Starting phenix.real_space_refine on Sat Jul 4 06:18:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ody_70380/07_2026/9ody_70380_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ody_70380/07_2026/9ody_70380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ody_70380/07_2026/9ody_70380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ody_70380/07_2026/9ody_70380.map" model { file = "/net/cci-nas-00/data/ceres_data/9ody_70380/07_2026/9ody_70380_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ody_70380/07_2026/9ody_70380_trim.cif" } resolution = 3.29 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= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5754 2.51 5 N 1528 2.21 5 O 1671 1.98 5 H 9124 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18134 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1154, 18070 Classifications: {'peptide': 1154} Link IDs: {'PTRANS': 27, 'TRANS': 1126} Chain breaks: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.87, per 1000 atoms: 0.16 Number of scatterers: 18134 At special positions: 0 Unit cell: (71.38, 119.52, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 O 1671 8.00 N 1528 7.00 C 5754 6.00 H 9124 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 635.0 milliseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 69.8% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 49 through 80 removed outlier: 3.790A pdb=" N ASN A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 115 through 161 removed outlier: 3.868A pdb=" N LEU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 172 through 192 removed outlier: 4.317A pdb=" N ASP A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 216 Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.513A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 252 through 265 removed outlier: 3.556A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 274 through 322 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 332 through 375 removed outlier: 3.768A pdb=" N GLY A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix removed outlier: 3.709A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.119A pdb=" N ASP A 410 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.693A pdb=" N GLN A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 489 through 497 removed outlier: 3.806A pdb=" N ARG A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.599A pdb=" N ALA A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 537 through 552 removed outlier: 3.843A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 695 through 703 removed outlier: 4.034A pdb=" N ASN A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 737 Proline residue: A 725 - end of helix Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 742 through 790 Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.776A pdb=" N ASP A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.502A pdb=" N VAL A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 828 removed outlier: 3.806A pdb=" N THR A 827 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 828' Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 852 through 901 removed outlier: 3.882A pdb=" N THR A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Proline residue: A 864 - end of helix removed outlier: 3.721A pdb=" N GLN A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 894 " --> pdb=" O GLN A 890 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.682A pdb=" N TYR A 918 " --> pdb=" O PHE A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 964 removed outlier: 3.716A pdb=" N TYR A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 930 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 993 Processing helix chain 'A' and resid 995 through 1011 Processing helix chain 'A' and resid 1075 through 1080 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1103 through 1110 Processing helix chain 'A' and resid 1124 through 1131 Processing helix chain 'A' and resid 1139 through 1150 Processing helix chain 'A' and resid 1152 through 1159 Processing helix chain 'A' and resid 1175 through 1190 removed outlier: 4.289A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1220 Processing helix chain 'A' and resid 1231 through 1237 removed outlier: 3.950A pdb=" N ILE A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1260 Processing helix chain 'A' and resid 1262 through 1274 Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 403 removed outlier: 5.086A pdb=" N PHE A 399 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER A 457 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN A 401 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 455 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 7.451A pdb=" N ALA A 604 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA A 429 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE A 606 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 431 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 613 " --> pdb=" O GLY A 605 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 1051 through 1054 removed outlier: 3.501A pdb=" N LEU A1051 " --> pdb=" O PHE A1040 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL A1038 " --> pdb=" O GLY A1053 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS A1037 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG A1091 " --> pdb=" O HIS A1037 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1064 through 1066 removed outlier: 6.417A pdb=" N GLY A1112 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASP A1198 " --> pdb=" O GLY A1112 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A1114 " --> pdb=" O ASP A1198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1242 through 1244 removed outlier: 4.289A pdb=" N GLU A1251 " --> pdb=" O VAL A1243 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1725 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: 5.10 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.06: 9115 1.06 - 1.28: 1489 1.28 - 1.50: 3796 1.50 - 1.73: 3803 1.73 - 1.95: 87 Bond restraints: 18290 Sorted by residual: bond pdb=" O2G AGS A1303 " pdb=" PG AGS A1303 " ideal model delta sigma weight residual 1.604 1.504 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " ideal model delta sigma weight residual 1.673 1.575 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" O3A AGS A1304 " pdb=" PA AGS A1304 " ideal model delta sigma weight residual 1.664 1.580 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.593 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" O3G AGS A1303 " pdb=" PG AGS A1303 " ideal model delta sigma weight residual 1.570 1.498 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 18285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 32775 2.28 - 4.57: 285 4.57 - 6.85: 21 6.85 - 9.14: 5 9.14 - 11.42: 2 Bond angle restraints: 33088 Sorted by residual: angle pdb=" PB AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sigma weight residual 129.21 117.79 11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" N GLU A 619 " pdb=" CA GLU A 619 " pdb=" C GLU A 619 " ideal model delta sigma weight residual 111.07 107.47 3.60 1.07e+00 8.73e-01 1.13e+01 angle pdb=" O1A AGS A1304 " pdb=" PA AGS A1304 " pdb=" O2A AGS A1304 " ideal model delta sigma weight residual 122.09 112.50 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" C VAL A 236 " ideal model delta sigma weight residual 110.74 107.92 2.82 9.10e-01 1.21e+00 9.62e+00 angle pdb=" O3A AGS A1304 " pdb=" PB AGS A1304 " pdb=" O3B AGS A1304 " ideal model delta sigma weight residual 100.38 109.32 -8.94 3.00e+00 1.11e-01 8.88e+00 ... (remaining 33083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 8157 34.54 - 69.07: 380 69.07 - 103.61: 23 103.61 - 138.15: 3 138.15 - 172.68: 4 Dihedral angle restraints: 8567 sinusoidal: 4711 harmonic: 3856 Sorted by residual: dihedral pdb=" CA ILE A 237 " pdb=" C ILE A 237 " pdb=" N GLY A 238 " pdb=" CA GLY A 238 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA LEU A1081 " pdb=" C LEU A1081 " pdb=" N GLU A1082 " pdb=" CA GLU A1082 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" O1B AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual 138.55 -34.13 172.68 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 8564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1261 0.059 - 0.118: 157 0.118 - 0.177: 11 0.177 - 0.236: 1 0.236 - 0.295: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C3' AGS A1303 " pdb=" C2' AGS A1303 " pdb=" C4' AGS A1303 " pdb=" O3' AGS A1303 " both_signs ideal model delta sigma weight residual False -2.37 -2.67 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' AGS A1304 " pdb=" C2' AGS A1304 " pdb=" C4' AGS A1304 " pdb=" O3' AGS A1304 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA GLU A 619 " pdb=" N GLU A 619 " pdb=" C GLU A 619 " pdb=" CB GLU A 619 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1429 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 521 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 522 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 522 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 522 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 354 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 355 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 236 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C VAL A 236 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 236 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 237 " 0.011 2.00e-02 2.50e+03 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2109 2.25 - 2.84: 41121 2.84 - 3.42: 47587 3.42 - 4.01: 62570 4.01 - 4.60: 98768 Nonbonded interactions: 252155 Sorted by model distance: nonbonded pdb=" O TRP A 167 " pdb="HD22 ASN A 171 " model vdw 1.660 2.450 nonbonded pdb=" HE ARG A 405 " pdb=" O ASP A 410 " model vdw 1.664 2.450 nonbonded pdb=" OD1 ASP A 52 " pdb="HH11 ARG A 147 " model vdw 1.680 2.450 nonbonded pdb=" OD1 ASP A 462 " pdb=" H ARG A 464 " model vdw 1.694 2.450 nonbonded pdb=" O ASP A 523 " pdb=" H THR A 527 " model vdw 1.695 2.450 ... (remaining 252150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.080 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.005 0.100 9166 Z= 0.254 Angle : 0.698 11.425 12399 Z= 0.361 Chirality : 0.040 0.295 1432 Planarity : 0.005 0.048 1566 Dihedral : 18.777 172.685 3402 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.92 % Favored : 93.82 % Rotamer: Outliers : 2.62 % Allowed : 11.83 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1148 helix: 1.24 (0.19), residues: 731 sheet: -3.54 (0.53), residues: 55 loop : -2.16 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 497 TYR 0.009 0.001 TYR A 918 PHE 0.013 0.002 PHE A 957 TRP 0.009 0.001 TRP A 801 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.25 ( 9166) covalent geometry : angle 0.69784 / 0.36 (12399) hydrogen bonds : bond 0.14826 / 9.89 ( 586) hydrogen bonds : angle 5.98980 / 4.33 ( 1725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1062 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7655 (mm110) outliers start: 25 outliers final: 12 residues processed: 94 average time/residue: 0.1830 time to fit residues: 25.7436 Evaluate side-chains 64 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 ASN A1101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.063288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050702 restraints weight = 113147.714| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.71 r_work: 0.3000 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9166 Z= 0.265 Angle : 0.594 6.569 12399 Z= 0.329 Chirality : 0.038 0.136 1432 Planarity : 0.004 0.044 1566 Dihedral : 14.971 171.991 1340 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.01 % Favored : 93.73 % Rotamer: Outliers : 1.99 % Allowed : 16.86 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1148 helix: 1.39 (0.19), residues: 740 sheet: -3.17 (0.55), residues: 55 loop : -2.36 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 747 TYR 0.009 0.001 TYR A 851 PHE 0.011 0.001 PHE A 348 TRP 0.009 0.001 TRP A 801 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.27 ( 9166) covalent geometry : angle 0.59368 / 0.33 (12399) hydrogen bonds : bond 0.04897 / 3.22 ( 586) hydrogen bonds : angle 4.99052 / 3.60 ( 1725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 984 MET cc_start: 0.9071 (mtp) cc_final: 0.8869 (mmm) REVERT: A 1093 MET cc_start: 0.8368 (tpp) cc_final: 0.8104 (tpp) outliers start: 19 outliers final: 15 residues processed: 68 average time/residue: 0.2028 time to fit residues: 20.2599 Evaluate side-chains 64 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.051649 restraints weight = 112852.830| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.83 r_work: 0.3025 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9166 Z= 0.131 Angle : 0.489 5.735 12399 Z= 0.264 Chirality : 0.036 0.137 1432 Planarity : 0.004 0.044 1566 Dihedral : 12.435 164.030 1335 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.84 % Favored : 93.90 % Rotamer: Outliers : 1.88 % Allowed : 18.12 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1148 helix: 1.86 (0.19), residues: 744 sheet: -3.59 (0.49), residues: 66 loop : -2.17 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.008 0.001 TYR A 515 PHE 0.008 0.001 PHE A 319 TRP 0.005 0.001 TRP A 141 HIS 0.003 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 9166) covalent geometry : angle 0.48856 / 0.26 (12399) hydrogen bonds : bond 0.04163 / 2.72 ( 586) hydrogen bonds : angle 4.47174 / 3.21 ( 1725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 984 MET cc_start: 0.9056 (mtp) cc_final: 0.8844 (mmm) outliers start: 18 outliers final: 16 residues processed: 69 average time/residue: 0.2040 time to fit residues: 20.3799 Evaluate side-chains 68 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 893 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1155 PHE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 54 optimal weight: 0.0370 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 ASN A 376 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.064577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.052166 restraints weight = 113089.956| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.73 r_work: 0.3028 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9166 Z= 0.138 Angle : 0.488 6.506 12399 Z= 0.262 Chirality : 0.036 0.139 1432 Planarity : 0.003 0.039 1566 Dihedral : 10.874 162.699 1334 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.57 % Favored : 94.16 % Rotamer: Outliers : 1.99 % Allowed : 18.12 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1148 helix: 2.04 (0.19), residues: 744 sheet: -3.47 (0.49), residues: 66 loop : -2.13 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.009 0.001 TYR A 515 PHE 0.009 0.001 PHE A 128 TRP 0.005 0.001 TRP A 217 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 9166) covalent geometry : angle 0.48761 / 0.26 (12399) hydrogen bonds : bond 0.03900 / 2.55 ( 586) hydrogen bonds : angle 4.36055 / 3.12 ( 1725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 984 MET cc_start: 0.9051 (mtp) cc_final: 0.8842 (mmm) outliers start: 19 outliers final: 16 residues processed: 72 average time/residue: 0.1810 time to fit residues: 19.7709 Evaluate side-chains 67 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1155 PHE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.064071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051614 restraints weight = 113249.371| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.72 r_work: 0.3011 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9166 Z= 0.188 Angle : 0.496 5.429 12399 Z= 0.272 Chirality : 0.036 0.136 1432 Planarity : 0.004 0.043 1566 Dihedral : 10.494 156.785 1334 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.84 % Favored : 93.90 % Rotamer: Outliers : 2.30 % Allowed : 18.95 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1148 helix: 2.07 (0.19), residues: 744 sheet: -3.36 (0.49), residues: 65 loop : -2.17 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 785 TYR 0.006 0.001 TYR A 123 PHE 0.010 0.001 PHE A 340 TRP 0.006 0.001 TRP A 320 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 ( 9166) covalent geometry : angle 0.49630 / 0.27 (12399) hydrogen bonds : bond 0.03923 / 2.57 ( 586) hydrogen bonds : angle 4.42094 / 3.17 ( 1725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8613 (mmt) cc_final: 0.8268 (mmp) REVERT: A 984 MET cc_start: 0.9066 (mtp) cc_final: 0.8851 (mmm) REVERT: A 1166 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8669 (tm-30) outliers start: 22 outliers final: 18 residues processed: 68 average time/residue: 0.2012 time to fit residues: 19.9788 Evaluate side-chains 68 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1155 PHE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1166 GLN Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051982 restraints weight = 111571.079| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.70 r_work: 0.3023 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9166 Z= 0.147 Angle : 0.477 6.808 12399 Z= 0.258 Chirality : 0.036 0.141 1432 Planarity : 0.003 0.040 1566 Dihedral : 10.083 153.002 1334 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.01 % Favored : 93.73 % Rotamer: Outliers : 2.30 % Allowed : 19.16 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1148 helix: 2.20 (0.19), residues: 744 sheet: -3.30 (0.50), residues: 66 loop : -2.11 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 785 TYR 0.007 0.001 TYR A 515 PHE 0.010 0.001 PHE A 128 TRP 0.006 0.001 TRP A 320 HIS 0.003 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 ( 9166) covalent geometry : angle 0.47718 / 0.26 (12399) hydrogen bonds : bond 0.03806 / 2.49 ( 586) hydrogen bonds : angle 4.27484 / 3.07 ( 1725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8577 (mmt) cc_final: 0.8234 (mmp) REVERT: A 984 MET cc_start: 0.9045 (mtp) cc_final: 0.8833 (mmm) outliers start: 22 outliers final: 17 residues processed: 73 average time/residue: 0.2027 time to fit residues: 21.6957 Evaluate side-chains 67 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1155 PHE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.064207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051797 restraints weight = 113048.851| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.73 r_work: 0.3019 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9166 Z= 0.153 Angle : 0.480 6.604 12399 Z= 0.260 Chirality : 0.036 0.141 1432 Planarity : 0.003 0.041 1566 Dihedral : 9.580 149.978 1332 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.92 % Favored : 93.82 % Rotamer: Outliers : 2.30 % Allowed : 19.27 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1148 helix: 2.25 (0.19), residues: 744 sheet: -3.23 (0.51), residues: 66 loop : -2.10 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 747 TYR 0.009 0.001 TYR A 515 PHE 0.007 0.001 PHE A 340 TRP 0.006 0.001 TRP A 320 HIS 0.004 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 9166) covalent geometry : angle 0.47957 / 0.26 (12399) hydrogen bonds : bond 0.03791 / 2.47 ( 586) hydrogen bonds : angle 4.25262 / 3.05 ( 1725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8604 (mmt) cc_final: 0.8250 (mmp) REVERT: A 984 MET cc_start: 0.9043 (mtp) cc_final: 0.8820 (mmm) outliers start: 22 outliers final: 19 residues processed: 74 average time/residue: 0.2040 time to fit residues: 22.2908 Evaluate side-chains 69 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1155 PHE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 HIS A1191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.063622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051132 restraints weight = 113417.035| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.72 r_work: 0.2995 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9166 Z= 0.215 Angle : 0.519 7.875 12399 Z= 0.284 Chirality : 0.037 0.138 1432 Planarity : 0.003 0.036 1566 Dihedral : 9.426 146.035 1332 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.27 % Favored : 93.47 % Rotamer: Outliers : 2.62 % Allowed : 19.48 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1148 helix: 2.16 (0.19), residues: 744 sheet: -3.21 (0.51), residues: 66 loop : -2.16 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1162 TYR 0.008 0.001 TYR A 321 PHE 0.010 0.001 PHE A 128 TRP 0.007 0.001 TRP A 320 HIS 0.007 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.22 ( 9166) covalent geometry : angle 0.51866 / 0.28 (12399) hydrogen bonds : bond 0.03897 / 2.55 ( 586) hydrogen bonds : angle 4.40450 / 3.16 ( 1725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8636 (mmt) cc_final: 0.8283 (mmp) REVERT: A 984 MET cc_start: 0.9033 (mtp) cc_final: 0.8806 (mmm) outliers start: 25 outliers final: 19 residues processed: 73 average time/residue: 0.2349 time to fit residues: 24.7420 Evaluate side-chains 67 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1155 PHE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 HIS A 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.066940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.054308 restraints weight = 108195.509| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.62 r_work: 0.3223 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9166 Z= 0.163 Angle : 0.499 7.561 12399 Z= 0.269 Chirality : 0.036 0.141 1432 Planarity : 0.003 0.041 1566 Dihedral : 9.257 145.116 1332 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.10 % Favored : 93.64 % Rotamer: Outliers : 2.09 % Allowed : 19.69 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.25), residues: 1148 helix: 2.24 (0.19), residues: 745 sheet: -3.15 (0.51), residues: 66 loop : -2.15 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 747 TYR 0.008 0.001 TYR A 515 PHE 0.017 0.001 PHE A 992 TRP 0.007 0.001 TRP A 320 HIS 0.010 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 9166) covalent geometry : angle 0.49890 / 0.27 (12399) hydrogen bonds : bond 0.03837 / 2.51 ( 586) hydrogen bonds : angle 4.29197 / 3.08 ( 1725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8586 (mmt) cc_final: 0.8236 (mmp) REVERT: A 984 MET cc_start: 0.9071 (mtp) cc_final: 0.8834 (mmm) outliers start: 20 outliers final: 19 residues processed: 68 average time/residue: 0.2048 time to fit residues: 20.3996 Evaluate side-chains 67 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1155 PHE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.067144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.054546 restraints weight = 107904.655| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.63 r_work: 0.3190 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9166 Z= 0.129 Angle : 0.486 7.309 12399 Z= 0.259 Chirality : 0.036 0.164 1432 Planarity : 0.003 0.037 1566 Dihedral : 9.086 144.937 1332 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.75 % Favored : 93.99 % Rotamer: Outliers : 1.78 % Allowed : 20.00 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.26), residues: 1148 helix: 2.35 (0.19), residues: 745 sheet: -3.08 (0.52), residues: 66 loop : -2.04 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 747 TYR 0.009 0.001 TYR A 515 PHE 0.018 0.001 PHE A 992 TRP 0.007 0.001 TRP A 320 HIS 0.009 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 9166) covalent geometry : angle 0.48555 / 0.26 (12399) hydrogen bonds : bond 0.03764 / 2.45 ( 586) hydrogen bonds : angle 4.17895 / 3.00 ( 1725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 439 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8575 (mmt) cc_final: 0.8224 (mmp) REVERT: A 984 MET cc_start: 0.9059 (mtp) cc_final: 0.8823 (mmm) outliers start: 17 outliers final: 16 residues processed: 67 average time/residue: 0.1980 time to fit residues: 19.5148 Evaluate side-chains 65 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1062 GLN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1155 PHE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.0070 chunk 105 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.067883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.055343 restraints weight = 107664.698| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.63 r_work: 0.3244 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9166 Z= 0.099 Angle : 0.465 7.127 12399 Z= 0.244 Chirality : 0.035 0.147 1432 Planarity : 0.003 0.043 1566 Dihedral : 8.780 145.516 1332 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.05 % Favored : 94.69 % Rotamer: Outliers : 1.47 % Allowed : 20.42 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.26), residues: 1148 helix: 2.47 (0.19), residues: 754 sheet: -2.97 (0.57), residues: 60 loop : -1.88 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 747 TYR 0.009 0.001 TYR A 515 PHE 0.016 0.001 PHE A 992 TRP 0.007 0.001 TRP A 853 HIS 0.011 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 9166) covalent geometry : angle 0.46506 / 0.24 (12399) hydrogen bonds : bond 0.03567 / 2.32 ( 586) hydrogen bonds : angle 4.02095 / 2.89 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.49 seconds wall clock time: 60 minutes 14.15 seconds (3614.15 seconds total)