A 893 " --> pdb=" O SER A 889 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 894 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Proline residue: A 902 - end of helix Processing helix chain 'A' and resid 948 through 968 Processing helix chain 'A' and resid 968 through 975 removed outlier: 4.047A pdb=" N GLU A 972 " --> pdb=" O SER A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 988 removed outlier: 3.553A pdb=" N LEU A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 988 " --> pdb=" O PHE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1053 Processing helix chain 'A' and resid 1054 through 1059 removed outlier: 4.405A pdb=" N GLU A1059 " --> pdb=" O ILE A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1080 through 1086 removed outlier: 3.899A pdb=" N LEU A1084 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 removed outlier: 4.361A pdb=" N ILE A1119 " --> pdb=" O GLU A1115 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A1120 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1133 removed outlier: 3.598A pdb=" N GLY A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1166 removed outlier: 3.955A pdb=" N LYS A1154 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1194 removed outlier: 3.671A pdb=" N GLU A1189 " --> pdb=" O CYS A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1235 removed outlier: 4.462A pdb=" N SER A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1252 removed outlier: 3.724A pdb=" N ARG A1243 " --> pdb=" O GLY A1239 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 390 removed outlier: 4.875A pdb=" N VAL A 370 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER A 421 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 557 through 558 removed outlier: 5.517A pdb=" N ALA A 397 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 574 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 399 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A 573 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 443 through 445 Processing sheet with id=AA4, first strand: chain 'A' and resid 1031 through 1034 removed outlier: 5.979A pdb=" N PHE A1031 " --> pdb=" O HIS A1014 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A1014 " --> pdb=" O PHE A1031 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A1033 " --> pdb=" O PHE A1012 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1041 Processing sheet with id=AA6, first strand: chain 'A' and resid 1216 through 1220 removed outlier: 3.603A pdb=" N GLY A1228 " --> pdb=" O ILE A1216 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A1218 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU A1226 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN A1220 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE A1224 " --> pdb=" O GLN A1220 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 2.81 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: 1519 1.32 - 1.45: 2400 1.45 - 1.57: 5203 1.57 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 9187 Sorted by residual: bond pdb=" N THR A1249 " pdb=" CA THR A1249 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.17e-02 7.31e+03 7.39e+00 bond pdb=" N LEU A1245 " pdb=" CA LEU A1245 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.85e+00 bond pdb=" N ARG A1251 " pdb=" CA ARG A1251 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.17e-02 7.31e+03 6.62e+00 bond pdb=" N HIS A1250 " pdb=" CA HIS A1250 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.23e-02 6.61e+03 6.34e+00 bond pdb=" N LEU A1244 " pdb=" CA LEU A1244 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.96e+00 ... (remaining 9182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12152 1.90 - 3.80: 234 3.80 - 5.69: 36 5.69 - 7.59: 10 7.59 - 9.49: 8 Bond angle restraints: 12440 Sorted by residual: angle pdb=" N ARG A1243 " pdb=" CA ARG A1243 " pdb=" C ARG A1243 " ideal model delta sigma weight residual 111.11 105.50 5.61 1.20e+00 6.94e-01 2.18e+01 angle pdb=" N GLU A 729 " pdb=" CA GLU A 729 " pdb=" CB GLU A 729 " ideal model delta sigma weight residual 110.39 117.36 -6.97 1.66e+00 3.63e-01 1.76e+01 angle pdb=" C LYS A 728 " pdb=" N GLU A 729 " pdb=" CA GLU A 729 " ideal model delta sigma weight residual 120.72 113.78 6.94 1.67e+00 3.59e-01 1.73e+01 angle pdb=" C SER A 183 " pdb=" N ALA A 184 " pdb=" CA ALA A 184 " ideal model delta sigma weight residual 121.54 114.20 7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLY A 977 " pdb=" N GLU A 978 " pdb=" CA GLU A 978 " ideal model delta sigma weight residual 121.31 126.88 -5.57 1.49e+00 4.50e-01 1.40e+01 ... (remaining 12435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 5255 26.44 - 52.87: 220 52.87 - 79.31: 25 79.31 - 105.75: 9 105.75 - 132.18: 1 Dihedral angle restraints: 5510 sinusoidal: 2165 harmonic: 3345 Sorted by residual: dihedral pdb=" CA GLU A 978 " pdb=" C GLU A 978 " pdb=" N ALA A 979 " pdb=" CA ALA A 979 " ideal model delta harmonic sigma weight residual -180.00 -136.98 -43.02 0 5.00e+00 4.00e-02 7.40e+01 dihedral pdb=" CA TRP A 185 " pdb=" C TRP A 185 " pdb=" N LYS A 186 " pdb=" CA LYS A 186 " ideal model delta harmonic sigma weight residual 180.00 149.73 30.27 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" C06 BLD A1301 " pdb=" C07 BLD A1301 " pdb=" O07 BLD A1301 " pdb=" C08 BLD A1301 " ideal model delta sinusoidal sigma weight residual -67.68 64.50 -132.18 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 5507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1123 0.048 - 0.097: 254 0.097 - 0.145: 54 0.145 - 0.193: 4 0.193 - 0.241: 3 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C10 BLD A1301 " pdb=" C01 BLD A1301 " pdb=" C05 BLD A1301 " pdb=" C09 BLD A1301 " both_signs ideal model delta sigma weight residual False -3.02 -2.78 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C09 BLD A1301 " pdb=" C08 BLD A1301 " pdb=" C10 BLD A1301 " pdb=" C11 BLD A1301 " both_signs ideal model delta sigma weight residual False -2.42 -2.64 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LEU A1247 " pdb=" N LEU A1247 " pdb=" C LEU A1247 " pdb=" CB LEU A1247 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1435 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1243 " 0.530 9.50e-02 1.11e+02 2.38e-01 3.46e+01 pdb=" NE ARG A1243 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A1243 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A1243 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1243 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1251 " -0.365 9.50e-02 1.11e+02 1.64e-01 1.64e+01 pdb=" NE ARG A1251 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A1251 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A1251 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1251 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 701 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO A 702 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 702 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 702 " -0.039 5.00e-02 4.00e+02 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 961 2.74 - 3.28: 9510 3.28 - 3.82: 14576 3.82 - 4.36: 16271 4.36 - 4.90: 27699 Nonbonded interactions: 69017 Sorted by model distance: nonbonded pdb=" OG1 THR A 395 " pdb=" OD1 ASP A 569 " model vdw 2.206 3.040 nonbonded pdb=" CZ PHE A 305 " pdb=" C26 BLD A1301 " model vdw 2.246 3.760 nonbonded pdb=" O GLY A1152 " pdb=" NE2 GLN A1155 " model vdw 2.253 3.120 nonbonded pdb=" O ALA A 475 " pdb=" OG SER A 478 " model vdw 2.284 3.040 nonbonded pdb=" O PRO A 522 " pdb=" NH1 ARG A 553 " model vdw 2.288 3.120 ... (remaining 69012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 0.044 9187 Z= 0.188 Angle : 0.682 9.488 12440 Z= 0.387 Chirality : 0.043 0.241 1438 Planarity : 0.008 0.238 1579 Dihedral : 14.664 132.183 3374 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.63 % Allowed : 0.42 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1164 helix: 1.38 (0.20), residues: 688 sheet: -1.18 (0.61), residues: 78 loop : -2.62 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.008 0.001 HIS A 51 PHE 0.017 0.001 PHE A 69 TYR 0.014 0.001 TYR A 220 ARG 0.010 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.17519 ( 529) hydrogen bonds : angle 5.90402 ( 1563) covalent geometry : bond 0.00339 ( 9187) covalent geometry : angle 0.68186 (12440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 381 MET cc_start: 0.4896 (mmm) cc_final: 0.4634 (tmm) REVERT: A 526 LEU cc_start: 0.8801 (mm) cc_final: 0.8577 (mm) REVERT: A 755 MET cc_start: 0.6994 (ttp) cc_final: 0.6756 (ttt) outliers start: 6 outliers final: 1 residues processed: 106 average time/residue: 0.1804 time to fit residues: 28.6093 Evaluate side-chains 87 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN A 878 ASN A 921 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.211154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160705 restraints weight = 13584.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159484 restraints weight = 15981.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.160802 restraints weight = 13390.883| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9187 Z= 0.151 Angle : 0.595 9.250 12440 Z= 0.314 Chirality : 0.041 0.165 1438 Planarity : 0.004 0.071 1579 Dihedral : 5.333 59.080 1355 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.16 % Allowed : 7.89 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1164 helix: 1.58 (0.20), residues: 695 sheet: -1.49 (0.62), residues: 66 loop : -2.61 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 684 HIS 0.008 0.001 HIS A 51 PHE 0.015 0.001 PHE A1061 TYR 0.015 0.001 TYR A 740 ARG 0.006 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.07003 ( 529) hydrogen bonds : angle 4.67728 ( 1563) covalent geometry : bond 0.00309 ( 9187) covalent geometry : angle 0.59473 (12440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 526 LEU cc_start: 0.8778 (mm) cc_final: 0.8530 (mm) REVERT: A 729 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: A 755 MET cc_start: 0.7045 (ttp) cc_final: 0.6759 (ttt) REVERT: A 969 LEU cc_start: 0.6972 (mm) cc_final: 0.6655 (tp) outliers start: 11 outliers final: 5 residues processed: 108 average time/residue: 0.1838 time to fit residues: 29.1981 Evaluate side-chains 89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 966 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.0070 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN A 362 HIS A 481 ASN A 878 ASN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.210341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.146863 restraints weight = 13694.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142616 restraints weight = 9035.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144812 restraints weight = 6417.694| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9187 Z= 0.150 Angle : 0.578 9.191 12440 Z= 0.306 Chirality : 0.041 0.191 1438 Planarity : 0.004 0.071 1579 Dihedral : 5.118 51.462 1353 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.68 % Allowed : 11.78 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1164 helix: 1.71 (0.20), residues: 696 sheet: -1.23 (0.60), residues: 76 loop : -2.69 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 684 HIS 0.008 0.001 HIS A 51 PHE 0.014 0.001 PHE A 69 TYR 0.016 0.001 TYR A 220 ARG 0.004 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.06856 ( 529) hydrogen bonds : angle 4.57355 ( 1563) covalent geometry : bond 0.00312 ( 9187) covalent geometry : angle 0.57817 (12440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 526 LEU cc_start: 0.8921 (mm) cc_final: 0.8563 (mm) REVERT: A 729 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: A 755 MET cc_start: 0.7054 (ttp) cc_final: 0.6770 (ttt) REVERT: A 969 LEU cc_start: 0.6705 (mm) cc_final: 0.6336 (tp) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.2265 time to fit residues: 35.1110 Evaluate side-chains 96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1209 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 109 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 298 GLN A 878 ASN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.207072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142217 restraints weight = 13554.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.137056 restraints weight = 9046.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139684 restraints weight = 6518.790| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9187 Z= 0.181 Angle : 0.602 9.255 12440 Z= 0.320 Chirality : 0.041 0.168 1438 Planarity : 0.004 0.073 1579 Dihedral : 5.169 40.017 1353 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.00 % Allowed : 13.88 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1164 helix: 1.55 (0.20), residues: 701 sheet: -1.24 (0.59), residues: 76 loop : -2.79 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 684 HIS 0.010 0.001 HIS A 51 PHE 0.018 0.001 PHE A 69 TYR 0.015 0.001 TYR A 220 ARG 0.003 0.000 ARG A1161 Details of bonding type rmsd hydrogen bonds : bond 0.07595 ( 529) hydrogen bonds : angle 4.67868 ( 1563) covalent geometry : bond 0.00396 ( 9187) covalent geometry : angle 0.60235 (12440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: A 526 LEU cc_start: 0.8974 (mm) cc_final: 0.8585 (mm) REVERT: A 729 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 755 MET cc_start: 0.7091 (ttp) cc_final: 0.6839 (ttt) REVERT: A 819 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7851 (mt) REVERT: A 969 LEU cc_start: 0.6669 (mm) cc_final: 0.6234 (tp) REVERT: A 1029 ARG cc_start: 0.7934 (ptm-80) cc_final: 0.7569 (tmm160) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.1621 time to fit residues: 26.2692 Evaluate side-chains 99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1209 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 81 optimal weight: 0.0670 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 878 ASN A1105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.204041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128252 restraints weight = 13751.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132181 restraints weight = 7034.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134599 restraints weight = 4812.796| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9187 Z= 0.209 Angle : 0.634 9.354 12440 Z= 0.337 Chirality : 0.042 0.171 1438 Planarity : 0.004 0.075 1579 Dihedral : 5.293 36.424 1353 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.94 % Allowed : 15.46 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1164 helix: 1.39 (0.20), residues: 697 sheet: -1.28 (0.57), residues: 80 loop : -2.84 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.011 0.001 HIS A 51 PHE 0.020 0.002 PHE A 69 TYR 0.014 0.001 TYR A 220 ARG 0.003 0.000 ARG A1161 Details of bonding type rmsd hydrogen bonds : bond 0.08150 ( 529) hydrogen bonds : angle 4.83041 ( 1563) covalent geometry : bond 0.00468 ( 9187) covalent geometry : angle 0.63350 (12440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.027 Fit side-chains REVERT: A 74 MET cc_start: 0.7510 (tpp) cc_final: 0.7306 (tpp) REVERT: A 130 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: A 226 ILE cc_start: 0.6374 (mt) cc_final: 0.6122 (mt) REVERT: A 526 LEU cc_start: 0.8902 (mm) cc_final: 0.8487 (mm) REVERT: A 729 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: A 755 MET cc_start: 0.7075 (ttp) cc_final: 0.6838 (ttt) REVERT: A 819 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7885 (mt) REVERT: A 969 LEU cc_start: 0.6853 (mm) cc_final: 0.6417 (tp) outliers start: 28 outliers final: 17 residues processed: 113 average time/residue: 0.1615 time to fit residues: 28.1123 Evaluate side-chains 108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1164 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 111 optimal weight: 0.0170 chunk 62 optimal weight: 0.7980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.207339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135027 restraints weight = 13611.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138275 restraints weight = 8351.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138333 restraints weight = 5732.825| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9187 Z= 0.152 Angle : 0.581 9.315 12440 Z= 0.308 Chirality : 0.041 0.238 1438 Planarity : 0.004 0.074 1579 Dihedral : 5.157 35.153 1353 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.52 % Allowed : 16.40 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1164 helix: 1.65 (0.20), residues: 698 sheet: -1.17 (0.57), residues: 80 loop : -2.80 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.007 0.001 HIS A 51 PHE 0.018 0.001 PHE A 134 TYR 0.017 0.001 TYR A 220 ARG 0.002 0.000 ARG A1029 Details of bonding type rmsd hydrogen bonds : bond 0.07127 ( 529) hydrogen bonds : angle 4.51888 ( 1563) covalent geometry : bond 0.00315 ( 9187) covalent geometry : angle 0.58085 (12440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.983 Fit side-chains REVERT: A 74 MET cc_start: 0.7703 (tpp) cc_final: 0.7440 (tpp) REVERT: A 92 TYR cc_start: 0.8137 (m-10) cc_final: 0.7789 (m-10) REVERT: A 130 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: A 226 ILE cc_start: 0.6296 (mt) cc_final: 0.6050 (mt) REVERT: A 526 LEU cc_start: 0.8845 (mm) cc_final: 0.8475 (mm) REVERT: A 729 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: A 755 MET cc_start: 0.7013 (ttp) cc_final: 0.6767 (ttt) REVERT: A 819 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7904 (mt) outliers start: 24 outliers final: 16 residues processed: 108 average time/residue: 0.1742 time to fit residues: 29.1676 Evaluate side-chains 106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 991 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 112 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 88 optimal weight: 0.0030 chunk 89 optimal weight: 3.9990 overall best weight: 2.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 HIS A1032 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.201163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125212 restraints weight = 13865.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129097 restraints weight = 8918.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128979 restraints weight = 5398.137| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9187 Z= 0.268 Angle : 0.693 9.454 12440 Z= 0.372 Chirality : 0.045 0.208 1438 Planarity : 0.004 0.074 1579 Dihedral : 5.510 36.625 1353 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.16 % Favored : 91.75 % Rotamer: Outliers : 2.63 % Allowed : 17.03 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1164 helix: 1.18 (0.20), residues: 693 sheet: -1.07 (0.58), residues: 80 loop : -2.80 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 185 HIS 0.014 0.001 HIS A 51 PHE 0.022 0.002 PHE A 309 TYR 0.014 0.002 TYR A 220 ARG 0.003 0.000 ARG A1161 Details of bonding type rmsd hydrogen bonds : bond 0.09105 ( 529) hydrogen bonds : angle 5.09876 ( 1563) covalent geometry : bond 0.00619 ( 9187) covalent geometry : angle 0.69344 (12440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.887 Fit side-chains REVERT: A 130 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: A 226 ILE cc_start: 0.6605 (mt) cc_final: 0.6396 (mt) REVERT: A 526 LEU cc_start: 0.8899 (mm) cc_final: 0.8507 (mm) REVERT: A 729 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: A 755 MET cc_start: 0.7062 (ttp) cc_final: 0.6818 (ttt) REVERT: A 819 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7943 (mt) outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 0.1620 time to fit residues: 28.3374 Evaluate side-chains 110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 20.0000 chunk 42 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 0.0030 chunk 114 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN A 903 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.211075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161989 restraints weight = 13782.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162219 restraints weight = 17292.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163588 restraints weight = 12711.314| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9187 Z= 0.139 Angle : 0.598 9.822 12440 Z= 0.312 Chirality : 0.040 0.192 1438 Planarity : 0.004 0.075 1579 Dihedral : 5.178 36.638 1353 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.79 % Allowed : 18.82 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1164 helix: 1.78 (0.20), residues: 692 sheet: -1.02 (0.58), residues: 80 loop : -2.80 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 288 HIS 0.002 0.001 HIS A 81 PHE 0.017 0.001 PHE A 438 TYR 0.017 0.001 TYR A 220 ARG 0.005 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.06616 ( 529) hydrogen bonds : angle 4.38754 ( 1563) covalent geometry : bond 0.00272 ( 9187) covalent geometry : angle 0.59803 (12440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.214 Fit side-chains REVERT: A 74 MET cc_start: 0.7427 (tpp) cc_final: 0.7164 (tpp) REVERT: A 92 TYR cc_start: 0.8083 (m-10) cc_final: 0.7776 (m-10) REVERT: A 226 ILE cc_start: 0.6259 (mt) cc_final: 0.6047 (mt) REVERT: A 381 MET cc_start: 0.5206 (mmm) cc_final: 0.4902 (tmm) REVERT: A 526 LEU cc_start: 0.8754 (mm) cc_final: 0.8514 (mm) REVERT: A 729 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: A 755 MET cc_start: 0.6980 (ttp) cc_final: 0.6738 (ttt) REVERT: A 819 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7782 (mt) REVERT: A 1139 LYS cc_start: 0.7510 (mmtm) cc_final: 0.6788 (pttp) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.2059 time to fit residues: 34.0738 Evaluate side-chains 108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.201694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129412 restraints weight = 13550.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131435 restraints weight = 7703.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130762 restraints weight = 5329.030| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9187 Z= 0.316 Angle : 0.750 10.346 12440 Z= 0.402 Chirality : 0.047 0.212 1438 Planarity : 0.005 0.071 1579 Dihedral : 5.651 37.071 1353 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.68 % Favored : 91.24 % Rotamer: Outliers : 2.00 % Allowed : 19.24 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1164 helix: 1.00 (0.19), residues: 693 sheet: -1.00 (0.58), residues: 80 loop : -2.74 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 185 HIS 0.005 0.001 HIS A 865 PHE 0.024 0.003 PHE A 69 TYR 0.013 0.002 TYR A 220 ARG 0.010 0.001 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.09544 ( 529) hydrogen bonds : angle 5.22686 ( 1563) covalent geometry : bond 0.00742 ( 9187) covalent geometry : angle 0.75005 (12440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 ILE cc_start: 0.6723 (mt) cc_final: 0.6513 (mt) REVERT: A 526 LEU cc_start: 0.8997 (mm) cc_final: 0.8633 (mm) REVERT: A 729 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: A 819 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7990 (mt) outliers start: 19 outliers final: 14 residues processed: 111 average time/residue: 0.1725 time to fit residues: 28.7368 Evaluate side-chains 106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 991 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 33 optimal weight: 0.0020 chunk 64 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN A 748 GLN A1032 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.209289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151063 restraints weight = 13556.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148113 restraints weight = 11830.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.149008 restraints weight = 9458.755| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9187 Z= 0.145 Angle : 0.628 10.142 12440 Z= 0.329 Chirality : 0.041 0.182 1438 Planarity : 0.004 0.077 1579 Dihedral : 5.258 37.534 1353 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.58 % Allowed : 20.29 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1164 helix: 1.67 (0.20), residues: 691 sheet: -0.85 (0.58), residues: 80 loop : -2.82 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 108 HIS 0.002 0.001 HIS A 749 PHE 0.016 0.001 PHE A 134 TYR 0.018 0.001 TYR A 220 ARG 0.007 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.07045 ( 529) hydrogen bonds : angle 4.49097 ( 1563) covalent geometry : bond 0.00291 ( 9187) covalent geometry : angle 0.62765 (12440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7482 (tpp) cc_final: 0.7106 (tpp) REVERT: A 92 TYR cc_start: 0.8162 (m-10) cc_final: 0.7865 (m-10) REVERT: A 226 ILE cc_start: 0.6410 (mt) cc_final: 0.6173 (mt) REVERT: A 381 MET cc_start: 0.5081 (mmm) cc_final: 0.4783 (tmm) REVERT: A 526 LEU cc_start: 0.9022 (mm) cc_final: 0.8688 (mm) REVERT: A 729 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: A 819 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8005 (mt) outliers start: 15 outliers final: 13 residues processed: 107 average time/residue: 0.1682 time to fit residues: 27.3679 Evaluate side-chains 108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 991 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.208769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.135696 restraints weight = 13613.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139402 restraints weight = 7151.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141601 restraints weight = 4962.624| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9187 Z= 0.157 Angle : 0.637 10.434 12440 Z= 0.332 Chirality : 0.041 0.182 1438 Planarity : 0.004 0.074 1579 Dihedral : 5.229 37.200 1353 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.37 % Allowed : 20.93 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1164 helix: 1.72 (0.20), residues: 691 sheet: -0.84 (0.59), residues: 80 loop : -2.81 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 108 HIS 0.003 0.001 HIS A 51 PHE 0.022 0.001 PHE A 134 TYR 0.016 0.001 TYR A 220 ARG 0.003 0.000 ARG A1060 Details of bonding type rmsd hydrogen bonds : bond 0.07048 ( 529) hydrogen bonds : angle 4.49673 ( 1563) covalent geometry : bond 0.00336 ( 9187) covalent geometry : angle 0.63669 (12440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3290.76 seconds wall clock time: 60 minutes 0.42 seconds (3600.42 seconds total)