Starting phenix.real_space_refine on Tue Mar 3 18:39:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhr_24467/03_2026/7rhr_24467.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhr_24467/03_2026/7rhr_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_2026/7rhr_24467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhr_24467/03_2026/7rhr_24467.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhr_24467/03_2026/7rhr_24467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhr_24467/03_2026/7rhr_24467.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.79, per 1000 atoms: 0.23 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: 0.65 Conformation dependent library (CDL) restraints added in 299.8 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: 0.26 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: 1.28 Time building geometry restraints manager: 0.89 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- 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 8020 Z= 0.267 Angle : 0.840 8.980 10934 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.001 ARG A 284 TYR 0.031 0.002 TYR A 912 PHE 0.029 0.003 PHE A 249 TRP 0.014 0.002 TRP A 268 HIS 0.006 0.001 HIS A 813 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 8013) covalent geometry : angle 0.83843 (10916) SS BOND : bond 0.00287 ( 3) SS BOND : angle 1.15647 ( 6) hydrogen bonds : bond 0.16437 ( 444) hydrogen bonds : angle 5.74722 ( 1293) link_BETA1-4 : bond 0.01190 ( 1) link_BETA1-4 : angle 1.35373 ( 3) link_NAG-ASN : bond 0.00168 ( 3) link_NAG-ASN : angle 1.72887 ( 9) *********************** 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 : 0.275 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: 0.5772 time to fit residues: 71.3066 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 : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 A1000 ASN A1009 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.163372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124663 restraints weight = 8718.760| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.10 r_work: 0.3033 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8020 Z= 0.152 Angle : 0.622 6.299 10934 Z= 0.320 Chirality : 0.043 0.148 1277 Planarity : 0.005 0.091 1347 Dihedral : 6.725 72.546 1326 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 1.57 % Allowed : 7.61 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 970 helix: 0.94 (0.22), residues: 567 sheet: 0.99 (0.80), residues: 46 loop : -1.12 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1103 TYR 0.019 0.002 TYR A 912 PHE 0.022 0.002 PHE A 78 TRP 0.007 0.001 TRP A 246 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8013) covalent geometry : angle 0.62075 (10916) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.94878 ( 6) hydrogen bonds : bond 0.05127 ( 444) hydrogen bonds : angle 4.27813 ( 1293) link_BETA1-4 : bond 0.00918 ( 1) link_BETA1-4 : angle 1.24233 ( 3) link_NAG-ASN : bond 0.00429 ( 3) link_NAG-ASN : angle 1.19609 ( 9) *********************** 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 119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.293 Fit side-chains REVERT: A 107 ARG cc_start: 0.7380 (pmt170) cc_final: 0.6482 (mmt180) REVERT: A 235 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8542 (tpp) REVERT: A 395 GLN cc_start: 0.7793 (mt0) cc_final: 0.7330 (tt0) REVERT: A 738 LYS cc_start: 0.7224 (mttt) cc_final: 0.6392 (tmtt) REVERT: A 785 PHE cc_start: 0.7968 (m-10) cc_final: 0.7258 (t80) REVERT: A 851 HIS cc_start: 0.7281 (m170) cc_final: 0.6972 (t-90) REVERT: A 956 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7808 (mp0) outliers start: 13 outliers final: 7 residues processed: 113 average time/residue: 0.5250 time to fit residues: 63.0672 Evaluate side-chains 105 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 297 THR 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 13 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 57 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 135 GLN A 846 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.164723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125857 restraints weight = 8617.495| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.01 r_work: 0.3044 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8020 Z= 0.121 Angle : 0.557 6.215 10934 Z= 0.287 Chirality : 0.041 0.139 1277 Planarity : 0.004 0.083 1347 Dihedral : 5.988 68.429 1326 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 2.05 % Allowed : 11.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.27), residues: 970 helix: 1.28 (0.22), residues: 567 sheet: 1.04 (0.78), residues: 46 loop : -0.98 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 762 TYR 0.014 0.001 TYR A 990 PHE 0.011 0.001 PHE A 963 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8013) covalent geometry : angle 0.55599 (10916) SS BOND : bond 0.00180 ( 3) SS BOND : angle 0.64555 ( 6) hydrogen bonds : bond 0.04357 ( 444) hydrogen bonds : angle 3.99645 ( 1293) link_BETA1-4 : bond 0.00894 ( 1) link_BETA1-4 : angle 1.38455 ( 3) link_NAG-ASN : bond 0.00371 ( 3) link_NAG-ASN : angle 1.01113 ( 9) *********************** 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 122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.282 Fit side-chains REVERT: A 86 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7816 (tmtm) REVERT: A 107 ARG cc_start: 0.7400 (pmt170) cc_final: 0.6452 (mmt180) REVERT: A 110 ASN cc_start: 0.7045 (m110) cc_final: 0.6836 (p0) REVERT: A 235 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8501 (tpp) REVERT: A 253 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: A 395 GLN cc_start: 0.7677 (mt0) cc_final: 0.7192 (tt0) REVERT: A 407 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: A 738 LYS cc_start: 0.7247 (mttt) cc_final: 0.6423 (tmtt) REVERT: A 785 PHE cc_start: 0.8003 (m-10) cc_final: 0.7362 (t80) REVERT: A 851 HIS cc_start: 0.7267 (m170) cc_final: 0.6937 (t-90) outliers start: 17 outliers final: 6 residues processed: 110 average time/residue: 0.5258 time to fit residues: 61.4277 Evaluate side-chains 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 242 ASP 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 437 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 956 GLU 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 40 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.168516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130888 restraints weight = 8651.480| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.90 r_work: 0.3063 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8020 Z= 0.133 Angle : 0.568 10.014 10934 Z= 0.289 Chirality : 0.041 0.168 1277 Planarity : 0.004 0.085 1347 Dihedral : 5.668 67.574 1326 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 3.14 % Allowed : 12.44 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.28), residues: 970 helix: 1.37 (0.22), residues: 571 sheet: 1.09 (0.79), residues: 46 loop : -0.84 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1103 TYR 0.017 0.002 TYR A 363 PHE 0.023 0.002 PHE A 78 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8013) covalent geometry : angle 0.56672 (10916) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.71578 ( 6) hydrogen bonds : bond 0.04311 ( 444) hydrogen bonds : angle 3.93843 ( 1293) link_BETA1-4 : bond 0.00897 ( 1) link_BETA1-4 : angle 1.46100 ( 3) link_NAG-ASN : bond 0.00302 ( 3) link_NAG-ASN : angle 1.09820 ( 9) *********************** 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 129 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.290 Fit side-chains REVERT: A 107 ARG cc_start: 0.7471 (pmt170) cc_final: 0.6364 (mmt-90) REVERT: A 110 ASN cc_start: 0.7111 (m110) cc_final: 0.6904 (p0) REVERT: A 235 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8613 (tpp) REVERT: A 395 GLN cc_start: 0.7781 (mt0) cc_final: 0.7236 (tt0) REVERT: A 422 LYS cc_start: 0.7597 (ttpt) cc_final: 0.6977 (mtpp) REVERT: A 574 ASN cc_start: 0.8199 (t0) cc_final: 0.7973 (m-40) REVERT: A 738 LYS cc_start: 0.7336 (mttt) cc_final: 0.6444 (tmtt) REVERT: A 785 PHE cc_start: 0.8160 (m-10) cc_final: 0.7390 (t80) REVERT: A 851 HIS cc_start: 0.7291 (m170) cc_final: 0.6835 (t-90) REVERT: A 905 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8229 (tm-30) outliers start: 26 outliers final: 11 residues processed: 114 average time/residue: 0.4535 time to fit residues: 55.4367 Evaluate side-chains 112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET 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 444 CYS Chi-restraints excluded: chain A residue 530 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 54 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN 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 = 0.3815 r_free = 0.3815 target = 0.165401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126068 restraints weight = 8613.565| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.00 r_work: 0.3030 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8020 Z= 0.126 Angle : 0.556 9.998 10934 Z= 0.284 Chirality : 0.041 0.165 1277 Planarity : 0.004 0.084 1347 Dihedral : 5.444 66.336 1326 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 2.66 % Allowed : 13.65 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 970 helix: 1.44 (0.22), residues: 576 sheet: 1.10 (0.80), residues: 46 loop : -0.80 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.014 0.001 TYR A 990 PHE 0.014 0.001 PHE A 963 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8013) covalent geometry : angle 0.55464 (10916) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.65050 ( 6) hydrogen bonds : bond 0.04132 ( 444) hydrogen bonds : angle 3.89361 ( 1293) link_BETA1-4 : bond 0.00993 ( 1) link_BETA1-4 : angle 1.41964 ( 3) link_NAG-ASN : bond 0.00318 ( 3) link_NAG-ASN : angle 1.11353 ( 9) *********************** 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 125 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.182 Fit side-chains REVERT: A 235 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8530 (tpp) REVERT: A 395 GLN cc_start: 0.7676 (mt0) cc_final: 0.7201 (tt0) REVERT: A 422 LYS cc_start: 0.7623 (ttpt) cc_final: 0.7066 (mtpp) REVERT: A 574 ASN cc_start: 0.8116 (t0) cc_final: 0.7909 (m-40) REVERT: A 738 LYS cc_start: 0.7276 (mttt) cc_final: 0.6460 (tmtt) REVERT: A 785 PHE cc_start: 0.8030 (m-10) cc_final: 0.7394 (t80) REVERT: A 851 HIS cc_start: 0.7326 (m170) cc_final: 0.6919 (t-90) outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 0.4566 time to fit residues: 55.7610 Evaluate side-chains 118 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET 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 444 CYS 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 1000 ASN 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 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.168629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130965 restraints weight = 8618.528| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.90 r_work: 0.3064 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8020 Z= 0.123 Angle : 0.547 10.586 10934 Z= 0.279 Chirality : 0.040 0.160 1277 Planarity : 0.004 0.083 1347 Dihedral : 5.281 65.956 1326 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 2.78 % Allowed : 14.13 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 970 helix: 1.56 (0.22), residues: 576 sheet: 1.09 (0.80), residues: 46 loop : -0.76 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.018 0.001 TYR A 363 PHE 0.014 0.001 PHE A 963 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8013) covalent geometry : angle 0.54629 (10916) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.63550 ( 6) hydrogen bonds : bond 0.04034 ( 444) hydrogen bonds : angle 3.85781 ( 1293) link_BETA1-4 : bond 0.00892 ( 1) link_BETA1-4 : angle 1.36957 ( 3) link_NAG-ASN : bond 0.00293 ( 3) link_NAG-ASN : angle 1.12864 ( 9) *********************** 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 131 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.179 Fit side-chains REVERT: A 107 ARG cc_start: 0.7455 (pmt170) cc_final: 0.6387 (mpp-170) REVERT: A 235 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8583 (tpp) REVERT: A 395 GLN cc_start: 0.7756 (mt0) cc_final: 0.7223 (tt0) REVERT: A 422 LYS cc_start: 0.7606 (ttpt) cc_final: 0.7048 (mtpp) REVERT: A 551 MET cc_start: 0.8826 (tpp) cc_final: 0.8602 (tpp) REVERT: A 574 ASN cc_start: 0.8128 (t0) cc_final: 0.7698 (m-40) REVERT: A 738 LYS cc_start: 0.7331 (mttt) cc_final: 0.6397 (tmtt) REVERT: A 785 PHE cc_start: 0.8091 (m-10) cc_final: 0.7306 (t80) outliers start: 23 outliers final: 12 residues processed: 119 average time/residue: 0.4477 time to fit residues: 56.9960 Evaluate side-chains 114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET 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 444 CYS 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 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 48 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.0570 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 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 = 0.3825 r_free = 0.3825 target = 0.166191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127023 restraints weight = 8637.229| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.99 r_work: 0.3109 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8020 Z= 0.115 Angle : 0.543 11.225 10934 Z= 0.276 Chirality : 0.040 0.158 1277 Planarity : 0.004 0.081 1347 Dihedral : 5.155 64.785 1326 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 2.54 % Allowed : 15.10 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.28), residues: 970 helix: 1.69 (0.22), residues: 578 sheet: 0.79 (0.81), residues: 48 loop : -0.71 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 762 TYR 0.013 0.001 TYR A 990 PHE 0.014 0.001 PHE A 733 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8013) covalent geometry : angle 0.54206 (10916) SS BOND : bond 0.00124 ( 3) SS BOND : angle 0.54349 ( 6) hydrogen bonds : bond 0.03845 ( 444) hydrogen bonds : angle 3.82546 ( 1293) link_BETA1-4 : bond 0.00749 ( 1) link_BETA1-4 : angle 1.27946 ( 3) link_NAG-ASN : bond 0.00297 ( 3) link_NAG-ASN : angle 1.11050 ( 9) *********************** 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 124 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.241 Fit side-chains REVERT: A 235 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8517 (tpp) REVERT: A 395 GLN cc_start: 0.7657 (mt0) cc_final: 0.7206 (tt0) REVERT: A 422 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7084 (mtpp) REVERT: A 738 LYS cc_start: 0.7245 (mttt) cc_final: 0.6441 (tmtt) REVERT: A 785 PHE cc_start: 0.8023 (m-10) cc_final: 0.7437 (t80) outliers start: 21 outliers final: 11 residues processed: 113 average time/residue: 0.4641 time to fit residues: 56.1654 Evaluate side-chains 115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET 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 444 CYS 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 961 VAL 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 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN 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 = 0.3753 r_free = 0.3753 target = 0.160176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120817 restraints weight = 8733.368| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.09 r_work: 0.3046 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8020 Z= 0.189 Angle : 0.617 10.643 10934 Z= 0.312 Chirality : 0.043 0.160 1277 Planarity : 0.005 0.092 1347 Dihedral : 5.433 68.355 1326 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 2.66 % Allowed : 15.22 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.28), residues: 970 helix: 1.50 (0.22), residues: 571 sheet: 0.83 (0.83), residues: 48 loop : -0.74 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.031 0.002 TYR A 990 PHE 0.024 0.002 PHE A 963 TRP 0.006 0.001 TRP A 389 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8013) covalent geometry : angle 0.61577 (10916) SS BOND : bond 0.00235 ( 3) SS BOND : angle 1.06627 ( 6) hydrogen bonds : bond 0.04835 ( 444) hydrogen bonds : angle 4.03513 ( 1293) link_BETA1-4 : bond 0.00900 ( 1) link_BETA1-4 : angle 1.46429 ( 3) link_NAG-ASN : bond 0.00364 ( 3) link_NAG-ASN : angle 1.25069 ( 9) *********************** 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 126 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.251 Fit side-chains REVERT: A 235 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8667 (tpp) REVERT: A 360 LYS cc_start: 0.8000 (tttm) cc_final: 0.7495 (ttpp) REVERT: A 395 GLN cc_start: 0.7851 (mt0) cc_final: 0.7367 (tt0) REVERT: A 422 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7154 (mtpp) REVERT: A 738 LYS cc_start: 0.7373 (mttt) cc_final: 0.6479 (tmtt) REVERT: A 785 PHE cc_start: 0.8201 (m-10) cc_final: 0.7405 (t80) REVERT: A 905 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8113 (tm-30) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.4826 time to fit residues: 59.2740 Evaluate side-chains 114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 235 MET 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 444 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN A1088 HIS A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137321 restraints weight = 8600.596| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.75 r_work: 0.3053 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8020 Z= 0.141 Angle : 0.578 10.963 10934 Z= 0.293 Chirality : 0.041 0.153 1277 Planarity : 0.005 0.087 1347 Dihedral : 5.322 67.131 1326 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 2.05 % Allowed : 16.30 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.28), residues: 970 helix: 1.62 (0.22), residues: 571 sheet: 0.90 (0.84), residues: 48 loop : -0.71 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 284 TYR 0.022 0.001 TYR A 990 PHE 0.027 0.002 PHE A 78 TRP 0.007 0.001 TRP A 327 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8013) covalent geometry : angle 0.57693 (10916) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.73031 ( 6) hydrogen bonds : bond 0.04325 ( 444) hydrogen bonds : angle 3.96882 ( 1293) link_BETA1-4 : bond 0.00931 ( 1) link_BETA1-4 : angle 1.36599 ( 3) link_NAG-ASN : bond 0.00313 ( 3) link_NAG-ASN : angle 1.11818 ( 9) *********************** 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 118 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.230 Fit side-chains REVERT: A 235 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8531 (tpp) REVERT: A 360 LYS cc_start: 0.7818 (tttm) cc_final: 0.7268 (ttpp) REVERT: A 395 GLN cc_start: 0.7631 (mt0) cc_final: 0.7104 (tt0) REVERT: A 422 LYS cc_start: 0.7569 (ttpt) cc_final: 0.6984 (mtpp) REVERT: A 738 LYS cc_start: 0.7313 (mttt) cc_final: 0.6368 (tmtt) REVERT: A 785 PHE cc_start: 0.8050 (m-10) cc_final: 0.7193 (t80) REVERT: A 905 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: A 1122 THR cc_start: 0.8184 (t) cc_final: 0.7803 (p) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.4793 time to fit residues: 55.2802 Evaluate side-chains 115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET 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 444 CYS Chi-restraints excluded: chain A residue 530 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3868 r_free = 0.3868 target = 0.169162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132201 restraints weight = 8628.305| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.86 r_work: 0.3066 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8020 Z= 0.123 Angle : 0.552 11.443 10934 Z= 0.280 Chirality : 0.040 0.147 1277 Planarity : 0.004 0.083 1347 Dihedral : 5.143 65.444 1326 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.28), residues: 970 helix: 1.77 (0.22), residues: 571 sheet: 0.89 (0.84), residues: 48 loop : -0.68 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.019 0.001 TYR A 990 PHE 0.028 0.001 PHE A 78 TRP 0.007 0.001 TRP A 327 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8013) covalent geometry : angle 0.55078 (10916) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.61005 ( 6) hydrogen bonds : bond 0.04022 ( 444) hydrogen bonds : angle 3.90447 ( 1293) link_BETA1-4 : bond 0.00861 ( 1) link_BETA1-4 : angle 1.30168 ( 3) link_NAG-ASN : bond 0.00293 ( 3) link_NAG-ASN : angle 1.11385 ( 9) ********************** 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 124 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.277 Fit side-chains REVERT: A 235 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8586 (tpp) REVERT: A 282 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8774 (mmm) REVERT: A 360 LYS cc_start: 0.7880 (tttm) cc_final: 0.7362 (ttpp) REVERT: A 395 GLN cc_start: 0.7738 (mt0) cc_final: 0.7222 (tt0) REVERT: A 738 LYS cc_start: 0.7337 (mttt) cc_final: 0.6402 (tmtt) REVERT: A 785 PHE cc_start: 0.8119 (m-10) cc_final: 0.7320 (t80) REVERT: A 905 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: A 1122 THR cc_start: 0.8376 (t) cc_final: 0.8031 (p) outliers start: 18 outliers final: 12 residues processed: 115 average time/residue: 0.4838 time to fit residues: 59.5186 Evaluate side-chains 119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 282 MET 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 444 CYS Chi-restraints excluded: chain A residue 530 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3836 r_free = 0.3836 target = 0.166776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128424 restraints weight = 8714.395| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.96 r_work: 0.3043 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8020 Z= 0.121 Angle : 0.557 11.369 10934 Z= 0.282 Chirality : 0.040 0.146 1277 Planarity : 0.004 0.083 1347 Dihedral : 5.086 64.982 1326 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 2.54 % Allowed : 15.82 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.28), residues: 970 helix: 1.84 (0.22), residues: 571 sheet: 0.91 (0.85), residues: 48 loop : -0.67 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.016 0.001 TYR A 990 PHE 0.028 0.001 PHE A 78 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8013) covalent geometry : angle 0.55610 (10916) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.60707 ( 6) hydrogen bonds : bond 0.03967 ( 444) hydrogen bonds : angle 3.88147 ( 1293) link_BETA1-4 : bond 0.00805 ( 1) link_BETA1-4 : angle 1.28243 ( 3) link_NAG-ASN : bond 0.00282 ( 3) link_NAG-ASN : angle 1.14223 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.15 seconds wall clock time: 41 minutes 40.54 seconds (2500.54 seconds total)