Starting phenix.real_space_refine on Sat Dec 28 02:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm6_17758/12_2024/8pm6_17758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm6_17758/12_2024/8pm6_17758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pm6_17758/12_2024/8pm6_17758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm6_17758/12_2024/8pm6_17758.map" model { file = "/net/cci-nas-00/data/ceres_data/8pm6_17758/12_2024/8pm6_17758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm6_17758/12_2024/8pm6_17758.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 Cl 1 4.86 5 C 4624 2.51 5 N 1125 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7029 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6772 Classifications: {'peptide': 872} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 847} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 257 Unusual residues: {'CLR': 8, 'GBM': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 5.36, per 1000 atoms: 0.76 Number of scatterers: 7029 At special positions: 0 Unit cell: (70.422, 103.092, 136.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 40 16.00 O 1239 8.00 N 1125 7.00 C 4624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 842.4 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 74.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 55 through 101 removed outlier: 3.777A pdb=" N GLN A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Proline residue: A 77 - end of helix removed outlier: 3.506A pdb=" N GLN A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 183 removed outlier: 3.804A pdb=" N MET A 183 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 215 through 238 Processing helix chain 'A' and resid 240 through 287 Proline residue: A 250 - end of helix removed outlier: 3.810A pdb=" N SER A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.718A pdb=" N VAL A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 350 removed outlier: 4.187A pdb=" N VAL A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N PHE A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 376 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.955A pdb=" N LEU A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 746 " --> pdb=" O ARG A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 766 Processing helix chain 'A' and resid 767 through 782 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 787 through 842 Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 853 through 895 removed outlier: 4.256A pdb=" N ALA A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY A 870 " --> pdb=" O SER A 866 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 871 " --> pdb=" O GLN A 867 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 917 removed outlier: 3.967A pdb=" N PHE A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) Proline residue: A 909 - end of helix removed outlier: 4.165A pdb=" N GLY A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.674A pdb=" N ALA A 962 " --> pdb=" O ARG A 958 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 963 " --> pdb=" O PHE A 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 958 through 963' Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 967 through 1010 removed outlier: 4.284A pdb=" N MET A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1036 removed outlier: 3.585A pdb=" N VAL A1017 " --> pdb=" O HIS A1013 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A1036 " --> pdb=" O GLY A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1056 removed outlier: 4.400A pdb=" N LYS A1043 " --> pdb=" O PRO A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1143 through 1147 Processing helix chain 'A' and resid 1148 through 1155 Processing helix chain 'A' and resid 1170 through 1174 Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1197 through 1204 removed outlier: 3.553A pdb=" N LEU A1204 " --> pdb=" O PHE A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1235 removed outlier: 3.503A pdb=" N LYS A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG A1226 " --> pdb=" O GLY A1222 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.686A pdb=" N THR A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A1266 " --> pdb=" O ASP A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1306 removed outlier: 4.348A pdb=" N ALA A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1314 removed outlier: 3.646A pdb=" N LEU A1313 " --> pdb=" O ALA A1309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1080 through 1081 removed outlier: 3.640A pdb=" N LYS A1136 " --> pdb=" O VAL A1081 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1108 through 1110 removed outlier: 6.355A pdb=" N LEU A1109 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A1242 " --> pdb=" O ILE A1271 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A1159 " --> pdb=" O LEU A1241 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1096 1.32 - 1.44: 1905 1.44 - 1.57: 4126 1.57 - 1.69: 1 1.69 - 1.82: 64 Bond restraints: 7192 Sorted by residual: bond pdb=" N ILE A 393 " pdb=" CA ILE A 393 " ideal model delta sigma weight residual 1.457 1.510 -0.053 1.29e-02 6.01e+03 1.68e+01 bond pdb=" N PRO A 740 " pdb=" CA PRO A 740 " ideal model delta sigma weight residual 1.469 1.423 0.046 1.28e-02 6.10e+03 1.27e+01 bond pdb=" CA SER A 377 " pdb=" CB SER A 377 " ideal model delta sigma weight residual 1.531 1.485 0.046 1.33e-02 5.65e+03 1.19e+01 bond pdb=" C TRP A 752 " pdb=" O TRP A 752 " ideal model delta sigma weight residual 1.244 1.211 0.032 9.80e-03 1.04e+04 1.10e+01 bond pdb=" C PRO A1184 " pdb=" O PRO A1184 " ideal model delta sigma weight residual 1.232 1.192 0.041 1.25e-02 6.40e+03 1.06e+01 ... (remaining 7187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 9490 2.03 - 4.06: 216 4.06 - 6.09: 48 6.09 - 8.12: 11 8.12 - 10.15: 7 Bond angle restraints: 9772 Sorted by residual: angle pdb=" N THR A 391 " pdb=" CA THR A 391 " pdb=" C THR A 391 " ideal model delta sigma weight residual 111.82 102.14 9.68 1.16e+00 7.43e-01 6.96e+01 angle pdb=" N GLU A 395 " pdb=" CA GLU A 395 " pdb=" C GLU A 395 " ideal model delta sigma weight residual 112.88 102.73 10.15 1.29e+00 6.01e-01 6.19e+01 angle pdb=" N ARG A 201 " pdb=" CA ARG A 201 " pdb=" C ARG A 201 " ideal model delta sigma weight residual 111.36 103.90 7.46 1.09e+00 8.42e-01 4.68e+01 angle pdb=" N LEU A 745 " pdb=" CA LEU A 745 " pdb=" C LEU A 745 " ideal model delta sigma weight residual 111.14 104.42 6.72 1.08e+00 8.57e-01 3.87e+01 angle pdb=" N THR A 396 " pdb=" CA THR A 396 " pdb=" C THR A 396 " ideal model delta sigma weight residual 113.16 105.86 7.30 1.24e+00 6.50e-01 3.47e+01 ... (remaining 9767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.41: 4200 24.41 - 48.81: 343 48.81 - 73.22: 47 73.22 - 97.62: 17 97.62 - 122.03: 11 Dihedral angle restraints: 4618 sinusoidal: 2115 harmonic: 2503 Sorted by residual: dihedral pdb=" C PRO A 378 " pdb=" N PRO A 378 " pdb=" CA PRO A 378 " pdb=" CB PRO A 378 " ideal model delta harmonic sigma weight residual -120.70 -109.77 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C1 CLR A1404 " pdb=" C2 CLR A1404 " pdb=" C3 CLR A1404 " pdb=" O1 CLR A1404 " ideal model delta sinusoidal sigma weight residual 180.04 58.01 122.03 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C10 CLR A1405 " pdb=" C1 CLR A1405 " pdb=" C2 CLR A1405 " pdb=" C3 CLR A1405 " ideal model delta sinusoidal sigma weight residual -56.83 64.17 -121.00 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 4615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 922 0.055 - 0.109: 170 0.109 - 0.163: 31 0.163 - 0.218: 6 0.218 - 0.272: 2 Chirality restraints: 1131 Sorted by residual: chirality pdb=" CA ARG A 387 " pdb=" N ARG A 387 " pdb=" C ARG A 387 " pdb=" CB ARG A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE A 213 " pdb=" CA ILE A 213 " pdb=" CG1 ILE A 213 " pdb=" CG2 ILE A 213 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1128 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 GBM A1409 " 0.493 2.00e-02 2.50e+03 3.37e-01 1.71e+03 pdb=" C17 GBM A1409 " -0.175 2.00e-02 2.50e+03 pdb=" N8 GBM A1409 " -0.494 2.00e-02 2.50e+03 pdb=" N9 GBM A1409 " -0.257 2.00e-02 2.50e+03 pdb=" O3 GBM A1409 " 0.167 2.00e-02 2.50e+03 pdb=" S2 GBM A1409 " 0.266 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1070 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C LYS A1070 " -0.066 2.00e-02 2.50e+03 pdb=" O LYS A1070 " 0.025 2.00e-02 2.50e+03 pdb=" N TRP A1071 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM A1409 " -0.037 2.00e-02 2.50e+03 3.21e-02 1.29e+01 pdb=" C26 GBM A1409 " -0.012 2.00e-02 2.50e+03 pdb=" C27 GBM A1409 " -0.022 2.00e-02 2.50e+03 pdb=" N10 GBM A1409 " 0.053 2.00e-02 2.50e+03 pdb=" O6 GBM A1409 " 0.017 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 656 2.74 - 3.28: 7409 3.28 - 3.82: 11725 3.82 - 4.36: 13312 4.36 - 4.90: 23081 Nonbonded interactions: 56183 Sorted by model distance: nonbonded pdb=" OD1 ASP A 88 " pdb=" OG1 THR A 355 " model vdw 2.200 3.040 nonbonded pdb=" O LEU A 198 " pdb=" CD2 PHE A 202 " model vdw 2.215 3.340 nonbonded pdb=" O ALA A 995 " pdb=" OG SER A 999 " model vdw 2.223 3.040 nonbonded pdb=" O PHE A1018 " pdb=" OG SER A1022 " model vdw 2.272 3.040 nonbonded pdb=" O SER A 897 " pdb=" OG SER A 901 " model vdw 2.272 3.040 ... (remaining 56178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.510 Find NCS groups from input model: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 0.060 7192 Z= 0.308 Angle : 0.800 10.146 9772 Z= 0.510 Chirality : 0.046 0.272 1131 Planarity : 0.011 0.337 1184 Dihedral : 18.408 122.028 3010 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.42 % Allowed : 22.73 % Favored : 76.85 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.29), residues: 862 helix: 1.65 (0.21), residues: 593 sheet: -2.87 (1.00), residues: 17 loop : -1.65 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1071 HIS 0.003 0.001 HIS A1198 PHE 0.016 0.001 PHE A 202 TYR 0.014 0.001 TYR A1041 ARG 0.009 0.001 ARG A1033 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.6747 (mmmm) cc_final: 0.6030 (tmtt) REVERT: A 268 ASP cc_start: 0.7274 (t0) cc_final: 0.6984 (t0) REVERT: A 322 MET cc_start: 0.7571 (ttm) cc_final: 0.7364 (ttm) REVERT: A 743 ARG cc_start: 0.7170 (ptp-110) cc_final: 0.6560 (ttm110) REVERT: A 744 ILE cc_start: 0.7072 (mm) cc_final: 0.6704 (mt) REVERT: A 789 GLU cc_start: 0.7519 (pt0) cc_final: 0.6819 (mt-10) REVERT: A 891 ILE cc_start: 0.8551 (mm) cc_final: 0.8348 (mt) REVERT: A 1010 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6390 (tt0) REVERT: A 1033 ARG cc_start: 0.7314 (ttm110) cc_final: 0.6982 (mmm160) REVERT: A 1050 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7374 (mtm110) REVERT: A 1175 LYS cc_start: 0.7609 (pttp) cc_final: 0.6761 (mttt) REVERT: A 1194 GLN cc_start: 0.8423 (mt0) cc_final: 0.8154 (mt0) outliers start: 3 outliers final: 1 residues processed: 139 average time/residue: 0.2094 time to fit residues: 38.7697 Evaluate side-chains 103 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 210 ASN A 375 ASN A 813 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN A1198 HIS A1218 GLN A1258 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7192 Z= 0.206 Angle : 0.580 10.368 9772 Z= 0.290 Chirality : 0.041 0.170 1131 Planarity : 0.004 0.049 1184 Dihedral : 8.330 107.382 1477 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.77 % Allowed : 21.62 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.29), residues: 862 helix: 1.88 (0.21), residues: 608 sheet: -2.88 (0.98), residues: 17 loop : -1.57 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1071 HIS 0.002 0.001 HIS A1198 PHE 0.013 0.001 PHE A 776 TYR 0.013 0.001 TYR A 754 ARG 0.004 0.000 ARG A1033 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.6683 (mmmm) cc_final: 0.5985 (tmtt) REVERT: A 268 ASP cc_start: 0.7297 (t0) cc_final: 0.7007 (t0) REVERT: A 322 MET cc_start: 0.7638 (ttm) cc_final: 0.7416 (ttm) REVERT: A 743 ARG cc_start: 0.7195 (ptp-110) cc_final: 0.6784 (ttm110) REVERT: A 744 ILE cc_start: 0.7315 (mm) cc_final: 0.7035 (mt) REVERT: A 789 GLU cc_start: 0.7507 (pt0) cc_final: 0.6822 (mt-10) REVERT: A 875 GLN cc_start: 0.8014 (tp40) cc_final: 0.7468 (tp40) REVERT: A 1010 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6675 (tt0) REVERT: A 1033 ARG cc_start: 0.7504 (ttm110) cc_final: 0.7181 (mmm160) REVERT: A 1050 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7502 (mtp85) REVERT: A 1175 LYS cc_start: 0.7604 (pttp) cc_final: 0.6864 (ptpt) REVERT: A 1194 GLN cc_start: 0.8441 (mt0) cc_final: 0.8195 (mt0) REVERT: A 1258 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: A 1262 ASP cc_start: 0.8084 (m-30) cc_final: 0.7649 (m-30) outliers start: 27 outliers final: 13 residues processed: 128 average time/residue: 0.2046 time to fit residues: 35.7668 Evaluate side-chains 114 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1258 GLN Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 842 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 ASN A1155 ASN A1215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 7192 Z= 0.242 Angle : 0.563 7.391 9772 Z= 0.286 Chirality : 0.041 0.152 1131 Planarity : 0.004 0.049 1184 Dihedral : 7.914 98.762 1474 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.77 % Allowed : 21.20 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 862 helix: 1.90 (0.21), residues: 610 sheet: -3.04 (0.98), residues: 17 loop : -1.60 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 898 HIS 0.003 0.001 HIS A1198 PHE 0.011 0.001 PHE A1151 TYR 0.020 0.002 TYR A 754 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7339 (t0) cc_final: 0.7060 (t0) REVERT: A 282 ASP cc_start: 0.7567 (m-30) cc_final: 0.7327 (m-30) REVERT: A 322 MET cc_start: 0.7624 (ttm) cc_final: 0.7389 (ttm) REVERT: A 743 ARG cc_start: 0.7230 (ptp-110) cc_final: 0.6797 (ttm110) REVERT: A 789 GLU cc_start: 0.7488 (pt0) cc_final: 0.6774 (mt-10) REVERT: A 1010 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6773 (tt0) REVERT: A 1033 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7209 (mmm160) REVERT: A 1050 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7476 (mtp85) REVERT: A 1051 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7450 (t80) REVERT: A 1175 LYS cc_start: 0.7591 (pttp) cc_final: 0.6774 (mttt) REVERT: A 1194 GLN cc_start: 0.8432 (mt0) cc_final: 0.8160 (mt0) REVERT: A 1243 ASP cc_start: 0.8199 (t0) cc_final: 0.7846 (m-30) REVERT: A 1262 ASP cc_start: 0.8231 (m-30) cc_final: 0.7923 (m-30) outliers start: 27 outliers final: 21 residues processed: 117 average time/residue: 0.2063 time to fit residues: 32.1693 Evaluate side-chains 113 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1051 PHE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 307 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7192 Z= 0.209 Angle : 0.536 6.952 9772 Z= 0.273 Chirality : 0.040 0.173 1131 Planarity : 0.004 0.049 1184 Dihedral : 7.637 88.013 1474 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.44 % Allowed : 20.64 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 862 helix: 1.97 (0.21), residues: 610 sheet: -3.06 (0.98), residues: 17 loop : -1.55 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 898 HIS 0.003 0.001 HIS A1198 PHE 0.016 0.001 PHE A 63 TYR 0.016 0.001 TYR A 754 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7341 (t0) cc_final: 0.7063 (t0) REVERT: A 282 ASP cc_start: 0.7587 (m-30) cc_final: 0.7235 (m-30) REVERT: A 322 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7341 (ttm) REVERT: A 743 ARG cc_start: 0.7231 (ptp-110) cc_final: 0.6839 (ttm110) REVERT: A 744 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7127 (mt) REVERT: A 789 GLU cc_start: 0.7532 (pt0) cc_final: 0.6739 (mt-10) REVERT: A 1010 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6757 (tt0) REVERT: A 1033 ARG cc_start: 0.7474 (ttm110) cc_final: 0.7211 (mmm160) REVERT: A 1041 TYR cc_start: 0.7126 (t80) cc_final: 0.6892 (t80) REVERT: A 1050 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7402 (mtm110) REVERT: A 1051 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7527 (t80) REVERT: A 1175 LYS cc_start: 0.7599 (pttp) cc_final: 0.6801 (mttt) REVERT: A 1194 GLN cc_start: 0.8465 (mt0) cc_final: 0.8238 (mt0) REVERT: A 1199 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6729 (t0) REVERT: A 1201 VAL cc_start: 0.3426 (OUTLIER) cc_final: 0.3213 (p) REVERT: A 1243 ASP cc_start: 0.8174 (t0) cc_final: 0.7809 (m-30) REVERT: A 1244 GLU cc_start: 0.5287 (tp30) cc_final: 0.4863 (tt0) REVERT: A 1262 ASP cc_start: 0.8230 (m-30) cc_final: 0.7894 (m-30) outliers start: 39 outliers final: 21 residues processed: 128 average time/residue: 0.1966 time to fit residues: 33.6701 Evaluate side-chains 122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1051 PHE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 ASN A1155 ASN ** A1215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 7192 Z= 0.309 Angle : 0.602 6.808 9772 Z= 0.308 Chirality : 0.043 0.166 1131 Planarity : 0.004 0.049 1184 Dihedral : 8.200 101.110 1474 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.58 % Allowed : 21.34 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 862 helix: 1.77 (0.21), residues: 609 sheet: -3.07 (0.92), residues: 18 loop : -1.55 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 898 HIS 0.003 0.001 HIS A1198 PHE 0.014 0.002 PHE A 63 TYR 0.018 0.002 TYR A 754 ARG 0.002 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.6580 (mtt180) cc_final: 0.6345 (mtt-85) REVERT: A 268 ASP cc_start: 0.7443 (t0) cc_final: 0.7149 (t0) REVERT: A 322 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7474 (ttm) REVERT: A 743 ARG cc_start: 0.7320 (ptp-110) cc_final: 0.6869 (ttm110) REVERT: A 789 GLU cc_start: 0.7615 (pt0) cc_final: 0.6859 (mt-10) REVERT: A 1010 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6763 (tt0) REVERT: A 1033 ARG cc_start: 0.7473 (ttm110) cc_final: 0.7189 (mmm160) REVERT: A 1050 ARG cc_start: 0.7686 (mtp180) cc_final: 0.7393 (mtm110) REVERT: A 1051 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7568 (t80) REVERT: A 1175 LYS cc_start: 0.7669 (pttp) cc_final: 0.6879 (mttt) REVERT: A 1199 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.6838 (t0) REVERT: A 1244 GLU cc_start: 0.5437 (tp30) cc_final: 0.5084 (tt0) outliers start: 40 outliers final: 22 residues processed: 125 average time/residue: 0.2031 time to fit residues: 33.9362 Evaluate side-chains 119 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1051 PHE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN A1196 GLN A1258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7192 Z= 0.181 Angle : 0.530 7.258 9772 Z= 0.270 Chirality : 0.040 0.170 1131 Planarity : 0.004 0.049 1184 Dihedral : 7.712 89.614 1474 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.04 % Allowed : 22.32 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 862 helix: 2.07 (0.21), residues: 610 sheet: -3.11 (0.99), residues: 17 loop : -1.52 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 898 HIS 0.004 0.001 HIS A1198 PHE 0.014 0.001 PHE A 63 TYR 0.017 0.001 TYR A1041 ARG 0.002 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.802 Fit side-chains REVERT: A 169 ARG cc_start: 0.6470 (mtt180) cc_final: 0.6256 (mtt-85) REVERT: A 268 ASP cc_start: 0.7338 (t0) cc_final: 0.7067 (t0) REVERT: A 282 ASP cc_start: 0.7516 (m-30) cc_final: 0.7281 (m-30) REVERT: A 322 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7329 (ttm) REVERT: A 743 ARG cc_start: 0.7247 (ptp-110) cc_final: 0.6884 (ttm110) REVERT: A 789 GLU cc_start: 0.7620 (pt0) cc_final: 0.6865 (mt-10) REVERT: A 992 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7595 (ptm) REVERT: A 1010 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6692 (tt0) REVERT: A 1033 ARG cc_start: 0.7449 (ttm110) cc_final: 0.7167 (mmm160) REVERT: A 1050 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7365 (mtm110) REVERT: A 1051 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7484 (t80) REVERT: A 1175 LYS cc_start: 0.7606 (pttp) cc_final: 0.6864 (ptpt) REVERT: A 1199 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6797 (t0) REVERT: A 1202 MET cc_start: 0.5601 (mmm) cc_final: 0.5156 (mmt) REVERT: A 1243 ASP cc_start: 0.8140 (t0) cc_final: 0.7757 (m-30) REVERT: A 1244 GLU cc_start: 0.5356 (tp30) cc_final: 0.5025 (tt0) REVERT: A 1304 MET cc_start: 0.4082 (mmm) cc_final: 0.3170 (mtp) outliers start: 29 outliers final: 22 residues processed: 120 average time/residue: 0.2014 time to fit residues: 32.9237 Evaluate side-chains 123 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1051 PHE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1142 HIS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.0170 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 ASN A1155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7192 Z= 0.171 Angle : 0.518 7.446 9772 Z= 0.269 Chirality : 0.040 0.166 1131 Planarity : 0.004 0.048 1184 Dihedral : 7.354 83.067 1474 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.18 % Allowed : 22.04 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.29), residues: 862 helix: 2.13 (0.21), residues: 611 sheet: -3.08 (0.99), residues: 17 loop : -1.40 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 314 HIS 0.002 0.000 HIS A1198 PHE 0.015 0.001 PHE A 63 TYR 0.013 0.001 TYR A 144 ARG 0.001 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.744 Fit side-chains REVERT: A 169 ARG cc_start: 0.6541 (mtt180) cc_final: 0.6317 (mtt-85) REVERT: A 268 ASP cc_start: 0.7353 (t0) cc_final: 0.7095 (t0) REVERT: A 282 ASP cc_start: 0.7537 (m-30) cc_final: 0.7277 (m-30) REVERT: A 322 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7348 (ttm) REVERT: A 743 ARG cc_start: 0.7186 (ptp-110) cc_final: 0.6836 (ttm110) REVERT: A 789 GLU cc_start: 0.7618 (pt0) cc_final: 0.6872 (mt-10) REVERT: A 842 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7407 (mm110) REVERT: A 1010 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6716 (tt0) REVERT: A 1012 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6852 (pt) REVERT: A 1033 ARG cc_start: 0.7433 (ttm110) cc_final: 0.7160 (mmm160) REVERT: A 1050 ARG cc_start: 0.7698 (mtp180) cc_final: 0.7361 (mtm110) REVERT: A 1051 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 1175 LYS cc_start: 0.7625 (pttp) cc_final: 0.6927 (ptpt) REVERT: A 1199 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6729 (t0) REVERT: A 1202 MET cc_start: 0.5627 (mmm) cc_final: 0.5240 (mmt) REVERT: A 1243 ASP cc_start: 0.8160 (t0) cc_final: 0.7812 (m-30) REVERT: A 1244 GLU cc_start: 0.5340 (tp30) cc_final: 0.5039 (tt0) REVERT: A 1304 MET cc_start: 0.4145 (mmm) cc_final: 0.3201 (mtp) outliers start: 30 outliers final: 21 residues processed: 119 average time/residue: 0.2127 time to fit residues: 33.9089 Evaluate side-chains 117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1051 PHE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1142 HIS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 76 optimal weight: 0.0370 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7192 Z= 0.195 Angle : 0.534 8.305 9772 Z= 0.276 Chirality : 0.040 0.164 1131 Planarity : 0.004 0.048 1184 Dihedral : 7.234 85.604 1474 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.60 % Allowed : 21.90 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.29), residues: 862 helix: 2.13 (0.21), residues: 611 sheet: -3.14 (0.98), residues: 17 loop : -1.38 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 898 HIS 0.002 0.000 HIS A1198 PHE 0.014 0.001 PHE A 63 TYR 0.013 0.001 TYR A1041 ARG 0.001 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.746 Fit side-chains REVERT: A 169 ARG cc_start: 0.6483 (mtt180) cc_final: 0.6269 (mtt-85) REVERT: A 268 ASP cc_start: 0.7356 (t0) cc_final: 0.7095 (t0) REVERT: A 282 ASP cc_start: 0.7572 (m-30) cc_final: 0.7310 (m-30) REVERT: A 322 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7362 (ttm) REVERT: A 743 ARG cc_start: 0.7184 (ptp-110) cc_final: 0.6837 (ttm110) REVERT: A 789 GLU cc_start: 0.7603 (pt0) cc_final: 0.6858 (mt-10) REVERT: A 1010 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6592 (tt0) REVERT: A 1012 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7024 (pt) REVERT: A 1033 ARG cc_start: 0.7436 (ttm110) cc_final: 0.7162 (mmm160) REVERT: A 1050 ARG cc_start: 0.7681 (mtp180) cc_final: 0.7348 (mtm110) REVERT: A 1051 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7496 (t80) REVERT: A 1171 MET cc_start: 0.4499 (mmt) cc_final: 0.4093 (mmt) REVERT: A 1175 LYS cc_start: 0.7637 (pttp) cc_final: 0.6936 (ptpt) REVERT: A 1199 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6781 (t0) REVERT: A 1202 MET cc_start: 0.5612 (mmm) cc_final: 0.5270 (mmt) REVERT: A 1243 ASP cc_start: 0.8165 (t0) cc_final: 0.7813 (m-30) REVERT: A 1244 GLU cc_start: 0.5340 (tp30) cc_final: 0.5031 (tt0) REVERT: A 1262 ASP cc_start: 0.8183 (m-30) cc_final: 0.7960 (m-30) REVERT: A 1304 MET cc_start: 0.4291 (mmm) cc_final: 0.3323 (mtp) outliers start: 33 outliers final: 26 residues processed: 117 average time/residue: 0.1947 time to fit residues: 30.7159 Evaluate side-chains 122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1051 PHE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1142 HIS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 7192 Z= 0.262 Angle : 0.566 6.377 9772 Z= 0.297 Chirality : 0.042 0.161 1131 Planarity : 0.004 0.047 1184 Dihedral : 7.564 84.983 1474 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.60 % Allowed : 22.04 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 862 helix: 1.96 (0.21), residues: 611 sheet: -3.14 (0.93), residues: 18 loop : -1.44 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 898 HIS 0.003 0.001 HIS A1198 PHE 0.016 0.002 PHE A1151 TYR 0.015 0.002 TYR A1041 ARG 0.002 0.000 ARG A1265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.754 Fit side-chains REVERT: A 169 ARG cc_start: 0.6514 (mtt180) cc_final: 0.6308 (mtt-85) REVERT: A 268 ASP cc_start: 0.7410 (t0) cc_final: 0.7148 (t0) REVERT: A 282 ASP cc_start: 0.7540 (m-30) cc_final: 0.7202 (m-30) REVERT: A 322 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7381 (ttm) REVERT: A 743 ARG cc_start: 0.7228 (ptp-110) cc_final: 0.6858 (ttm110) REVERT: A 789 GLU cc_start: 0.7594 (pt0) cc_final: 0.6862 (mt-10) REVERT: A 1010 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6840 (tt0) REVERT: A 1033 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7154 (mmm160) REVERT: A 1050 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7359 (mtm110) REVERT: A 1051 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7536 (t80) REVERT: A 1171 MET cc_start: 0.4560 (mmt) cc_final: 0.4309 (mmt) REVERT: A 1175 LYS cc_start: 0.7642 (pttp) cc_final: 0.6923 (ptpt) REVERT: A 1199 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6857 (t0) REVERT: A 1202 MET cc_start: 0.5617 (mmm) cc_final: 0.5207 (mmt) REVERT: A 1243 ASP cc_start: 0.8169 (t0) cc_final: 0.7772 (m-30) REVERT: A 1244 GLU cc_start: 0.5342 (tp30) cc_final: 0.5002 (tt0) REVERT: A 1262 ASP cc_start: 0.8281 (m-30) cc_final: 0.8071 (m-30) REVERT: A 1266 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6550 (mm-30) REVERT: A 1304 MET cc_start: 0.4309 (mmm) cc_final: 0.3325 (mtp) outliers start: 33 outliers final: 27 residues processed: 115 average time/residue: 0.1979 time to fit residues: 30.9591 Evaluate side-chains 125 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1051 PHE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1142 HIS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 8.9990 chunk 79 optimal weight: 0.0370 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 7192 Z= 0.212 Angle : 0.540 8.264 9772 Z= 0.282 Chirality : 0.041 0.161 1131 Planarity : 0.004 0.047 1184 Dihedral : 7.406 86.793 1474 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.18 % Allowed : 22.45 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.29), residues: 862 helix: 2.03 (0.21), residues: 612 sheet: -3.21 (0.92), residues: 18 loop : -1.44 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1071 HIS 0.003 0.001 HIS A1198 PHE 0.015 0.001 PHE A 63 TYR 0.011 0.001 TYR A 754 ARG 0.002 0.000 ARG A 832 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.759 Fit side-chains REVERT: A 268 ASP cc_start: 0.7381 (t0) cc_final: 0.7118 (t0) REVERT: A 282 ASP cc_start: 0.7538 (m-30) cc_final: 0.7160 (m-30) REVERT: A 322 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7342 (ttm) REVERT: A 743 ARG cc_start: 0.7225 (ptp-110) cc_final: 0.6871 (ttm110) REVERT: A 789 GLU cc_start: 0.7574 (pt0) cc_final: 0.6870 (mt-10) REVERT: A 1010 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6611 (tt0) REVERT: A 1012 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7062 (pt) REVERT: A 1033 ARG cc_start: 0.7441 (ttm110) cc_final: 0.7156 (mmm160) REVERT: A 1050 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7347 (mtm110) REVERT: A 1051 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7579 (t80) REVERT: A 1171 MET cc_start: 0.4444 (mmt) cc_final: 0.4218 (mmt) REVERT: A 1175 LYS cc_start: 0.7653 (pttp) cc_final: 0.6929 (ptpt) REVERT: A 1199 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6808 (t0) REVERT: A 1202 MET cc_start: 0.5699 (mmm) cc_final: 0.5277 (mmt) REVERT: A 1243 ASP cc_start: 0.8161 (t0) cc_final: 0.7789 (m-30) REVERT: A 1244 GLU cc_start: 0.5323 (tp30) cc_final: 0.5018 (tt0) REVERT: A 1262 ASP cc_start: 0.8302 (m-30) cc_final: 0.8083 (m-30) REVERT: A 1266 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6478 (mm-30) REVERT: A 1304 MET cc_start: 0.4404 (mmm) cc_final: 0.3385 (mtp) outliers start: 30 outliers final: 26 residues processed: 115 average time/residue: 0.2085 time to fit residues: 32.2830 Evaluate side-chains 124 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1051 PHE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1142 HIS Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1180 THR Chi-restraints excluded: chain A residue 1199 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.200243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158066 restraints weight = 8739.460| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.05 r_work: 0.3691 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7192 Z= 0.200 Angle : 0.541 8.427 9772 Z= 0.282 Chirality : 0.041 0.162 1131 Planarity : 0.004 0.048 1184 Dihedral : 7.307 88.532 1474 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.46 % Allowed : 22.32 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.29), residues: 862 helix: 2.09 (0.21), residues: 612 sheet: -3.30 (0.91), residues: 18 loop : -1.43 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 898 HIS 0.002 0.000 HIS A1198 PHE 0.016 0.001 PHE A1151 TYR 0.019 0.001 TYR A 144 ARG 0.008 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1785.92 seconds wall clock time: 33 minutes 30.37 seconds (2010.37 seconds total)