Starting phenix.real_space_refine on Wed Mar 12 15:59:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhr_24467/03_2025/7rhr_24467.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhr_24467/03_2025/7rhr_24467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhr_24467/03_2025/7rhr_24467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhr_24467/03_2025/7rhr_24467.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhr_24467/03_2025/7rhr_24467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhr_24467/03_2025/7rhr_24467.cif" } resolution = 3.0 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= 0.006 sd= 0.137 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 40 5.16 5 C 5121 2.51 5 N 1265 2.21 5 O 1394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7820 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7680 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 41, 'TRANS': 932} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'CLR': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.14, per 1000 atoms: 0.66 Number of scatterers: 7820 At special positions: 0 Unit cell: (79.5, 81.62, 138.86, 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 40 16.00 O 1394 8.00 N 1265 7.00 C 5121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1503 " - " ASN A 302 " " NAG A1504 " - " ASN A 339 " " NAG B 1 " - " ASN A 989 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 939.2 milliseconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 63.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 69 through 87 Processing helix chain 'A' and resid 89 through 106 removed outlier: 3.879A pdb=" N VAL A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.755A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.601A pdb=" N LEU A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.607A pdb=" N GLN A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 5.935A pdb=" N TRP A 226 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLU A 227 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.988A pdb=" N GLY A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.668A pdb=" N ILE A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 378 through 400 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.596A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 Processing helix chain 'A' and resid 456 through 481 Processing helix chain 'A' and resid 492 through 518 removed outlier: 4.180A pdb=" N ASP A 503 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 553 removed outlier: 5.490A pdb=" N ALA A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 581 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.507A pdb=" N ILE A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.995A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Proline residue: A 732 - end of helix removed outlier: 3.737A pdb=" N LEU A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 758 removed outlier: 4.295A pdb=" N VAL A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 removed outlier: 3.552A pdb=" N ASP A 769 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 788 removed outlier: 3.706A pdb=" N ASP A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 815 removed outlier: 3.610A pdb=" N LEU A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 810 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 855 removed outlier: 3.647A pdb=" N TYR A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 879 removed outlier: 3.892A pdb=" N GLN A 879 " --> pdb=" O LYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.916A pdb=" N ASN A 890 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN A 891 " --> pdb=" O ASN A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 891' Processing helix chain 'A' and resid 908 through 920 Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'A' and resid 972 through 992 removed outlier: 3.586A pdb=" N SER A 992 " --> pdb=" O ASN A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1006 Processing helix chain 'A' and resid 1008 through 1011 removed outlier: 3.635A pdb=" N ILE A1011 " --> pdb=" O GLU A1008 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1008 through 1011' Processing helix chain 'A' and resid 1012 through 1037 removed outlier: 3.656A pdb=" N TRP A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1064 Processing helix chain 'A' and resid 1068 through 1096 removed outlier: 3.950A pdb=" N VAL A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A1086 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A1089 " --> pdb=" O PHE A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1112 Processing helix chain 'A' and resid 1112 through 1126 removed outlier: 3.537A pdb=" N VAL A1126 " --> pdb=" O THR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1130 Processing helix chain 'A' and resid 1141 through 1159 Processing helix chain 'A' and resid 1159 through 1167 removed outlier: 3.619A pdb=" N PHE A1166 " --> pdb=" O VAL A1162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 removed outlier: 3.669A pdb=" N ASN A 144 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 182 Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA6, first strand: chain 'A' and resid 337 through 338 removed outlier: 6.972A pdb=" N VAL A 337 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 961 through 968 446 hydrogen bonds defined for protein. 1293 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: 2.52 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2384 1.34 - 1.46: 1327 1.46 - 1.58: 4236 1.58 - 1.70: 1 1.70 - 1.82: 65 Bond restraints: 8013 Sorted by residual: bond pdb=" CA ASP A 223 " pdb=" C ASP A 223 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.38e-02 5.25e+03 6.06e+00 bond pdb=" CB PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.91e+00 bond pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta sigma weight residual 1.526 1.543 -0.016 9.30e-03 1.16e+04 3.12e+00 bond pdb=" CB VAL A 159 " pdb=" CG2 VAL A 159 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.75e+00 bond pdb=" C10 CLR A1502 " pdb=" C9 CLR A1502 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 8008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 10417 1.80 - 3.59: 422 3.59 - 5.39: 64 5.39 - 7.18: 9 7.18 - 8.98: 4 Bond angle restraints: 10916 Sorted by residual: angle pdb=" CA PRO A 732 " pdb=" N PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 112.00 103.07 8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" N PHE A1004 " pdb=" CA PHE A1004 " pdb=" C PHE A1004 " ideal model delta sigma weight residual 114.75 107.40 7.35 1.26e+00 6.30e-01 3.41e+01 angle pdb=" N ASN A 907 " pdb=" CA ASN A 907 " pdb=" C ASN A 907 " ideal model delta sigma weight residual 114.04 108.06 5.98 1.24e+00 6.50e-01 2.32e+01 angle pdb=" C TYR A 237 " pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 120.49 114.92 5.57 1.42e+00 4.96e-01 1.54e+01 angle pdb=" CA ARG A 932 " pdb=" CB ARG A 932 " pdb=" CG ARG A 932 " ideal model delta sigma weight residual 114.10 107.41 6.69 2.00e+00 2.50e-01 1.12e+01 ... (remaining 10911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4606 17.76 - 35.52: 272 35.52 - 53.28: 37 53.28 - 71.04: 13 71.04 - 88.80: 7 Dihedral angle restraints: 4935 sinusoidal: 2097 harmonic: 2838 Sorted by residual: dihedral pdb=" CA ARG A 932 " pdb=" C ARG A 932 " pdb=" N PRO A 933 " pdb=" CA PRO A 933 " ideal model delta harmonic sigma weight residual -180.00 -103.48 -76.52 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" CA LYS A 828 " pdb=" C LYS A 828 " pdb=" N GLN A 829 " pdb=" CA GLN A 829 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN A 882 " pdb=" C ASN A 882 " pdb=" N SER A 883 " pdb=" CA SER A 883 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 920 0.050 - 0.101: 296 0.101 - 0.151: 52 0.151 - 0.201: 6 0.201 - 0.252: 3 Chirality restraints: 1277 Sorted by residual: chirality pdb=" C13 CLR A1502 " pdb=" C12 CLR A1502 " pdb=" C14 CLR A1502 " pdb=" C17 CLR A1502 " both_signs ideal model delta sigma weight residual False -2.93 -2.68 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C13 CLR A1505 " pdb=" C12 CLR A1505 " pdb=" C14 CLR A1505 " pdb=" C17 CLR A1505 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C13 CLR A1501 " pdb=" C12 CLR A1501 " pdb=" C14 CLR A1501 " pdb=" C17 CLR A1501 " both_signs ideal model delta sigma weight residual False -2.93 -2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1274 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 932 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO A 933 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 933 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 933 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 731 " 0.039 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 732 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 912 " 0.014 2.00e-02 2.50e+03 1.26e-02 3.15e+00 pdb=" CG TYR A 912 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 912 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 912 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 912 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 912 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 912 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 912 " 0.000 2.00e-02 2.50e+03 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 113 2.69 - 3.24: 7635 3.24 - 3.79: 11802 3.79 - 4.35: 16297 4.35 - 4.90: 27294 Nonbonded interactions: 63141 Sorted by model distance: nonbonded pdb=" OH TYR A 442 " pdb=" OD1 ASP A1117 " model vdw 2.131 3.040 nonbonded pdb=" NE2 GLN A 150 " pdb=" OE1 GLN A 407 " model vdw 2.172 3.120 nonbonded pdb=" NH2 ARG A 134 " pdb=" OE2 GLU A 140 " model vdw 2.191 3.120 nonbonded pdb=" NH2 ARG A 431 " pdb=" O MET A1128 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR A 880 " pdb=" O ASP A 884 " model vdw 2.315 3.040 ... (remaining 63136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.940 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:18.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 8013 Z= 0.396 Angle : 0.838 8.980 10916 Z= 0.480 Chirality : 0.050 0.252 1277 Planarity : 0.005 0.101 1347 Dihedral : 11.889 88.803 3098 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -0.44 (0.27), residues: 970 helix: 0.41 (0.22), residues: 563 sheet: 0.63 (0.77), residues: 47 loop : -1.49 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 268 HIS 0.006 0.001 HIS A 813 PHE 0.029 0.003 PHE A 249 TYR 0.031 0.002 TYR A 912 ARG 0.011 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.775 Fit side-chains REVERT: A 107 ARG cc_start: 0.7263 (pmt170) cc_final: 0.6571 (mmt180) REVERT: A 395 GLN cc_start: 0.7629 (mt0) cc_final: 0.7238 (tt0) REVERT: A 738 LYS cc_start: 0.7101 (mttt) cc_final: 0.6386 (tmtt) REVERT: A 785 PHE cc_start: 0.7810 (m-10) cc_final: 0.7451 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 1.2975 time to fit residues: 161.0162 Evaluate side-chains 93 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 245 GLN A 846 GLN ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN ** A1038 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 = 0.3825 r_free = 0.3825 target = 0.166150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126882 restraints weight = 8561.218| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.01 r_work: 0.3081 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8013 Z= 0.206 Angle : 0.601 6.298 10916 Z= 0.309 Chirality : 0.042 0.148 1277 Planarity : 0.005 0.087 1347 Dihedral : 6.521 71.043 1326 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.57 % Allowed : 7.85 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.39 (0.27), residues: 970 helix: 1.06 (0.22), residues: 568 sheet: 0.97 (0.80), residues: 46 loop : -1.11 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.004 0.001 HIS A 168 PHE 0.022 0.002 PHE A 78 TYR 0.017 0.002 TYR A 912 ARG 0.006 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.827 Fit side-chains REVERT: A 107 ARG cc_start: 0.7319 (pmt170) cc_final: 0.6419 (mmt180) REVERT: A 110 ASN cc_start: 0.7045 (m110) cc_final: 0.6802 (p0) REVERT: A 395 GLN cc_start: 0.7791 (mt0) cc_final: 0.7351 (tt0) REVERT: A 738 LYS cc_start: 0.7226 (mttt) cc_final: 0.6439 (tmtt) REVERT: A 785 PHE cc_start: 0.7974 (m-10) cc_final: 0.7280 (t80) REVERT: A 851 HIS cc_start: 0.7265 (m170) cc_final: 0.6968 (t-90) outliers start: 13 outliers final: 8 residues processed: 116 average time/residue: 1.0556 time to fit residues: 131.2705 Evaluate side-chains 105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 0.0570 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.167945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130293 restraints weight = 8594.462| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.94 r_work: 0.3040 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8013 Z= 0.238 Angle : 0.585 6.057 10916 Z= 0.300 Chirality : 0.042 0.142 1277 Planarity : 0.005 0.090 1347 Dihedral : 5.943 69.710 1326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 2.29 % Allowed : 10.87 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.61 (0.27), residues: 970 helix: 1.19 (0.22), residues: 569 sheet: 1.13 (0.80), residues: 46 loop : -0.95 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.003 0.001 HIS A 398 PHE 0.016 0.002 PHE A 963 TYR 0.018 0.002 TYR A 990 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.858 Fit side-chains REVERT: A 86 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7379 (tmtm) REVERT: A 107 ARG cc_start: 0.7508 (pmt170) cc_final: 0.6498 (mmt-90) REVERT: A 110 ASN cc_start: 0.7206 (m110) cc_final: 0.6923 (p0) REVERT: A 191 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: A 253 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: A 395 GLN cc_start: 0.7818 (mt0) cc_final: 0.7290 (tt0) REVERT: A 407 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: A 738 LYS cc_start: 0.7316 (mttt) cc_final: 0.6409 (tmtt) REVERT: A 785 PHE cc_start: 0.8105 (m-10) cc_final: 0.7284 (t80) REVERT: A 851 HIS cc_start: 0.7218 (m170) cc_final: 0.6823 (t-90) outliers start: 19 outliers final: 8 residues processed: 108 average time/residue: 1.1544 time to fit residues: 133.4317 Evaluate side-chains 111 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 92 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN A1000 ASN A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.171793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134817 restraints weight = 8552.464| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.89 r_work: 0.3082 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8013 Z= 0.165 Angle : 0.524 6.580 10916 Z= 0.271 Chirality : 0.040 0.146 1277 Planarity : 0.004 0.081 1347 Dihedral : 5.488 66.386 1326 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 2.54 % Allowed : 12.80 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.94 (0.28), residues: 970 helix: 1.48 (0.22), residues: 570 sheet: 1.11 (0.80), residues: 46 loop : -0.83 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 168 PHE 0.024 0.001 PHE A 78 TYR 0.015 0.001 TYR A 990 ARG 0.002 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.491 Fit side-chains REVERT: A 86 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7384 (tmtm) REVERT: A 110 ASN cc_start: 0.7277 (m110) cc_final: 0.7071 (p0) REVERT: A 395 GLN cc_start: 0.7753 (mt0) cc_final: 0.7218 (tt0) REVERT: A 407 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: A 738 LYS cc_start: 0.7311 (mttt) cc_final: 0.6464 (tmtt) REVERT: A 785 PHE cc_start: 0.8145 (m-10) cc_final: 0.7388 (t80) REVERT: A 851 HIS cc_start: 0.7309 (m170) cc_final: 0.6830 (t-90) REVERT: A 953 ARG cc_start: 0.8554 (ptm160) cc_final: 0.8353 (ptm-80) outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 1.1153 time to fit residues: 142.5967 Evaluate side-chains 117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 846 GLN A1000 ASN A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.169747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132305 restraints weight = 8524.269| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.88 r_work: 0.3058 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8013 Z= 0.215 Angle : 0.551 7.272 10916 Z= 0.284 Chirality : 0.041 0.144 1277 Planarity : 0.004 0.086 1347 Dihedral : 5.406 66.643 1326 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 2.66 % Allowed : 13.41 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.92 (0.28), residues: 970 helix: 1.43 (0.22), residues: 577 sheet: 1.13 (0.79), residues: 46 loop : -0.83 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A1015 PHE 0.017 0.002 PHE A 963 TYR 0.016 0.002 TYR A 990 ARG 0.003 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.764 Fit side-chains REVERT: A 86 LYS cc_start: 0.7635 (ttmt) cc_final: 0.7377 (tmtm) REVERT: A 235 MET cc_start: 0.8776 (tpp) cc_final: 0.8514 (mmt) REVERT: A 360 LYS cc_start: 0.7890 (tttm) cc_final: 0.7382 (ttpp) REVERT: A 395 GLN cc_start: 0.7775 (mt0) cc_final: 0.7237 (tt0) REVERT: A 422 LYS cc_start: 0.7617 (ttpt) cc_final: 0.6992 (mtpp) REVERT: A 738 LYS cc_start: 0.7307 (mttt) cc_final: 0.6422 (tmtt) REVERT: A 785 PHE cc_start: 0.8114 (m-10) cc_final: 0.7327 (t80) REVERT: A 905 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: A 953 ARG cc_start: 0.8566 (ptm160) cc_final: 0.8361 (ptm-80) outliers start: 22 outliers final: 13 residues processed: 116 average time/residue: 1.0407 time to fit residues: 129.4140 Evaluate side-chains 118 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 905 GLN Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 82 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN A1101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126713 restraints weight = 8544.422| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.00 r_work: 0.3117 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8013 Z= 0.189 Angle : 0.528 7.747 10916 Z= 0.273 Chirality : 0.040 0.145 1277 Planarity : 0.004 0.084 1347 Dihedral : 5.253 66.241 1326 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 2.90 % Allowed : 13.77 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 970 helix: 1.56 (0.22), residues: 578 sheet: 0.80 (0.80), residues: 48 loop : -0.80 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.001 PHE A 963 TYR 0.019 0.001 TYR A 363 ARG 0.002 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.845 Fit side-chains REVERT: A 86 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7456 (tmtm) REVERT: A 115 VAL cc_start: 0.7996 (t) cc_final: 0.7755 (t) REVERT: A 360 LYS cc_start: 0.7953 (tttm) cc_final: 0.7460 (ttpp) REVERT: A 395 GLN cc_start: 0.7808 (mt0) cc_final: 0.7297 (tt0) REVERT: A 422 LYS cc_start: 0.7637 (ttpt) cc_final: 0.7028 (mtpp) REVERT: A 738 LYS cc_start: 0.7330 (mttt) cc_final: 0.6493 (tmtt) REVERT: A 785 PHE cc_start: 0.8170 (m-10) cc_final: 0.7415 (t80) outliers start: 24 outliers final: 12 residues processed: 121 average time/residue: 1.0446 time to fit residues: 135.7668 Evaluate side-chains 116 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.163294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124448 restraints weight = 8655.042| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.09 r_work: 0.3014 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8013 Z= 0.242 Angle : 0.562 8.290 10916 Z= 0.288 Chirality : 0.041 0.149 1277 Planarity : 0.005 0.089 1347 Dihedral : 5.321 67.387 1326 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 2.29 % Allowed : 15.10 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.28), residues: 970 helix: 1.51 (0.22), residues: 577 sheet: 0.85 (0.82), residues: 48 loop : -0.79 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A 279 PHE 0.026 0.002 PHE A 78 TYR 0.019 0.002 TYR A 990 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.773 Fit side-chains REVERT: A 235 MET cc_start: 0.8593 (mmt) cc_final: 0.8357 (mmt) REVERT: A 360 LYS cc_start: 0.7888 (tttm) cc_final: 0.7395 (ttpp) REVERT: A 395 GLN cc_start: 0.7710 (mt0) cc_final: 0.7261 (tt0) REVERT: A 422 LYS cc_start: 0.7689 (ttpt) cc_final: 0.7098 (mtpp) REVERT: A 738 LYS cc_start: 0.7263 (mttt) cc_final: 0.6449 (tmtt) REVERT: A 785 PHE cc_start: 0.8029 (m-10) cc_final: 0.7337 (t80) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 1.0648 time to fit residues: 125.4347 Evaluate side-chains 117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 114 ASN A 846 GLN A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.162412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123463 restraints weight = 8730.082| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.09 r_work: 0.3015 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8013 Z= 0.243 Angle : 0.565 8.663 10916 Z= 0.289 Chirality : 0.041 0.153 1277 Planarity : 0.005 0.088 1347 Dihedral : 5.334 67.293 1326 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 2.78 % Allowed : 15.34 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.28), residues: 970 helix: 1.57 (0.22), residues: 571 sheet: 0.89 (0.82), residues: 48 loop : -0.80 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.003 0.001 HIS A 279 PHE 0.028 0.002 PHE A 78 TYR 0.019 0.001 TYR A 990 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.771 Fit side-chains REVERT: A 235 MET cc_start: 0.8618 (mmt) cc_final: 0.8364 (mmt) REVERT: A 360 LYS cc_start: 0.7899 (tttm) cc_final: 0.7414 (ttpp) REVERT: A 395 GLN cc_start: 0.7694 (mt0) cc_final: 0.7264 (tt0) REVERT: A 422 LYS cc_start: 0.7708 (ttpt) cc_final: 0.7145 (mtpp) REVERT: A 738 LYS cc_start: 0.7297 (mttt) cc_final: 0.6415 (tmtt) REVERT: A 785 PHE cc_start: 0.8030 (m-10) cc_final: 0.7341 (t80) outliers start: 23 outliers final: 14 residues processed: 114 average time/residue: 1.0194 time to fit residues: 124.8996 Evaluate side-chains 114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN A1088 HIS A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127065 restraints weight = 8744.949| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.93 r_work: 0.3006 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8013 Z= 0.316 Angle : 0.609 9.123 10916 Z= 0.311 Chirality : 0.043 0.158 1277 Planarity : 0.005 0.094 1347 Dihedral : 5.506 68.864 1326 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 2.17 % Allowed : 15.94 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: 0.90 (0.27), residues: 970 helix: 1.44 (0.22), residues: 571 sheet: 0.95 (0.82), residues: 48 loop : -0.83 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 327 HIS 0.004 0.001 HIS A 398 PHE 0.024 0.002 PHE A 963 TYR 0.024 0.002 TYR A 990 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.787 Fit side-chains REVERT: A 235 MET cc_start: 0.8709 (mmt) cc_final: 0.8434 (mmt) REVERT: A 360 LYS cc_start: 0.7914 (tttm) cc_final: 0.7401 (ttpp) REVERT: A 395 GLN cc_start: 0.7830 (mt0) cc_final: 0.7324 (tt0) REVERT: A 738 LYS cc_start: 0.7310 (mttt) cc_final: 0.6416 (tmtt) REVERT: A 785 PHE cc_start: 0.8123 (m-10) cc_final: 0.7312 (t80) REVERT: A 1122 THR cc_start: 0.8379 (t) cc_final: 0.8042 (p) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 1.0695 time to fit residues: 125.9308 Evaluate side-chains 117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 74 optimal weight: 0.0570 chunk 50 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 846 GLN A 891 GLN A1088 HIS A1101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.170474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133563 restraints weight = 8638.214| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.88 r_work: 0.3070 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8013 Z= 0.159 Angle : 0.529 9.580 10916 Z= 0.273 Chirality : 0.040 0.147 1277 Planarity : 0.004 0.081 1347 Dihedral : 5.138 65.193 1326 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 2.42 % Allowed : 15.70 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.28), residues: 970 helix: 1.79 (0.22), residues: 571 sheet: 0.95 (0.84), residues: 48 loop : -0.72 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.002 0.001 HIS A 374 PHE 0.017 0.001 PHE A 733 TYR 0.018 0.001 TYR A 363 ARG 0.002 0.000 ARG A 932 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 235 MET cc_start: 0.8672 (mmt) cc_final: 0.8445 (mmt) REVERT: A 360 LYS cc_start: 0.7896 (tttm) cc_final: 0.7386 (ttpp) REVERT: A 395 GLN cc_start: 0.7741 (mt0) cc_final: 0.7234 (tt0) REVERT: A 422 LYS cc_start: 0.7632 (ttpt) cc_final: 0.7074 (mtpp) REVERT: A 738 LYS cc_start: 0.7338 (mttt) cc_final: 0.6407 (tmtt) REVERT: A 785 PHE cc_start: 0.8147 (m-10) cc_final: 0.7405 (t80) REVERT: A 1122 THR cc_start: 0.8341 (t) cc_final: 0.8057 (p) outliers start: 20 outliers final: 14 residues processed: 117 average time/residue: 0.9777 time to fit residues: 122.8839 Evaluate side-chains 120 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1110 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A 891 GLN A1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.163072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124699 restraints weight = 8642.118| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.03 r_work: 0.3018 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8013 Z= 0.263 Angle : 0.574 9.547 10916 Z= 0.294 Chirality : 0.042 0.159 1277 Planarity : 0.005 0.090 1347 Dihedral : 5.298 67.008 1326 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 2.17 % Allowed : 16.06 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 970 helix: 1.66 (0.22), residues: 571 sheet: 0.94 (0.85), residues: 48 loop : -0.77 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 389 HIS 0.003 0.001 HIS A 279 PHE 0.020 0.002 PHE A 963 TYR 0.030 0.002 TYR A 990 ARG 0.003 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5227.21 seconds wall clock time: 90 minutes 56.50 seconds (5456.50 seconds total)