Starting phenix.real_space_refine on Sat Apr 6 04:36:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm6_17758/04_2024/8pm6_17758_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm6_17758/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm6_17758/04_2024/8pm6_17758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm6_17758/04_2024/8pm6_17758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm6_17758/04_2024/8pm6_17758_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm6_17758/04_2024/8pm6_17758_updated.pdb" } 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 Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A GLU 956": "OE1" <-> "OE2" Residue "A GLU 1206": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.10, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 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... running ksdssp... Secondary structure from input PDB file: 28 helices and 2 sheets defined 68.3% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 56 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 134 through 182 Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 216 through 237 Processing helix chain 'A' and resid 241 through 286 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) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 297 through 349 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 356 through 393 removed outlier: 4.165A pdb=" N SER A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 742 through 765 removed outlier: 3.889A pdb=" N LYS A 746 " --> pdb=" O ARG A 742 " (cutoff:3.500A) Proline residue: A 750 - end of helix Proline residue: A 753 - end of helix Processing helix chain 'A' and resid 767 through 784 removed outlier: 3.686A pdb=" N PHE A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 784 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 841 Processing helix chain 'A' and resid 844 through 847 Processing helix chain 'A' and resid 854 through 894 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 898 through 916 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 918 through 922 Processing helix chain 'A' and resid 959 through 962 No H-bonds generated for 'chain 'A' and resid 959 through 962' Processing helix chain 'A' and resid 965 through 1009 removed outlier: 3.807A pdb=" N GLU A 968 " --> pdb=" O THR A 965 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 969 " --> pdb=" O GLU A 966 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.845A pdb=" N ILE A 991 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET A 992 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 999 " --> pdb=" O ASN A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1035 Processing helix chain 'A' and resid 1038 through 1055 removed outlier: 4.400A pdb=" N LYS A1043 " --> pdb=" O PRO A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1127 Processing helix chain 'A' and resid 1144 through 1146 No H-bonds generated for 'chain 'A' and resid 1144 through 1146' Processing helix chain 'A' and resid 1149 through 1155 Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1198 through 1203 Processing helix chain 'A' and resid 1221 through 1234 removed outlier: 4.363A pdb=" N ARG A1226 " --> pdb=" O GLY A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1265 removed outlier: 3.686A pdb=" N THR A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1305 No H-bonds generated for 'chain 'A' and resid 1302 through 1305' Processing helix chain 'A' and resid 1310 through 1313 No H-bonds generated for 'chain 'A' and resid 1310 through 1313' Processing sheet with id= A, first strand: chain 'A' and resid 1108 through 1110 removed outlier: 6.231A pdb=" N CYS A1270 " --> pdb=" O LEU A1109 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 6.510A pdb=" N ILE A1239 " --> pdb=" O GLY A1157 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A1159 " --> pdb=" O ILE A1239 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A1241 " --> pdb=" O VAL A1159 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 435 hydrogen bonds defined for protein. 1200 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: 2.20 Time building geometry restraints manager: 3.21 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: 97.96 - 105.26: 135 105.26 - 112.55: 3744 112.55 - 119.84: 2562 119.84 - 127.13: 3283 127.13 - 134.42: 48 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: 661 2.74 - 3.28: 7469 3.28 - 3.82: 11762 3.82 - 4.36: 13381 4.36 - 4.90: 23094 Nonbonded interactions: 56367 Sorted by model distance: nonbonded pdb=" OD1 ASP A 88 " pdb=" OG1 THR A 355 " model vdw 2.200 2.440 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 2.440 nonbonded pdb=" O PHE A1018 " pdb=" OG SER A1022 " model vdw 2.272 2.440 nonbonded pdb=" O SER A 897 " pdb=" OG SER A 901 " model vdw 2.272 2.440 ... (remaining 56362 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.190 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.370 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- 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= 0.312 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 fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 0.699 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: 0.2069 time to fit residues: 38.1403 Evaluate side-chains 103 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 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 170 GLN A 210 ASN A 375 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 GLN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN ** A1161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1198 HIS A1218 GLN A1258 GLN ** A1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7192 Z= 0.192 Angle : 0.569 10.029 9772 Z= 0.289 Chirality : 0.041 0.184 1131 Planarity : 0.005 0.049 1184 Dihedral : 8.352 108.902 1477 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.32 % Allowed : 21.90 % 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: 1.13 (0.29), residues: 862 helix: 1.77 (0.21), residues: 603 sheet: -2.98 (0.98), residues: 17 loop : -1.62 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1071 HIS 0.002 0.000 HIS A1198 PHE 0.012 0.001 PHE A 310 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 139 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7289 (t0) cc_final: 0.7014 (t0) REVERT: A 322 MET cc_start: 0.7637 (ttm) cc_final: 0.7414 (ttm) REVERT: A 743 ARG cc_start: 0.7223 (ptp-110) cc_final: 0.6790 (ttm110) REVERT: A 744 ILE cc_start: 0.7276 (mm) cc_final: 0.6979 (mt) REVERT: A 789 GLU cc_start: 0.7500 (pt0) cc_final: 0.6812 (mt-10) REVERT: A 875 GLN cc_start: 0.8025 (tp40) cc_final: 0.7466 (tp40) REVERT: A 891 ILE cc_start: 0.8577 (mm) cc_final: 0.8373 (mt) REVERT: A 1010 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6593 (tt0) REVERT: A 1033 ARG cc_start: 0.7378 (ttm110) cc_final: 0.7023 (mmm160) REVERT: A 1050 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7470 (mtp85) REVERT: A 1171 MET cc_start: 0.4727 (mmt) cc_final: 0.4447 (mmt) REVERT: A 1175 LYS cc_start: 0.7622 (pttp) cc_final: 0.6887 (ptpt) REVERT: A 1194 GLN cc_start: 0.8436 (mt0) cc_final: 0.8165 (mt0) REVERT: A 1258 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: A 1262 ASP cc_start: 0.8153 (m-30) cc_final: 0.7544 (m-30) outliers start: 31 outliers final: 18 residues processed: 128 average time/residue: 0.2001 time to fit residues: 34.8441 Evaluate side-chains 115 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 215 ASP 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 286 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 999 SER 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: 1.9990 chunk 65 optimal weight: 9.9990 chunk 53 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 0.0270 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 375 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN A1281 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7192 Z= 0.173 Angle : 0.528 6.813 9772 Z= 0.272 Chirality : 0.040 0.153 1131 Planarity : 0.004 0.049 1184 Dihedral : 7.668 93.785 1474 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.63 % Allowed : 23.29 % 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: 1.79 (0.21), residues: 604 sheet: -3.06 (0.99), residues: 17 loop : -1.54 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 314 HIS 0.003 0.001 HIS A1198 PHE 0.024 0.001 PHE A 63 TYR 0.017 0.001 TYR A 754 ARG 0.002 0.000 ARG A1033 *********************** 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 130 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7296 (t0) cc_final: 0.7016 (t0) REVERT: A 282 ASP cc_start: 0.7720 (m-30) cc_final: 0.7488 (m-30) REVERT: A 322 MET cc_start: 0.7629 (ttm) cc_final: 0.7397 (ttm) REVERT: A 743 ARG cc_start: 0.7223 (ptp-110) cc_final: 0.6774 (ttm110) REVERT: A 744 ILE cc_start: 0.7274 (mm) cc_final: 0.7002 (mt) REVERT: A 789 GLU cc_start: 0.7500 (pt0) cc_final: 0.6805 (mt-10) REVERT: A 1010 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6701 (tt0) REVERT: A 1033 ARG cc_start: 0.7380 (ttm110) cc_final: 0.7055 (mmm160) REVERT: A 1041 TYR cc_start: 0.7344 (t80) cc_final: 0.7141 (t80) REVERT: A 1050 ARG cc_start: 0.7692 (mtp180) cc_final: 0.7366 (mtm110) REVERT: A 1051 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 1175 LYS cc_start: 0.7612 (pttp) cc_final: 0.6905 (ptpt) REVERT: A 1194 GLN cc_start: 0.8402 (mt0) cc_final: 0.8148 (mt0) REVERT: A 1243 ASP cc_start: 0.8172 (t0) cc_final: 0.7928 (m-30) REVERT: A 1244 GLU cc_start: 0.5113 (tp30) cc_final: 0.4736 (tt0) REVERT: A 1262 ASP cc_start: 0.8230 (m-30) cc_final: 0.7946 (m-30) outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 0.2017 time to fit residues: 33.5043 Evaluate side-chains 116 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP 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 286 SER Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 1051 PHE 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: 4.9990 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7192 Z= 0.257 Angle : 0.573 6.022 9772 Z= 0.294 Chirality : 0.041 0.167 1131 Planarity : 0.004 0.049 1184 Dihedral : 7.815 87.179 1474 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.44 % Allowed : 22.04 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 862 helix: 1.58 (0.21), residues: 604 sheet: -3.13 (0.93), residues: 18 loop : -1.70 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 898 HIS 0.006 0.001 HIS A1198 PHE 0.014 0.002 PHE A 63 TYR 0.021 0.002 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 138 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 99 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7359 (t0) cc_final: 0.7060 (t0) REVERT: A 282 ASP cc_start: 0.7628 (m-30) cc_final: 0.7328 (m-30) REVERT: A 743 ARG cc_start: 0.7228 (ptp-110) cc_final: 0.6837 (ttm110) REVERT: A 789 GLU cc_start: 0.7558 (pt0) cc_final: 0.6756 (mt-10) REVERT: A 1010 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6554 (tt0) REVERT: A 1033 ARG cc_start: 0.7402 (ttm110) cc_final: 0.7079 (mmm160) REVERT: A 1041 TYR cc_start: 0.7396 (t80) cc_final: 0.7169 (t80) REVERT: A 1050 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7390 (mtm110) REVERT: A 1051 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7577 (t80) REVERT: A 1175 LYS cc_start: 0.7659 (pttp) cc_final: 0.6879 (mttt) REVERT: A 1194 GLN cc_start: 0.8500 (mt0) cc_final: 0.8279 (mt0) REVERT: A 1243 ASP cc_start: 0.8201 (t0) cc_final: 0.7888 (m-30) REVERT: A 1262 ASP cc_start: 0.8267 (m-30) cc_final: 0.8006 (m-30) outliers start: 39 outliers final: 22 residues processed: 126 average time/residue: 0.2078 time to fit residues: 34.9326 Evaluate side-chains 115 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 215 ASP 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 286 SER 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 392 SER Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1051 PHE 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 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: 1.9990 chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7249 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7192 Z= 0.195 Angle : 0.531 6.683 9772 Z= 0.274 Chirality : 0.040 0.164 1131 Planarity : 0.004 0.049 1184 Dihedral : 7.615 82.728 1474 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.18 % Allowed : 23.01 % Favored : 72.80 % 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: 1.08 (0.29), residues: 862 helix: 1.67 (0.21), residues: 603 sheet: -3.12 (1.03), residues: 17 loop : -1.46 (0.41), residues: 242 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 0.015 0.001 TYR A 754 ARG 0.003 0.000 ARG A1057 *********************** 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 126 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 268 ASP cc_start: 0.7347 (t0) cc_final: 0.7059 (t0) REVERT: A 282 ASP cc_start: 0.7643 (m-30) cc_final: 0.7307 (m-30) REVERT: A 743 ARG cc_start: 0.7229 (ptp-110) cc_final: 0.6836 (ttm110) REVERT: A 789 GLU cc_start: 0.7567 (pt0) cc_final: 0.6759 (mt-10) REVERT: A 875 GLN cc_start: 0.7890 (tp40) cc_final: 0.7610 (tp-100) REVERT: A 1010 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6568 (tt0) REVERT: A 1033 ARG cc_start: 0.7392 (ttm110) cc_final: 0.7070 (mmm160) REVERT: A 1041 TYR cc_start: 0.7365 (t80) cc_final: 0.7071 (t80) REVERT: A 1050 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7343 (mtm110) REVERT: A 1051 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7525 (t80) REVERT: A 1175 LYS cc_start: 0.7646 (pttp) cc_final: 0.6944 (ptpt) REVERT: A 1194 GLN cc_start: 0.8512 (mt0) cc_final: 0.8279 (mt0) REVERT: A 1243 ASP cc_start: 0.8117 (t0) cc_final: 0.7829 (m-30) REVERT: A 1244 GLU cc_start: 0.5216 (tp30) cc_final: 0.4939 (tt0) REVERT: A 1262 ASP cc_start: 0.8185 (m-30) cc_final: 0.7857 (m-30) outliers start: 30 outliers final: 19 residues processed: 116 average time/residue: 0.2170 time to fit residues: 33.4399 Evaluate side-chains 112 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 286 SER 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 999 SER 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 1142 HIS 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 1272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 0.0370 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.0050 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7205 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7192 Z= 0.151 Angle : 0.497 7.024 9772 Z= 0.258 Chirality : 0.039 0.163 1131 Planarity : 0.004 0.047 1184 Dihedral : 7.229 84.252 1474 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.49 % Allowed : 23.71 % Favored : 72.80 % 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: 1.29 (0.30), residues: 862 helix: 1.85 (0.21), residues: 598 sheet: -3.26 (1.03), residues: 17 loop : -1.35 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 314 HIS 0.004 0.001 HIS A1198 PHE 0.013 0.001 PHE A1151 TYR 0.011 0.001 TYR A 754 ARG 0.003 0.000 ARG A1057 *********************** 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 122 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.696 Fit side-chains REVERT: A 169 ARG cc_start: 0.6523 (mtt180) cc_final: 0.6310 (mtt-85) REVERT: A 268 ASP cc_start: 0.7325 (t0) cc_final: 0.7063 (t0) REVERT: A 282 ASP cc_start: 0.7588 (m-30) cc_final: 0.7262 (m-30) REVERT: A 743 ARG cc_start: 0.7190 (ptp-110) cc_final: 0.6833 (ttm110) REVERT: A 789 GLU cc_start: 0.7550 (pt0) cc_final: 0.6778 (mt-10) REVERT: A 875 GLN cc_start: 0.7887 (tp40) cc_final: 0.7618 (tp-100) REVERT: A 1010 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6559 (tt0) REVERT: A 1033 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6975 (mmm160) REVERT: A 1041 TYR cc_start: 0.7341 (t80) cc_final: 0.7079 (t80) REVERT: A 1050 ARG cc_start: 0.7613 (mtp180) cc_final: 0.7315 (mtm110) REVERT: A 1051 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7472 (t80) REVERT: A 1175 LYS cc_start: 0.7639 (pttp) cc_final: 0.6918 (ptpt) REVERT: A 1202 MET cc_start: 0.5077 (mmt) cc_final: 0.4862 (mmm) REVERT: A 1243 ASP cc_start: 0.8129 (t0) cc_final: 0.7854 (m-30) REVERT: A 1244 GLU cc_start: 0.5252 (tp30) cc_final: 0.4952 (tt0) REVERT: A 1262 ASP cc_start: 0.8144 (m-30) cc_final: 0.7828 (m-30) REVERT: A 1263 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8562 (mmtt) outliers start: 25 outliers final: 14 residues processed: 116 average time/residue: 0.2109 time to fit residues: 32.4567 Evaluate side-chains 108 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 999 SER 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 1142 HIS 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 1272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7192 Z= 0.182 Angle : 0.514 7.465 9772 Z= 0.267 Chirality : 0.040 0.159 1131 Planarity : 0.004 0.047 1184 Dihedral : 7.208 85.417 1474 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.18 % Allowed : 22.59 % 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: 1.27 (0.29), residues: 862 helix: 1.83 (0.21), residues: 598 sheet: -3.25 (1.03), residues: 17 loop : -1.35 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 898 HIS 0.003 0.001 HIS A1198 PHE 0.014 0.001 PHE A1151 TYR 0.012 0.001 TYR A 144 ARG 0.002 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 124 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 0.817 Fit side-chains REVERT: A 169 ARG cc_start: 0.6479 (mtt180) cc_final: 0.5761 (mtp85) REVERT: A 268 ASP cc_start: 0.7334 (t0) cc_final: 0.7060 (t0) REVERT: A 282 ASP cc_start: 0.7601 (m-30) cc_final: 0.7278 (m-30) REVERT: A 743 ARG cc_start: 0.7209 (ptp-110) cc_final: 0.6850 (ttm110) REVERT: A 789 GLU cc_start: 0.7580 (pt0) cc_final: 0.6840 (mt-10) REVERT: A 875 GLN cc_start: 0.7916 (tp40) cc_final: 0.7629 (tp-100) REVERT: A 1010 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6584 (tt0) REVERT: A 1033 ARG cc_start: 0.7303 (ttm110) cc_final: 0.6989 (mmm160) REVERT: A 1050 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7303 (mtm110) REVERT: A 1051 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7537 (t80) REVERT: A 1171 MET cc_start: 0.4450 (mmt) cc_final: 0.4009 (mmt) REVERT: A 1175 LYS cc_start: 0.7669 (pttp) cc_final: 0.6992 (ptpt) REVERT: A 1202 MET cc_start: 0.5092 (mmt) cc_final: 0.4874 (mmm) REVERT: A 1243 ASP cc_start: 0.8145 (t0) cc_final: 0.7875 (m-30) REVERT: A 1244 GLU cc_start: 0.5276 (tp30) cc_final: 0.4963 (tt0) REVERT: A 1262 ASP cc_start: 0.8163 (m-30) cc_final: 0.7853 (m-30) REVERT: A 1263 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8519 (mtmt) REVERT: A 1266 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 1304 MET cc_start: 0.4385 (mmm) cc_final: 0.3353 (mtp) outliers start: 30 outliers final: 24 residues processed: 117 average time/residue: 0.1965 time to fit residues: 31.0731 Evaluate side-chains 116 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 286 SER 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 973 THR Chi-restraints excluded: chain A residue 999 SER 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 1142 HIS 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 1272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.7215 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7192 Z= 0.173 Angle : 0.509 8.156 9772 Z= 0.265 Chirality : 0.039 0.158 1131 Planarity : 0.004 0.047 1184 Dihedral : 7.154 87.293 1474 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.77 % Allowed : 23.15 % 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: 1.33 (0.29), residues: 862 helix: 1.87 (0.21), residues: 598 sheet: -3.24 (1.01), residues: 17 loop : -1.31 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 898 HIS 0.003 0.001 HIS A1198 PHE 0.014 0.001 PHE A1151 TYR 0.017 0.001 TYR A1041 ARG 0.003 0.000 ARG A1057 *********************** 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 120 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 169 ARG cc_start: 0.6458 (mtt180) cc_final: 0.5693 (mtp85) REVERT: A 268 ASP cc_start: 0.7329 (t0) cc_final: 0.7064 (t0) REVERT: A 282 ASP cc_start: 0.7613 (m-30) cc_final: 0.7294 (m-30) REVERT: A 743 ARG cc_start: 0.7189 (ptp-110) cc_final: 0.6849 (ttm110) REVERT: A 789 GLU cc_start: 0.7588 (pt0) cc_final: 0.6818 (mt-10) REVERT: A 1010 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6530 (tt0) REVERT: A 1033 ARG cc_start: 0.7313 (ttm110) cc_final: 0.7006 (mmm160) REVERT: A 1041 TYR cc_start: 0.7127 (t80) cc_final: 0.6871 (t80) REVERT: A 1050 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7277 (mtm110) REVERT: A 1051 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7508 (t80) REVERT: A 1171 MET cc_start: 0.4516 (mmt) cc_final: 0.4230 (mmt) REVERT: A 1175 LYS cc_start: 0.7633 (pttp) cc_final: 0.6928 (ptpt) REVERT: A 1202 MET cc_start: 0.4987 (mmt) cc_final: 0.4764 (mmm) REVERT: A 1243 ASP cc_start: 0.8138 (t0) cc_final: 0.7871 (m-30) REVERT: A 1244 GLU cc_start: 0.5249 (tp30) cc_final: 0.4918 (tt0) REVERT: A 1262 ASP cc_start: 0.8145 (m-30) cc_final: 0.7840 (m-30) REVERT: A 1304 MET cc_start: 0.4454 (mmm) cc_final: 0.3388 (mtp) outliers start: 27 outliers final: 25 residues processed: 113 average time/residue: 0.2033 time to fit residues: 30.9643 Evaluate side-chains 116 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 215 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 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 973 THR Chi-restraints excluded: chain A residue 999 SER 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 1142 HIS 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 1272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 7192 Z= 0.262 Angle : 0.562 8.212 9772 Z= 0.295 Chirality : 0.042 0.175 1131 Planarity : 0.004 0.046 1184 Dihedral : 7.750 86.150 1474 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.46 % Allowed : 23.29 % Favored : 72.25 % 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: 1.04 (0.29), residues: 862 helix: 1.66 (0.21), residues: 599 sheet: -3.16 (0.97), residues: 18 loop : -1.46 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 898 HIS 0.004 0.001 HIS A1198 PHE 0.015 0.001 PHE A1151 TYR 0.016 0.002 TYR A1041 ARG 0.003 0.000 ARG A1001 *********************** 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 121 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 0.777 Fit side-chains REVERT: A 145 TYR cc_start: 0.8259 (m-80) cc_final: 0.8003 (m-80) REVERT: A 169 ARG cc_start: 0.6482 (mtt180) cc_final: 0.5717 (mtp85) REVERT: A 268 ASP cc_start: 0.7386 (t0) cc_final: 0.7110 (t0) REVERT: A 282 ASP cc_start: 0.7582 (m-30) cc_final: 0.7216 (m-30) REVERT: A 743 ARG cc_start: 0.7221 (ptp-110) cc_final: 0.6882 (ttm110) REVERT: A 789 GLU cc_start: 0.7637 (pt0) cc_final: 0.6832 (mt-10) REVERT: A 1010 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6667 (tt0) REVERT: A 1033 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6987 (mmm160) REVERT: A 1050 ARG cc_start: 0.7510 (mtp180) cc_final: 0.7268 (mtm110) REVERT: A 1051 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 1084 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7174 (mtpp) REVERT: A 1134 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6387 (tm-30) REVERT: A 1171 MET cc_start: 0.4896 (mmt) cc_final: 0.4610 (mmt) REVERT: A 1175 LYS cc_start: 0.7663 (pttp) cc_final: 0.6960 (ptpt) REVERT: A 1202 MET cc_start: 0.5059 (mmt) cc_final: 0.4843 (mmm) REVERT: A 1243 ASP cc_start: 0.8154 (t0) cc_final: 0.7815 (m-30) REVERT: A 1244 GLU cc_start: 0.5308 (tp30) cc_final: 0.4979 (tt0) REVERT: A 1262 ASP cc_start: 0.8168 (m-30) cc_final: 0.7839 (m-30) REVERT: A 1263 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8476 (mtmt) REVERT: A 1304 MET cc_start: 0.4363 (mmm) cc_final: 0.3353 (mtp) outliers start: 32 outliers final: 27 residues processed: 113 average time/residue: 0.2125 time to fit residues: 31.9274 Evaluate side-chains 119 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 215 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 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 967 LEU Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 999 SER 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 1084 LYS Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1104 SER 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 1263 LYS 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: 10.0000 chunk 79 optimal weight: 0.0270 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7231 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7192 Z= 0.180 Angle : 0.521 7.853 9772 Z= 0.273 Chirality : 0.040 0.156 1131 Planarity : 0.004 0.047 1184 Dihedral : 7.634 89.544 1474 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.77 % Allowed : 23.99 % Favored : 72.25 % 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: 1.17 (0.29), residues: 862 helix: 1.73 (0.21), residues: 603 sheet: -3.23 (0.97), residues: 18 loop : -1.37 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 898 HIS 0.004 0.001 HIS A1198 PHE 0.013 0.001 PHE A1151 TYR 0.012 0.001 TYR A 754 ARG 0.003 0.000 ARG A1057 ********************** 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 122 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.772 Fit side-chains REVERT: A 145 TYR cc_start: 0.8175 (m-80) cc_final: 0.7933 (m-80) REVERT: A 169 ARG cc_start: 0.6411 (mtt180) cc_final: 0.5705 (mtp85) REVERT: A 268 ASP cc_start: 0.7331 (t0) cc_final: 0.7064 (t0) REVERT: A 282 ASP cc_start: 0.7553 (m-30) cc_final: 0.7206 (m-30) REVERT: A 743 ARG cc_start: 0.7209 (ptp-110) cc_final: 0.6888 (ttm110) REVERT: A 789 GLU cc_start: 0.7594 (pt0) cc_final: 0.6813 (mt-10) REVERT: A 1010 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6604 (tt0) REVERT: A 1033 ARG cc_start: 0.7306 (ttm110) cc_final: 0.6979 (mmm160) REVERT: A 1041 TYR cc_start: 0.7378 (t80) cc_final: 0.7137 (t80) REVERT: A 1050 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7285 (mtm110) REVERT: A 1051 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7473 (t80) REVERT: A 1134 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6486 (tm-30) REVERT: A 1175 LYS cc_start: 0.7685 (pttp) cc_final: 0.6975 (ptpt) REVERT: A 1202 MET cc_start: 0.5026 (mmt) cc_final: 0.4793 (mmm) REVERT: A 1243 ASP cc_start: 0.8122 (t0) cc_final: 0.7826 (m-30) REVERT: A 1244 GLU cc_start: 0.5250 (tp30) cc_final: 0.4954 (tt0) REVERT: A 1262 ASP cc_start: 0.8136 (m-30) cc_final: 0.7804 (m-30) REVERT: A 1304 MET cc_start: 0.4375 (mmm) cc_final: 0.3391 (mtp) outliers start: 27 outliers final: 24 residues processed: 114 average time/residue: 0.2161 time to fit residues: 32.4733 Evaluate side-chains 116 residues out of total 719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 215 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 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 973 THR Chi-restraints excluded: chain A residue 999 SER 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 1104 SER 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 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: 2.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.198826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157091 restraints weight = 8749.820| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.94 r_work: 0.3703 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7192 Z= 0.193 Angle : 0.530 9.344 9772 Z= 0.278 Chirality : 0.040 0.164 1131 Planarity : 0.004 0.047 1184 Dihedral : 7.635 87.353 1474 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.91 % Allowed : 23.71 % Favored : 72.38 % 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: 1.15 (0.29), residues: 862 helix: 1.74 (0.21), residues: 603 sheet: -3.13 (0.77), residues: 28 loop : -1.36 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 898 HIS 0.004 0.001 HIS A1198 PHE 0.016 0.001 PHE A1151 TYR 0.012 0.001 TYR A 754 ARG 0.002 0.000 ARG A1057 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.38 seconds wall clock time: 36 minutes 49.38 seconds (2209.38 seconds total)