Starting phenix.real_space_refine on Wed Apr 30 00:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9juk_61828/04_2025/9juk_61828.cif Found real_map, /net/cci-nas-00/data/ceres_data/9juk_61828/04_2025/9juk_61828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9juk_61828/04_2025/9juk_61828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9juk_61828/04_2025/9juk_61828.map" model { file = "/net/cci-nas-00/data/ceres_data/9juk_61828/04_2025/9juk_61828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9juk_61828/04_2025/9juk_61828.cif" } resolution = 3.3 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= 0.005 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 5756 2.51 5 N 1555 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9035 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 8971 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 30, 'TRANS': 1134} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ANP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.98, per 1000 atoms: 0.66 Number of scatterers: 9035 At special positions: 0 Unit cell: (102.3, 101.37, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 6 15.00 Mg 2 11.99 O 1675 8.00 N 1555 7.00 C 5756 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: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 67.4% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 37 through 75 removed outlier: 4.120A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.780A pdb=" N ASN A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 133 Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.774A pdb=" N PHE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.671A pdb=" N ALA A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 187 through 236 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 236 through 243 removed outlier: 3.514A pdb=" N ALA A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 299 Processing helix chain 'A' and resid 303 through 323 Processing helix chain 'A' and resid 324 through 347 removed outlier: 3.747A pdb=" N HIS A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.956A pdb=" N ASN A 354 " --> pdb=" O ILE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 440 through 446 removed outlier: 3.931A pdb=" N GLN A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.757A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.505A pdb=" N LYS A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 3.874A pdb=" N LYS A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 693 removed outlier: 4.225A pdb=" N GLN A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 729 removed outlier: 3.507A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 786 Processing helix chain 'A' and resid 788 through 794 removed outlier: 3.508A pdb=" N PHE A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 798 through 818 Processing helix chain 'A' and resid 818 through 842 Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 852 through 869 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 878 through 891 Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 900 through 954 Proline residue: A 914 - end of helix Processing helix chain 'A' and resid 958 through 1001 Proline residue: A 984 - end of helix Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1067 through 1073 Processing helix chain 'A' and resid 1094 through 1100 Processing helix chain 'A' and resid 1115 through 1122 Processing helix chain 'A' and resid 1129 through 1139 Processing helix chain 'A' and resid 1142 through 1148 removed outlier: 3.992A pdb=" N LEU A1148 " --> pdb=" O PHE A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1180 removed outlier: 3.537A pdb=" N LYS A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1212 removed outlier: 3.954A pdb=" N ARG A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 4.297A pdb=" N GLY A1254 " --> pdb=" O ASN A1250 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A1255 " --> pdb=" O HIS A1251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1250 through 1255' Processing helix chain 'A' and resid 1255 through 1264 removed outlier: 4.102A pdb=" N MET A1259 " --> pdb=" O ILE A1255 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 400 removed outlier: 6.213A pdb=" N ILE A 399 " --> pdb=" O THR A 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 578 Processing sheet with id=AA4, first strand: chain 'A' and resid 1045 through 1049 removed outlier: 3.530A pdb=" N LEU A1045 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A1047 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS A1027 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA A1049 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU A1025 " --> pdb=" O ALA A1049 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1054 through 1055 removed outlier: 6.354A pdb=" N MET A1184 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A1103 " --> pdb=" O LEU A1185 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1764 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: 3.36 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2952 1.34 - 1.46: 1974 1.46 - 1.58: 4199 1.58 - 1.70: 10 1.70 - 1.82: 68 Bond restraints: 9203 Sorted by residual: bond pdb=" N3B ANP A1304 " pdb=" PG ANP A1304 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" N3B ANP A1303 " pdb=" PG ANP A1303 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O3A ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" N VAL A 813 " pdb=" CA VAL A 813 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.23e+00 ... (remaining 9198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12216 1.90 - 3.80: 196 3.80 - 5.71: 42 5.71 - 7.61: 13 7.61 - 9.51: 3 Bond angle restraints: 12470 Sorted by residual: angle pdb=" CA PRO A1034 " pdb=" N PRO A1034 " pdb=" CD PRO A1034 " ideal model delta sigma weight residual 112.00 106.64 5.36 1.40e+00 5.10e-01 1.46e+01 angle pdb=" N GLU A 478 " pdb=" CA GLU A 478 " pdb=" CB GLU A 478 " ideal model delta sigma weight residual 110.40 115.98 -5.58 1.63e+00 3.76e-01 1.17e+01 angle pdb=" C GLU A 477 " pdb=" N GLU A 478 " pdb=" CA GLU A 478 " ideal model delta sigma weight residual 121.14 115.22 5.92 1.75e+00 3.27e-01 1.15e+01 angle pdb=" N3B ANP A1304 " pdb=" PG ANP A1304 " pdb=" O2G ANP A1304 " ideal model delta sigma weight residual 101.05 110.56 -9.51 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N3B ANP A1303 " pdb=" PG ANP A1303 " pdb=" O2G ANP A1303 " ideal model delta sigma weight residual 101.05 110.25 -9.20 3.00e+00 1.11e-01 9.41e+00 ... (remaining 12465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.16: 5219 27.16 - 54.33: 237 54.33 - 81.49: 59 81.49 - 108.65: 10 108.65 - 135.81: 2 Dihedral angle restraints: 5527 sinusoidal: 2173 harmonic: 3354 Sorted by residual: dihedral pdb=" O1A ANP A1303 " pdb=" O3A ANP A1303 " pdb=" PA ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sinusoidal sigma weight residual 83.11 -52.70 135.81 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" O1A ANP A1304 " pdb=" O3A ANP A1304 " pdb=" PA ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sinusoidal sigma weight residual 83.11 -28.61 111.72 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" O1B ANP A1304 " pdb=" N3B ANP A1304 " pdb=" PB ANP A1304 " pdb=" PG ANP A1304 " ideal model delta sinusoidal sigma weight residual 35.15 -64.66 99.81 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1319 0.070 - 0.139: 108 0.139 - 0.208: 7 0.208 - 0.278: 0 0.278 - 0.347: 2 Chirality restraints: 1436 Sorted by residual: chirality pdb=" C3' ANP A1304 " pdb=" C2' ANP A1304 " pdb=" C4' ANP A1304 " pdb=" O3' ANP A1304 " both_signs ideal model delta sigma weight residual False -2.36 -2.70 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C3' ANP A1303 " pdb=" C2' ANP A1303 " pdb=" C4' ANP A1303 " pdb=" O3' ANP A1303 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB VAL A 500 " pdb=" CA VAL A 500 " pdb=" CG1 VAL A 500 " pdb=" CG2 VAL A 500 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 1433 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1033 " 0.083 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO A1034 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO A1034 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1034 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 393 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO A 394 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 721 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C LEU A 721 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 721 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 722 " 0.010 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 88 2.61 - 3.18: 8501 3.18 - 3.75: 15156 3.75 - 4.33: 19888 4.33 - 4.90: 32706 Nonbonded interactions: 76339 Sorted by model distance: nonbonded pdb=" OG SER A 410 " pdb="MG MG A1301 " model vdw 2.036 2.170 nonbonded pdb=" OD2 ASP A 531 " pdb="MG MG A1301 " model vdw 2.124 2.170 nonbonded pdb=" OE1 GLN A1107 " pdb="MG MG A1302 " model vdw 2.206 2.170 nonbonded pdb=" OG1 THR A1013 " pdb=" OD1 ASN A1094 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN A 758 " pdb=" NE2 GLN A 761 " model vdw 2.240 3.120 ... (remaining 76334 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: 1.050 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.700 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 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 : 0.004 0.164 9203 Z= 0.226 Angle : 0.642 9.511 12470 Z= 0.336 Chirality : 0.042 0.347 1436 Planarity : 0.005 0.123 1574 Dihedral : 16.731 135.814 3369 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.11 % Allowed : 0.42 % Favored : 99.47 % 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: 0.83 (0.25), residues: 1161 helix: 1.80 (0.19), residues: 747 sheet: -1.60 (1.19), residues: 27 loop : -1.89 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 791 HIS 0.004 0.001 HIS A 762 PHE 0.024 0.001 PHE A 552 TYR 0.025 0.002 TYR A 908 ARG 0.003 0.000 ARG A 481 Details of bonding type rmsd hydrogen bonds : bond 0.10898 ( 596) hydrogen bonds : angle 4.83914 ( 1764) covalent geometry : bond 0.00441 ( 9203) covalent geometry : angle 0.64233 (12470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7705 (tp30) cc_final: 0.7265 (tp30) REVERT: A 286 TYR cc_start: 0.6787 (m-10) cc_final: 0.6295 (m-80) REVERT: A 315 MET cc_start: 0.7800 (mmt) cc_final: 0.7456 (mmm) REVERT: A 344 ILE cc_start: 0.7541 (mp) cc_final: 0.7261 (mp) REVERT: A 440 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7260 (tpt170) REVERT: A 686 PHE cc_start: 0.6437 (t80) cc_final: 0.6236 (t80) REVERT: A 729 TYR cc_start: 0.6707 (m-80) cc_final: 0.6002 (m-80) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2393 time to fit residues: 42.2784 Evaluate side-chains 109 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.0040 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 overall best weight: 0.7810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 761 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.220936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.162218 restraints weight = 9305.055| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.80 r_work: 0.3843 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9203 Z= 0.122 Angle : 0.526 8.808 12470 Z= 0.276 Chirality : 0.039 0.158 1436 Planarity : 0.004 0.076 1574 Dihedral : 9.151 126.840 1318 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.37 % Allowed : 7.17 % Favored : 91.46 % 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: 1.22 (0.25), residues: 1161 helix: 2.13 (0.19), residues: 754 sheet: -1.02 (1.49), residues: 17 loop : -1.90 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 188 HIS 0.003 0.001 HIS A 171 PHE 0.019 0.001 PHE A 552 TYR 0.017 0.001 TYR A 908 ARG 0.005 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 596) hydrogen bonds : angle 3.96185 ( 1764) covalent geometry : bond 0.00246 ( 9203) covalent geometry : angle 0.52551 (12470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.7355 (mmm) cc_final: 0.7118 (tpt) REVERT: A 116 GLU cc_start: 0.8304 (tp30) cc_final: 0.7881 (tp30) REVERT: A 141 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5302 (mp0) REVERT: A 286 TYR cc_start: 0.7308 (m-10) cc_final: 0.6919 (m-80) REVERT: A 440 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7255 (tpt170) REVERT: A 478 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: A 532 GLU cc_start: 0.6379 (pp20) cc_final: 0.5818 (pp20) REVERT: A 970 MET cc_start: 0.6406 (mmp) cc_final: 0.6079 (mmp) outliers start: 13 outliers final: 6 residues processed: 118 average time/residue: 0.2166 time to fit residues: 36.4483 Evaluate side-chains 112 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 1058 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** 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 = 0.4527 r_free = 0.4527 target = 0.223529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167726 restraints weight = 9388.264| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.76 r_work: 0.3832 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9203 Z= 0.118 Angle : 0.506 8.906 12470 Z= 0.266 Chirality : 0.038 0.166 1436 Planarity : 0.004 0.056 1574 Dihedral : 7.973 122.070 1318 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.16 % Allowed : 11.49 % Favored : 87.36 % 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: 1.28 (0.25), residues: 1161 helix: 2.18 (0.19), residues: 754 sheet: -1.38 (1.37), residues: 17 loop : -1.88 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 188 HIS 0.004 0.001 HIS A1124 PHE 0.017 0.001 PHE A1112 TYR 0.015 0.001 TYR A 719 ARG 0.003 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 596) hydrogen bonds : angle 3.83715 ( 1764) covalent geometry : bond 0.00238 ( 9203) covalent geometry : angle 0.50607 (12470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.769 Fit side-chains REVERT: A 116 GLU cc_start: 0.8371 (tp30) cc_final: 0.7901 (tp30) REVERT: A 173 MET cc_start: 0.7441 (tpp) cc_final: 0.6992 (mmm) REVERT: A 266 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7661 (mtpt) REVERT: A 440 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7235 (tpt170) REVERT: A 478 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: A 970 MET cc_start: 0.6365 (mmp) cc_final: 0.6053 (mmp) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 0.2978 time to fit residues: 50.1732 Evaluate side-chains 114 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1029 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** 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 = 0.4493 r_free = 0.4493 target = 0.219294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.162782 restraints weight = 9233.185| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.69 r_work: 0.3773 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9203 Z= 0.148 Angle : 0.541 9.530 12470 Z= 0.283 Chirality : 0.040 0.169 1436 Planarity : 0.004 0.048 1574 Dihedral : 7.705 112.701 1318 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.11 % Allowed : 13.17 % Favored : 84.72 % 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: 1.01 (0.25), residues: 1161 helix: 1.91 (0.19), residues: 757 sheet: -1.45 (1.35), residues: 17 loop : -1.85 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 188 HIS 0.007 0.001 HIS A 171 PHE 0.019 0.002 PHE A 72 TYR 0.014 0.002 TYR A 286 ARG 0.003 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 596) hydrogen bonds : angle 3.96997 ( 1764) covalent geometry : bond 0.00320 ( 9203) covalent geometry : angle 0.54057 (12470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.860 Fit side-chains REVERT: A 141 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5441 (mp0) REVERT: A 152 ASN cc_start: 0.6394 (m-40) cc_final: 0.6136 (m-40) REVERT: A 173 MET cc_start: 0.7452 (tpp) cc_final: 0.7006 (mmm) REVERT: A 266 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7744 (mtpt) REVERT: A 440 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7248 (tpt170) REVERT: A 478 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: A 1101 HIS cc_start: 0.6639 (t-170) cc_final: 0.6423 (m170) outliers start: 20 outliers final: 15 residues processed: 124 average time/residue: 0.2977 time to fit residues: 53.7342 Evaluate side-chains 127 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 762 HIS ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.215583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.163414 restraints weight = 9307.747| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.97 r_work: 0.3711 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9203 Z= 0.191 Angle : 0.592 10.041 12470 Z= 0.309 Chirality : 0.041 0.182 1436 Planarity : 0.004 0.046 1574 Dihedral : 7.617 104.283 1318 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.42 % Allowed : 15.49 % Favored : 82.09 % 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: 0.62 (0.24), residues: 1161 helix: 1.53 (0.18), residues: 761 sheet: -1.43 (1.39), residues: 17 loop : -1.86 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 188 HIS 0.009 0.002 HIS A 171 PHE 0.021 0.002 PHE A 72 TYR 0.016 0.002 TYR A 286 ARG 0.004 0.001 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 596) hydrogen bonds : angle 4.19714 ( 1764) covalent geometry : bond 0.00426 ( 9203) covalent geometry : angle 0.59151 (12470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.984 Fit side-chains REVERT: A 116 GLU cc_start: 0.8284 (tp30) cc_final: 0.7852 (tp30) REVERT: A 141 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5572 (mp0) REVERT: A 173 MET cc_start: 0.7439 (tpp) cc_final: 0.6980 (mmm) REVERT: A 266 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7879 (mtpt) REVERT: A 444 GLN cc_start: 0.7595 (pm20) cc_final: 0.7000 (pm20) REVERT: A 478 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: A 760 LEU cc_start: 0.8070 (tp) cc_final: 0.7554 (tt) outliers start: 23 outliers final: 14 residues processed: 124 average time/residue: 0.2058 time to fit residues: 37.0359 Evaluate side-chains 124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 86 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN ** A 812 ASN ** 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 = 0.4465 r_free = 0.4465 target = 0.215927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162238 restraints weight = 9249.188| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.02 r_work: 0.3729 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9203 Z= 0.178 Angle : 0.580 10.941 12470 Z= 0.303 Chirality : 0.041 0.195 1436 Planarity : 0.004 0.046 1574 Dihedral : 7.308 95.708 1318 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.53 % Allowed : 16.65 % Favored : 80.82 % 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: 0.51 (0.24), residues: 1161 helix: 1.46 (0.18), residues: 760 sheet: -1.68 (1.33), residues: 17 loop : -1.93 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 188 HIS 0.009 0.001 HIS A 171 PHE 0.020 0.002 PHE A 552 TYR 0.015 0.002 TYR A 286 ARG 0.004 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 596) hydrogen bonds : angle 4.19365 ( 1764) covalent geometry : bond 0.00396 ( 9203) covalent geometry : angle 0.57953 (12470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8304 (m-10) cc_final: 0.7688 (m-10) REVERT: A 116 GLU cc_start: 0.8321 (tp30) cc_final: 0.7895 (tp30) REVERT: A 141 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5425 (mp0) REVERT: A 173 MET cc_start: 0.7485 (tpp) cc_final: 0.7050 (mmm) REVERT: A 266 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7794 (mtpt) REVERT: A 444 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: A 478 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7347 (pm20) outliers start: 24 outliers final: 16 residues processed: 127 average time/residue: 0.1990 time to fit residues: 36.4703 Evaluate side-chains 130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 114 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 812 ASN ** 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 = 0.4492 r_free = 0.4492 target = 0.218977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.162492 restraints weight = 9326.673| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.72 r_work: 0.3775 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9203 Z= 0.132 Angle : 0.564 13.603 12470 Z= 0.286 Chirality : 0.039 0.208 1436 Planarity : 0.004 0.046 1574 Dihedral : 7.061 90.911 1318 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.32 % Allowed : 17.70 % Favored : 79.98 % 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: 0.80 (0.25), residues: 1161 helix: 1.77 (0.19), residues: 758 sheet: -1.90 (1.28), residues: 17 loop : -1.97 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.008 0.001 HIS A 486 PHE 0.018 0.001 PHE A 35 TYR 0.014 0.001 TYR A 286 ARG 0.003 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 596) hydrogen bonds : angle 4.01393 ( 1764) covalent geometry : bond 0.00276 ( 9203) covalent geometry : angle 0.56410 (12470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8230 (m-10) cc_final: 0.7653 (m-10) REVERT: A 116 GLU cc_start: 0.8278 (tp30) cc_final: 0.7850 (tp30) REVERT: A 141 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5234 (mp0) REVERT: A 173 MET cc_start: 0.7418 (tpp) cc_final: 0.6976 (mmm) REVERT: A 266 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7765 (mtpt) REVERT: A 444 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: A 478 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: A 481 ARG cc_start: 0.7200 (mmm160) cc_final: 0.6570 (mmm160) REVERT: A 576 VAL cc_start: 0.6960 (OUTLIER) cc_final: 0.6759 (t) REVERT: A 1168 LYS cc_start: 0.6438 (ptpp) cc_final: 0.6099 (ptmm) outliers start: 22 outliers final: 15 residues processed: 129 average time/residue: 0.2176 time to fit residues: 38.9765 Evaluate side-chains 130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 1116 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 812 ASN ** 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 = 0.4484 r_free = 0.4484 target = 0.217854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.161209 restraints weight = 9406.255| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.69 r_work: 0.3757 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9203 Z= 0.152 Angle : 0.592 12.577 12470 Z= 0.299 Chirality : 0.040 0.212 1436 Planarity : 0.004 0.046 1574 Dihedral : 6.931 80.678 1318 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.74 % Allowed : 17.60 % Favored : 79.66 % 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: 0.69 (0.25), residues: 1161 helix: 1.69 (0.19), residues: 759 sheet: -2.03 (1.27), residues: 17 loop : -2.04 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.007 0.001 HIS A 486 PHE 0.017 0.002 PHE A 72 TYR 0.013 0.001 TYR A 286 ARG 0.004 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 596) hydrogen bonds : angle 4.04990 ( 1764) covalent geometry : bond 0.00329 ( 9203) covalent geometry : angle 0.59154 (12470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8249 (m-10) cc_final: 0.7616 (m-10) REVERT: A 116 GLU cc_start: 0.8281 (tp30) cc_final: 0.7872 (tp30) REVERT: A 141 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5311 (mp0) REVERT: A 173 MET cc_start: 0.7437 (tpp) cc_final: 0.6996 (mmm) REVERT: A 266 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7786 (mtpt) REVERT: A 444 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: A 478 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7318 (pm20) outliers start: 26 outliers final: 22 residues processed: 126 average time/residue: 0.2059 time to fit residues: 37.3636 Evaluate side-chains 137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1216 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 812 ASN ** 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 = 0.4500 r_free = 0.4500 target = 0.219951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.163978 restraints weight = 9263.690| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.68 r_work: 0.3788 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9203 Z= 0.132 Angle : 0.583 13.831 12470 Z= 0.290 Chirality : 0.039 0.221 1436 Planarity : 0.004 0.046 1574 Dihedral : 6.671 70.463 1318 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.53 % Allowed : 17.81 % Favored : 79.66 % 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: 0.82 (0.25), residues: 1161 helix: 1.81 (0.19), residues: 760 sheet: -2.22 (1.22), residues: 17 loop : -2.02 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.007 0.001 HIS A 486 PHE 0.023 0.001 PHE A 35 TYR 0.013 0.001 TYR A 286 ARG 0.003 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 596) hydrogen bonds : angle 3.96901 ( 1764) covalent geometry : bond 0.00278 ( 9203) covalent geometry : angle 0.58280 (12470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8222 (m-10) cc_final: 0.7619 (m-10) REVERT: A 116 GLU cc_start: 0.8253 (tp30) cc_final: 0.7825 (tp30) REVERT: A 141 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5242 (mp0) REVERT: A 173 MET cc_start: 0.7421 (tpp) cc_final: 0.6965 (mmm) REVERT: A 266 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7752 (mtpt) REVERT: A 444 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7028 (pm20) REVERT: A 478 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7259 (pm20) outliers start: 24 outliers final: 17 residues processed: 125 average time/residue: 0.2387 time to fit residues: 42.1841 Evaluate side-chains 130 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 697 TRP Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 24 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 812 ASN ** 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 = 0.4527 r_free = 0.4527 target = 0.222989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170167 restraints weight = 9320.953| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.08 r_work: 0.3816 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9203 Z= 0.115 Angle : 0.562 12.697 12470 Z= 0.279 Chirality : 0.039 0.224 1436 Planarity : 0.004 0.047 1574 Dihedral : 5.892 67.325 1318 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.00 % Allowed : 18.44 % Favored : 79.56 % 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: 1.05 (0.25), residues: 1161 helix: 2.04 (0.19), residues: 754 sheet: -2.34 (1.19), residues: 17 loop : -1.99 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 188 HIS 0.007 0.001 HIS A 762 PHE 0.023 0.001 PHE A 35 TYR 0.011 0.001 TYR A 286 ARG 0.002 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 596) hydrogen bonds : angle 3.83508 ( 1764) covalent geometry : bond 0.00233 ( 9203) covalent geometry : angle 0.56248 (12470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8228 (m-10) cc_final: 0.7644 (m-10) REVERT: A 116 GLU cc_start: 0.8252 (tp30) cc_final: 0.7812 (tp30) REVERT: A 141 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5286 (mp0) REVERT: A 173 MET cc_start: 0.7494 (tpp) cc_final: 0.7018 (mmm) REVERT: A 266 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7763 (mtpt) REVERT: A 444 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: A 478 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: A 729 TYR cc_start: 0.6774 (m-80) cc_final: 0.5988 (m-80) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 0.2597 time to fit residues: 46.9670 Evaluate side-chains 128 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 812 ASN ** 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 = 0.4527 r_free = 0.4527 target = 0.222869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167534 restraints weight = 9235.969| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.70 r_work: 0.3827 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9203 Z= 0.117 Angle : 0.571 12.263 12470 Z= 0.282 Chirality : 0.039 0.218 1436 Planarity : 0.004 0.047 1574 Dihedral : 5.686 66.378 1318 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.11 % Allowed : 18.55 % Favored : 79.35 % 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: 1.09 (0.25), residues: 1161 helix: 2.08 (0.19), residues: 754 sheet: -2.39 (1.16), residues: 17 loop : -1.98 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 188 HIS 0.007 0.001 HIS A 486 PHE 0.021 0.001 PHE A 35 TYR 0.016 0.001 TYR A 719 ARG 0.002 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 596) hydrogen bonds : angle 3.82542 ( 1764) covalent geometry : bond 0.00241 ( 9203) covalent geometry : angle 0.57092 (12470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8329.60 seconds wall clock time: 144 minutes 9.60 seconds (8649.60 seconds total)