Starting phenix.real_space_refine on Sun May 11 17:04:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdv_17622/05_2025/8pdv_17622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdv_17622/05_2025/8pdv_17622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdv_17622/05_2025/8pdv_17622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdv_17622/05_2025/8pdv_17622.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdv_17622/05_2025/8pdv_17622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdv_17622/05_2025/8pdv_17622.cif" } resolution = 3.26 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= 0.001 sd= 0.022 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 P 1 5.49 5 S 43 5.16 5 C 5317 2.51 5 N 1352 2.21 5 O 1427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8140 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8117 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 30, 'TRANS': 996} Chain breaks: 5 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.03, per 1000 atoms: 0.62 Number of scatterers: 8140 At special positions: 0 Unit cell: (84.826, 118.552, 123.662, 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) S 43 16.00 P 1 15.00 O 1427 8.00 N 1352 7.00 C 5317 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: 2.17 Conformation dependent library (CDL) restraints added in 890.5 milliseconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1938 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 76.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.853A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.953A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.531A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 171 through 188 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.607A pdb=" N ASP A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 254 removed outlier: 3.618A pdb=" N LYS A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.520A pdb=" N ASN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.582A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.553A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 380 removed outlier: 3.612A pdb=" N VAL A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 381 through 406 removed outlier: 4.023A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.538A pdb=" N ARG A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.538A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 469 removed outlier: 4.042A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 4.936A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 571 through 600 removed outlier: 4.268A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.517A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.735A pdb=" N ILE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 removed outlier: 4.226A pdb=" N LYS A 656 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 Processing helix chain 'A' and resid 677 through 691 removed outlier: 3.962A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 removed outlier: 3.707A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 755 Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.874A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 778 removed outlier: 3.841A pdb=" N LEU A 771 " --> pdb=" O ASP A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.991A pdb=" N LEU A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 858 Proline residue: A 819 - end of helix removed outlier: 3.952A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.603A pdb=" N LEU A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.555A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 941 removed outlier: 3.721A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 952 through 960 removed outlier: 3.526A pdb=" N LEU A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 975 Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 3.531A pdb=" N VAL A1047 " --> pdb=" O GLY A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1108 removed outlier: 3.548A pdb=" N ARG A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.043A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.872A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.078A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136 removed outlier: 3.751A pdb=" N ALA A1152 " --> pdb=" O ILE A1161 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1704 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: 2.46 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1770 1.33 - 1.45: 1665 1.45 - 1.57: 4784 1.57 - 1.69: 2 1.69 - 1.81: 79 Bond restraints: 8300 Sorted by residual: bond pdb=" O1A PCG A1401 " pdb=" PA PCG A1401 " ideal model delta sigma weight residual 1.582 1.468 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C5 PCG A1401 " pdb=" C6 PCG A1401 " ideal model delta sigma weight residual 1.425 1.322 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" CA SER A 995 " pdb=" CB SER A 995 " ideal model delta sigma weight residual 1.527 1.470 0.057 1.44e-02 4.82e+03 1.55e+01 bond pdb=" N VAL A1041 " pdb=" CA VAL A1041 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.20e-02 6.94e+03 9.27e+00 bond pdb=" C4 PCG A1401 " pdb=" C5 PCG A1401 " ideal model delta sigma weight residual 1.381 1.327 0.054 2.00e-02 2.50e+03 7.29e+00 ... (remaining 8295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11098 1.94 - 3.87: 128 3.87 - 5.81: 22 5.81 - 7.74: 6 7.74 - 9.68: 4 Bond angle restraints: 11258 Sorted by residual: angle pdb=" N VAL A1047 " pdb=" CA VAL A1047 " pdb=" C VAL A1047 " ideal model delta sigma weight residual 111.45 107.63 3.82 9.30e-01 1.16e+00 1.69e+01 angle pdb=" CA LEU A 998 " pdb=" C LEU A 998 " pdb=" O LEU A 998 " ideal model delta sigma weight residual 121.99 117.73 4.26 1.14e+00 7.69e-01 1.40e+01 angle pdb=" N MET A1045 " pdb=" CA MET A1045 " pdb=" C MET A1045 " ideal model delta sigma weight residual 113.02 108.57 4.45 1.20e+00 6.94e-01 1.38e+01 angle pdb=" CB MET A 925 " pdb=" CG MET A 925 " pdb=" SD MET A 925 " ideal model delta sigma weight residual 112.70 122.38 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CA VAL A1041 " pdb=" C VAL A1041 " pdb=" O VAL A1041 " ideal model delta sigma weight residual 120.72 117.08 3.64 1.14e+00 7.69e-01 1.02e+01 ... (remaining 11253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.31: 4876 33.31 - 66.62: 91 66.62 - 99.93: 8 99.93 - 133.25: 1 133.25 - 166.56: 2 Dihedral angle restraints: 4978 sinusoidal: 1990 harmonic: 2988 Sorted by residual: dihedral pdb=" C3' PCG A1401 " pdb=" O3' PCG A1401 " pdb=" PA PCG A1401 " pdb=" O2A PCG A1401 " ideal model delta sinusoidal sigma weight residual 279.09 112.53 166.56 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C5' PCG A1401 " pdb=" O5' PCG A1401 " pdb=" PA PCG A1401 " pdb=" O2A PCG A1401 " ideal model delta sinusoidal sigma weight residual 81.13 -56.54 137.67 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C5' PCG A1401 " pdb=" O5' PCG A1401 " pdb=" PA PCG A1401 " pdb=" O3' PCG A1401 " ideal model delta sinusoidal sigma weight residual -45.54 60.33 -105.87 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 4975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1281 0.080 - 0.159: 68 0.159 - 0.239: 3 0.239 - 0.318: 1 0.318 - 0.398: 1 Chirality restraints: 1354 Sorted by residual: chirality pdb=" PA PCG A1401 " pdb=" O2A PCG A1401 " pdb=" O3' PCG A1401 " pdb=" O5' PCG A1401 " both_signs ideal model delta sigma weight residual True 2.70 -3.10 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" C3' PCG A1401 " pdb=" C2' PCG A1401 " pdb=" C4' PCG A1401 " pdb=" O3' PCG A1401 " both_signs ideal model delta sigma weight residual False -2.45 -2.69 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE A1042 " pdb=" N ILE A1042 " pdb=" C ILE A1042 " pdb=" CB ILE A1042 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1351 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1097 " -0.191 9.50e-02 1.11e+02 8.56e-02 4.50e+00 pdb=" NE ARG A1097 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A1097 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1097 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A1097 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1096 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C ILE A1096 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A1096 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A1097 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1045 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C MET A1045 " -0.022 2.00e-02 2.50e+03 pdb=" O MET A1045 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY A1046 " 0.008 2.00e-02 2.50e+03 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1695 2.78 - 3.31: 8387 3.31 - 3.84: 12727 3.84 - 4.37: 15049 4.37 - 4.90: 25629 Nonbonded interactions: 63487 Sorted by model distance: nonbonded pdb=" OD1 ASP A1144 " pdb=" N VAL A1145 " model vdw 2.247 3.120 nonbonded pdb=" OD1 ASP A 923 " pdb=" N GLU A 924 " model vdw 2.308 3.120 nonbonded pdb=" OH TYR A 392 " pdb=" OD1 ASN A 470 " model vdw 2.361 3.040 nonbonded pdb=" O ASN A1154 " pdb=" N ARG A1158 " model vdw 2.381 3.120 nonbonded pdb=" O VAL A 468 " pdb=" OG1 THR A 472 " model vdw 2.391 3.040 ... (remaining 63482 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 0.114 8300 Z= 0.212 Angle : 0.594 9.677 11258 Z= 0.327 Chirality : 0.040 0.398 1354 Planarity : 0.004 0.086 1379 Dihedral : 14.127 166.557 3040 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.09 % 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: 1.63 (0.27), residues: 1015 helix: 1.49 (0.19), residues: 727 sheet: 0.62 (0.72), residues: 48 loop : 0.12 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 278 HIS 0.002 0.001 HIS A 676 PHE 0.017 0.001 PHE A 201 TYR 0.010 0.001 TYR A 309 ARG 0.004 0.000 ARG A 733 Details of bonding type rmsd hydrogen bonds : bond 0.18955 ( 578) hydrogen bonds : angle 6.74787 ( 1704) covalent geometry : bond 0.00397 ( 8300) covalent geometry : angle 0.59426 (11258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7905 (mttm) cc_final: 0.7689 (mttm) REVERT: A 84 SER cc_start: 0.7750 (p) cc_final: 0.7485 (t) REVERT: A 116 VAL cc_start: 0.6947 (p) cc_final: 0.6681 (m) REVERT: A 120 VAL cc_start: 0.7218 (t) cc_final: 0.7001 (p) REVERT: A 124 GLU cc_start: 0.7468 (tt0) cc_final: 0.6974 (tm-30) REVERT: A 155 ASP cc_start: 0.7711 (t70) cc_final: 0.7258 (t0) REVERT: A 175 VAL cc_start: 0.7056 (t) cc_final: 0.6828 (m) REVERT: A 187 ASN cc_start: 0.7318 (m-40) cc_final: 0.6808 (m-40) REVERT: A 263 GLN cc_start: 0.6218 (mm-40) cc_final: 0.5954 (mm-40) REVERT: A 289 PHE cc_start: 0.8187 (m-80) cc_final: 0.7983 (m-80) REVERT: A 295 ASN cc_start: 0.8260 (t0) cc_final: 0.7937 (t0) REVERT: A 344 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7454 (mm-30) REVERT: A 354 GLU cc_start: 0.7928 (tt0) cc_final: 0.7699 (mt-10) REVERT: A 355 MET cc_start: 0.7773 (tmm) cc_final: 0.7509 (tmm) REVERT: A 383 MET cc_start: 0.7899 (mmm) cc_final: 0.7540 (mmm) REVERT: A 474 ILE cc_start: 0.7717 (tp) cc_final: 0.7420 (tt) REVERT: A 485 ASP cc_start: 0.7604 (m-30) cc_final: 0.7344 (m-30) REVERT: A 511 MET cc_start: 0.7457 (tmm) cc_final: 0.7019 (tmm) REVERT: A 531 GLU cc_start: 0.7532 (tt0) cc_final: 0.7214 (tp30) REVERT: A 579 MET cc_start: 0.6495 (tpt) cc_final: 0.6271 (tpt) REVERT: A 585 ARG cc_start: 0.6990 (mtt-85) cc_final: 0.6460 (mtt-85) REVERT: A 588 LYS cc_start: 0.7849 (ttpp) cc_final: 0.7512 (ttpp) REVERT: A 628 VAL cc_start: 0.7706 (m) cc_final: 0.7354 (t) REVERT: A 634 SER cc_start: 0.8034 (m) cc_final: 0.7706 (p) REVERT: A 646 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.7357 (ttp-170) REVERT: A 647 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7424 (mptt) REVERT: A 684 ILE cc_start: 0.7197 (mm) cc_final: 0.6752 (pt) REVERT: A 697 MET cc_start: 0.5542 (tpp) cc_final: 0.5107 (tpp) REVERT: A 815 LYS cc_start: 0.8364 (tttm) cc_final: 0.8092 (tttp) REVERT: A 828 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8204 (mmmt) REVERT: A 838 ASP cc_start: 0.7577 (m-30) cc_final: 0.7228 (m-30) REVERT: A 841 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7410 (tptt) REVERT: A 845 ILE cc_start: 0.8044 (mt) cc_final: 0.7810 (mm) REVERT: A 862 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7556 (tppt) REVERT: A 865 ARG cc_start: 0.6725 (tmm-80) cc_final: 0.6519 (tmm-80) REVERT: A 866 GLU cc_start: 0.7360 (tp30) cc_final: 0.6711 (tp30) REVERT: A 867 LEU cc_start: 0.7761 (mp) cc_final: 0.7441 (mm) REVERT: A 868 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7373 (mtmm) REVERT: A 870 ILE cc_start: 0.8005 (mt) cc_final: 0.7634 (mt) REVERT: A 877 GLN cc_start: 0.7815 (mt0) cc_final: 0.7540 (tt0) REVERT: A 888 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7252 (mm-30) REVERT: A 911 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7244 (mm-30) REVERT: A 931 GLU cc_start: 0.7583 (tt0) cc_final: 0.7356 (tt0) REVERT: A 946 SER cc_start: 0.8169 (p) cc_final: 0.7956 (t) REVERT: A 961 SER cc_start: 0.8303 (m) cc_final: 0.7975 (p) REVERT: A 972 PHE cc_start: 0.7915 (t80) cc_final: 0.7625 (t80) REVERT: A 974 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7566 (mtpp) REVERT: A 999 PHE cc_start: 0.7627 (m-80) cc_final: 0.7298 (m-80) REVERT: A 1003 SER cc_start: 0.8647 (t) cc_final: 0.8266 (t) REVERT: A 1033 GLU cc_start: 0.7258 (tt0) cc_final: 0.6978 (tt0) REVERT: A 1096 ILE cc_start: 0.7975 (mt) cc_final: 0.7677 (mm) REVERT: A 1107 MET cc_start: 0.6480 (mtm) cc_final: 0.6141 (mtp) REVERT: A 1118 LYS cc_start: 0.3998 (tmtt) cc_final: 0.2876 (mttm) REVERT: A 1122 GLU cc_start: 0.7677 (tp30) cc_final: 0.7370 (tt0) REVERT: A 1133 HIS cc_start: 0.6864 (t-170) cc_final: 0.6622 (t-90) REVERT: A 1143 GLU cc_start: 0.7176 (tt0) cc_final: 0.6759 (mt-10) REVERT: A 1154 ASN cc_start: 0.7138 (t0) cc_final: 0.6626 (t0) REVERT: A 1182 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6179 (mp0) REVERT: A 1186 LEU cc_start: 0.8455 (tp) cc_final: 0.8189 (tp) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.2292 time to fit residues: 78.6787 Evaluate side-chains 224 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN A 900 GLN A 908 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116317 restraints weight = 11948.553| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.81 r_work: 0.3296 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8300 Z= 0.164 Angle : 0.554 7.845 11258 Z= 0.292 Chirality : 0.041 0.188 1354 Planarity : 0.004 0.047 1379 Dihedral : 9.664 169.318 1127 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.81 % Allowed : 11.33 % Favored : 86.86 % 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: 2.05 (0.27), residues: 1015 helix: 1.75 (0.19), residues: 731 sheet: 0.67 (0.69), residues: 51 loop : 0.45 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 278 HIS 0.003 0.001 HIS A 676 PHE 0.013 0.001 PHE A 575 TYR 0.017 0.002 TYR A 743 ARG 0.003 0.000 ARG A 733 Details of bonding type rmsd hydrogen bonds : bond 0.05537 ( 578) hydrogen bonds : angle 4.60628 ( 1704) covalent geometry : bond 0.00361 ( 8300) covalent geometry : angle 0.55375 (11258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 84 SER cc_start: 0.8419 (p) cc_final: 0.7996 (t) REVERT: A 120 VAL cc_start: 0.8169 (t) cc_final: 0.7807 (p) REVERT: A 169 LEU cc_start: 0.8526 (tp) cc_final: 0.8303 (tp) REVERT: A 187 ASN cc_start: 0.7887 (m-40) cc_final: 0.7498 (m-40) REVERT: A 205 MET cc_start: 0.8298 (tpp) cc_final: 0.8095 (mmt) REVERT: A 295 ASN cc_start: 0.8301 (t0) cc_final: 0.7982 (t0) REVERT: A 344 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7967 (mm-30) REVERT: A 354 GLU cc_start: 0.8337 (tt0) cc_final: 0.8008 (mt-10) REVERT: A 355 MET cc_start: 0.8431 (tmm) cc_final: 0.7842 (tmm) REVERT: A 375 LYS cc_start: 0.7896 (mttt) cc_final: 0.7686 (mttt) REVERT: A 383 MET cc_start: 0.8415 (mmm) cc_final: 0.8131 (mmm) REVERT: A 443 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7736 (tp30) REVERT: A 474 ILE cc_start: 0.8478 (tp) cc_final: 0.8232 (tt) REVERT: A 503 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 511 MET cc_start: 0.8296 (tmm) cc_final: 0.7941 (tmm) REVERT: A 579 MET cc_start: 0.7000 (tpt) cc_final: 0.6773 (tpt) REVERT: A 588 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7715 (ttpp) REVERT: A 628 VAL cc_start: 0.7902 (m) cc_final: 0.7574 (t) REVERT: A 629 ASP cc_start: 0.7913 (p0) cc_final: 0.7659 (p0) REVERT: A 633 LYS cc_start: 0.8428 (mttt) cc_final: 0.8159 (mmtm) REVERT: A 634 SER cc_start: 0.8146 (m) cc_final: 0.7819 (p) REVERT: A 646 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7636 (ttp-170) REVERT: A 684 ILE cc_start: 0.7348 (mm) cc_final: 0.6995 (pt) REVERT: A 697 MET cc_start: 0.5599 (tpp) cc_final: 0.5208 (tpp) REVERT: A 862 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7892 (ttmt) REVERT: A 866 GLU cc_start: 0.7478 (tp30) cc_final: 0.7108 (tp30) REVERT: A 870 ILE cc_start: 0.8501 (mt) cc_final: 0.7971 (mt) REVERT: A 974 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8106 (mtpp) REVERT: A 1102 LEU cc_start: 0.8326 (mt) cc_final: 0.8125 (mp) REVERT: A 1118 LYS cc_start: 0.5231 (tmtt) cc_final: 0.3698 (mttm) REVERT: A 1143 GLU cc_start: 0.7155 (tt0) cc_final: 0.6890 (mt-10) REVERT: A 1154 ASN cc_start: 0.7615 (t0) cc_final: 0.7166 (t0) REVERT: A 1182 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6352 (mp0) REVERT: A 1186 LEU cc_start: 0.8799 (tp) cc_final: 0.8592 (tp) outliers start: 16 outliers final: 8 residues processed: 238 average time/residue: 0.2106 time to fit residues: 66.4455 Evaluate side-chains 230 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 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 886 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116967 restraints weight = 12075.042| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.82 r_work: 0.3290 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8300 Z= 0.169 Angle : 0.527 7.965 11258 Z= 0.276 Chirality : 0.040 0.207 1354 Planarity : 0.004 0.053 1379 Dihedral : 9.707 174.322 1127 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.49 % Allowed : 14.38 % Favored : 83.13 % 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: 2.02 (0.26), residues: 1015 helix: 1.73 (0.19), residues: 731 sheet: 0.81 (0.68), residues: 51 loop : 0.36 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 278 HIS 0.004 0.001 HIS A1133 PHE 0.016 0.002 PHE A 575 TYR 0.013 0.002 TYR A 309 ARG 0.003 0.000 ARG A1169 Details of bonding type rmsd hydrogen bonds : bond 0.04903 ( 578) hydrogen bonds : angle 4.33062 ( 1704) covalent geometry : bond 0.00377 ( 8300) covalent geometry : angle 0.52684 (11258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 84 SER cc_start: 0.8296 (p) cc_final: 0.7961 (t) REVERT: A 120 VAL cc_start: 0.8143 (t) cc_final: 0.7770 (p) REVERT: A 124 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7355 (tp30) REVERT: A 161 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7874 (mtt180) REVERT: A 187 ASN cc_start: 0.7924 (m-40) cc_final: 0.7534 (m-40) REVERT: A 256 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 354 GLU cc_start: 0.8350 (tt0) cc_final: 0.8023 (mt-10) REVERT: A 355 MET cc_start: 0.8458 (tmm) cc_final: 0.7850 (tmm) REVERT: A 375 LYS cc_start: 0.7946 (mttt) cc_final: 0.7730 (mttt) REVERT: A 443 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7702 (tp30) REVERT: A 474 ILE cc_start: 0.8454 (tp) cc_final: 0.8200 (tt) REVERT: A 511 MET cc_start: 0.8203 (tmm) cc_final: 0.7806 (tmm) REVERT: A 514 SER cc_start: 0.8008 (m) cc_final: 0.7787 (p) REVERT: A 531 GLU cc_start: 0.7343 (tp30) cc_final: 0.7086 (tp30) REVERT: A 588 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7749 (ttpp) REVERT: A 628 VAL cc_start: 0.7909 (m) cc_final: 0.7670 (t) REVERT: A 629 ASP cc_start: 0.7924 (p0) cc_final: 0.7705 (p0) REVERT: A 633 LYS cc_start: 0.8415 (mttt) cc_final: 0.8171 (mmtm) REVERT: A 634 SER cc_start: 0.8119 (m) cc_final: 0.7840 (p) REVERT: A 643 TRP cc_start: 0.7635 (t60) cc_final: 0.7412 (t-100) REVERT: A 646 ARG cc_start: 0.7943 (ttp-170) cc_final: 0.7611 (ttp-170) REVERT: A 684 ILE cc_start: 0.7392 (mm) cc_final: 0.6983 (pt) REVERT: A 697 MET cc_start: 0.5579 (tpp) cc_final: 0.5250 (tpp) REVERT: A 828 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8337 (mmtm) REVERT: A 847 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 862 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7924 (tppt) REVERT: A 876 LEU cc_start: 0.8487 (mt) cc_final: 0.8269 (mm) REVERT: A 974 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8051 (mtpp) REVERT: A 983 ASP cc_start: 0.6972 (t0) cc_final: 0.6711 (p0) REVERT: A 1033 GLU cc_start: 0.7531 (tt0) cc_final: 0.7261 (tt0) REVERT: A 1102 LEU cc_start: 0.8330 (mt) cc_final: 0.8116 (mp) REVERT: A 1118 LYS cc_start: 0.5623 (tmtt) cc_final: 0.3260 (tppt) REVERT: A 1122 GLU cc_start: 0.6497 (tt0) cc_final: 0.5682 (tt0) REVERT: A 1154 ASN cc_start: 0.7515 (t0) cc_final: 0.7055 (t0) REVERT: A 1182 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6379 (mp0) REVERT: A 1186 LEU cc_start: 0.8796 (tp) cc_final: 0.8586 (tp) outliers start: 22 outliers final: 15 residues processed: 232 average time/residue: 0.2180 time to fit residues: 66.6701 Evaluate side-chains 234 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118569 restraints weight = 11776.328| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.79 r_work: 0.3299 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8300 Z= 0.150 Angle : 0.510 6.970 11258 Z= 0.267 Chirality : 0.040 0.219 1354 Planarity : 0.004 0.051 1379 Dihedral : 9.688 174.405 1127 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.94 % Allowed : 15.63 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.05 (0.26), residues: 1015 helix: 1.80 (0.19), residues: 730 sheet: 1.05 (0.70), residues: 51 loop : 0.19 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 278 HIS 0.005 0.001 HIS A 914 PHE 0.015 0.001 PHE A 575 TYR 0.011 0.001 TYR A 309 ARG 0.003 0.000 ARG A1097 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 578) hydrogen bonds : angle 4.17640 ( 1704) covalent geometry : bond 0.00334 ( 8300) covalent geometry : angle 0.51005 (11258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 84 SER cc_start: 0.8290 (p) cc_final: 0.7954 (t) REVERT: A 108 ILE cc_start: 0.8158 (mm) cc_final: 0.7864 (mt) REVERT: A 120 VAL cc_start: 0.8115 (t) cc_final: 0.7718 (p) REVERT: A 155 ASP cc_start: 0.8336 (t0) cc_final: 0.8046 (t0) REVERT: A 161 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7795 (mtt180) REVERT: A 187 ASN cc_start: 0.7935 (m-40) cc_final: 0.7539 (m-40) REVERT: A 354 GLU cc_start: 0.8373 (tt0) cc_final: 0.8096 (mt-10) REVERT: A 355 MET cc_start: 0.8488 (tmm) cc_final: 0.7917 (tmm) REVERT: A 443 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7625 (tp30) REVERT: A 500 ARG cc_start: 0.6491 (ttp-170) cc_final: 0.6284 (ttp-170) REVERT: A 511 MET cc_start: 0.8162 (tmm) cc_final: 0.7807 (tmm) REVERT: A 531 GLU cc_start: 0.7307 (tp30) cc_final: 0.7069 (tp30) REVERT: A 588 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7730 (ttpp) REVERT: A 633 LYS cc_start: 0.8404 (mttt) cc_final: 0.8142 (mmtm) REVERT: A 634 SER cc_start: 0.8118 (m) cc_final: 0.7800 (p) REVERT: A 643 TRP cc_start: 0.7626 (t60) cc_final: 0.7401 (t-100) REVERT: A 646 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7438 (ttp-170) REVERT: A 684 ILE cc_start: 0.7425 (mm) cc_final: 0.6969 (pt) REVERT: A 697 MET cc_start: 0.5606 (tpp) cc_final: 0.5290 (tpp) REVERT: A 828 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8274 (mmmm) REVERT: A 847 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 974 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8049 (mtpp) REVERT: A 1033 GLU cc_start: 0.7521 (tt0) cc_final: 0.7203 (tt0) REVERT: A 1107 MET cc_start: 0.7211 (mtm) cc_final: 0.6944 (mtp) REVERT: A 1110 GLN cc_start: 0.7933 (mp10) cc_final: 0.7467 (mp10) REVERT: A 1118 LYS cc_start: 0.5093 (tmtt) cc_final: 0.2926 (tppt) REVERT: A 1122 GLU cc_start: 0.7009 (tt0) cc_final: 0.6544 (mt-10) REVERT: A 1154 ASN cc_start: 0.7438 (t0) cc_final: 0.7027 (t0) REVERT: A 1182 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6350 (mp0) REVERT: A 1186 LEU cc_start: 0.8776 (tp) cc_final: 0.8520 (tp) outliers start: 26 outliers final: 19 residues processed: 236 average time/residue: 0.2118 time to fit residues: 66.1700 Evaluate side-chains 238 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.145446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118710 restraints weight = 11659.410| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.79 r_work: 0.3295 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8300 Z= 0.147 Angle : 0.511 7.590 11258 Z= 0.268 Chirality : 0.040 0.224 1354 Planarity : 0.004 0.057 1379 Dihedral : 9.693 175.328 1127 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.85 % Allowed : 16.76 % Favored : 79.39 % 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: 2.13 (0.26), residues: 1015 helix: 1.85 (0.19), residues: 733 sheet: 1.22 (0.72), residues: 51 loop : 0.18 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 278 HIS 0.004 0.001 HIS A1133 PHE 0.014 0.001 PHE A 575 TYR 0.011 0.001 TYR A 309 ARG 0.003 0.000 ARG A1169 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 578) hydrogen bonds : angle 4.09267 ( 1704) covalent geometry : bond 0.00328 ( 8300) covalent geometry : angle 0.51084 (11258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 155 ASP cc_start: 0.8333 (t0) cc_final: 0.8044 (t0) REVERT: A 161 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7753 (mtt180) REVERT: A 187 ASN cc_start: 0.7913 (m-40) cc_final: 0.7523 (m-40) REVERT: A 355 MET cc_start: 0.8481 (tmm) cc_final: 0.7920 (tmm) REVERT: A 443 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7757 (tp30) REVERT: A 500 ARG cc_start: 0.6481 (ttp-170) cc_final: 0.6278 (ttp-170) REVERT: A 511 MET cc_start: 0.8161 (tmm) cc_final: 0.7788 (tmm) REVERT: A 588 LYS cc_start: 0.8009 (ttpp) cc_final: 0.7771 (ttpp) REVERT: A 633 LYS cc_start: 0.8405 (mttt) cc_final: 0.8144 (mmtm) REVERT: A 634 SER cc_start: 0.8031 (m) cc_final: 0.7779 (p) REVERT: A 643 TRP cc_start: 0.7625 (t60) cc_final: 0.7351 (t-100) REVERT: A 646 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7426 (ttp-170) REVERT: A 684 ILE cc_start: 0.7316 (mm) cc_final: 0.6889 (pt) REVERT: A 697 MET cc_start: 0.5619 (tpp) cc_final: 0.5318 (tpp) REVERT: A 876 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8409 (mt) REVERT: A 974 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8055 (mtpp) REVERT: A 1033 GLU cc_start: 0.7535 (tt0) cc_final: 0.7272 (tt0) REVERT: A 1104 MET cc_start: 0.8051 (tpp) cc_final: 0.7706 (tpt) REVERT: A 1110 GLN cc_start: 0.7972 (mp10) cc_final: 0.7498 (mp10) REVERT: A 1118 LYS cc_start: 0.5142 (tmtt) cc_final: 0.2699 (tppt) REVERT: A 1122 GLU cc_start: 0.6988 (tt0) cc_final: 0.6569 (tm-30) REVERT: A 1182 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6332 (mp0) REVERT: A 1186 LEU cc_start: 0.8771 (tp) cc_final: 0.8557 (tp) outliers start: 34 outliers final: 25 residues processed: 233 average time/residue: 0.2147 time to fit residues: 66.3002 Evaluate side-chains 244 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 93 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118092 restraints weight = 11713.880| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.79 r_work: 0.3296 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8300 Z= 0.148 Angle : 0.526 9.522 11258 Z= 0.272 Chirality : 0.040 0.226 1354 Planarity : 0.004 0.052 1379 Dihedral : 9.688 175.322 1127 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.74 % Allowed : 17.33 % Favored : 78.94 % 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: 2.14 (0.26), residues: 1015 helix: 1.87 (0.19), residues: 733 sheet: 1.09 (0.73), residues: 51 loop : 0.15 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 278 HIS 0.003 0.001 HIS A 676 PHE 0.013 0.001 PHE A 575 TYR 0.011 0.001 TYR A 309 ARG 0.003 0.000 ARG A1169 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 578) hydrogen bonds : angle 4.06804 ( 1704) covalent geometry : bond 0.00338 ( 8300) covalent geometry : angle 0.52605 (11258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.813 Fit side-chains REVERT: A 108 ILE cc_start: 0.8135 (mm) cc_final: 0.7830 (mt) REVERT: A 120 VAL cc_start: 0.8026 (t) cc_final: 0.7551 (p) REVERT: A 124 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 155 ASP cc_start: 0.8326 (t0) cc_final: 0.8052 (t0) REVERT: A 161 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7726 (mtt180) REVERT: A 187 ASN cc_start: 0.7900 (m-40) cc_final: 0.7509 (m-40) REVERT: A 355 MET cc_start: 0.8486 (tmm) cc_final: 0.7903 (tmm) REVERT: A 366 MET cc_start: 0.8302 (mtp) cc_final: 0.8029 (mtp) REVERT: A 443 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7734 (tp30) REVERT: A 511 MET cc_start: 0.8132 (tmm) cc_final: 0.7763 (tmm) REVERT: A 532 ILE cc_start: 0.8179 (mm) cc_final: 0.7854 (mt) REVERT: A 588 LYS cc_start: 0.8010 (ttpp) cc_final: 0.7770 (ttpp) REVERT: A 633 LYS cc_start: 0.8405 (mttt) cc_final: 0.8146 (mmtm) REVERT: A 634 SER cc_start: 0.8085 (m) cc_final: 0.7779 (p) REVERT: A 643 TRP cc_start: 0.7630 (t60) cc_final: 0.7328 (t-100) REVERT: A 646 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7448 (ttp-170) REVERT: A 684 ILE cc_start: 0.7312 (mm) cc_final: 0.6896 (pt) REVERT: A 697 MET cc_start: 0.5646 (tpp) cc_final: 0.5365 (tpp) REVERT: A 812 ARG cc_start: 0.7805 (ptm160) cc_final: 0.7519 (ptm160) REVERT: A 841 LYS cc_start: 0.8046 (tptt) cc_final: 0.7752 (mptt) REVERT: A 876 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 900 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7452 (mp10) REVERT: A 974 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8018 (mtpp) REVERT: A 1102 LEU cc_start: 0.8241 (mt) cc_final: 0.8024 (mp) REVERT: A 1107 MET cc_start: 0.7411 (mtm) cc_final: 0.7113 (mtp) REVERT: A 1110 GLN cc_start: 0.8058 (mp10) cc_final: 0.7602 (mp10) REVERT: A 1118 LYS cc_start: 0.4575 (tmtt) cc_final: 0.2576 (mttm) REVERT: A 1122 GLU cc_start: 0.6887 (tt0) cc_final: 0.5805 (tt0) REVERT: A 1123 ARG cc_start: 0.7765 (mmt180) cc_final: 0.6830 (mmt-90) REVERT: A 1143 GLU cc_start: 0.7011 (tt0) cc_final: 0.6745 (mt-10) REVERT: A 1182 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6352 (mp0) REVERT: A 1186 LEU cc_start: 0.8774 (tp) cc_final: 0.8552 (tp) outliers start: 33 outliers final: 25 residues processed: 237 average time/residue: 0.2200 time to fit residues: 68.8043 Evaluate side-chains 248 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1063 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 87 optimal weight: 0.0470 chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118492 restraints weight = 11784.637| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.83 r_work: 0.3312 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8300 Z= 0.122 Angle : 0.505 8.644 11258 Z= 0.263 Chirality : 0.039 0.232 1354 Planarity : 0.004 0.064 1379 Dihedral : 9.647 175.130 1127 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.17 % Allowed : 17.89 % Favored : 78.94 % 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: 2.24 (0.26), residues: 1015 helix: 1.98 (0.19), residues: 731 sheet: 0.73 (0.71), residues: 53 loop : 0.17 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 278 HIS 0.004 0.001 HIS A1120 PHE 0.011 0.001 PHE A 972 TYR 0.008 0.001 TYR A 309 ARG 0.004 0.000 ARG A1169 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 578) hydrogen bonds : angle 3.98602 ( 1704) covalent geometry : bond 0.00269 ( 8300) covalent geometry : angle 0.50514 (11258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8086 (mm) cc_final: 0.7794 (mt) REVERT: A 120 VAL cc_start: 0.8025 (t) cc_final: 0.7550 (p) REVERT: A 124 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 155 ASP cc_start: 0.8363 (t0) cc_final: 0.8106 (t0) REVERT: A 161 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7696 (mtt180) REVERT: A 187 ASN cc_start: 0.7887 (m-40) cc_final: 0.7496 (m-40) REVERT: A 355 MET cc_start: 0.8463 (tmm) cc_final: 0.7932 (tmm) REVERT: A 366 MET cc_start: 0.8279 (mtp) cc_final: 0.8003 (mtp) REVERT: A 443 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7721 (tp30) REVERT: A 474 ILE cc_start: 0.8357 (tp) cc_final: 0.8145 (tt) REVERT: A 511 MET cc_start: 0.8128 (tmm) cc_final: 0.7755 (tmm) REVERT: A 532 ILE cc_start: 0.8181 (mm) cc_final: 0.7945 (mt) REVERT: A 586 MET cc_start: 0.7574 (ttm) cc_final: 0.7349 (ttp) REVERT: A 588 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7751 (ttpp) REVERT: A 633 LYS cc_start: 0.8368 (mttt) cc_final: 0.8137 (mmtm) REVERT: A 634 SER cc_start: 0.8064 (m) cc_final: 0.7798 (p) REVERT: A 643 TRP cc_start: 0.7594 (t60) cc_final: 0.7284 (t-100) REVERT: A 646 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7451 (ttp-170) REVERT: A 684 ILE cc_start: 0.7264 (mm) cc_final: 0.6851 (pt) REVERT: A 697 MET cc_start: 0.5666 (tpp) cc_final: 0.5396 (tpp) REVERT: A 841 LYS cc_start: 0.7868 (tptt) cc_final: 0.7543 (mptt) REVERT: A 900 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7452 (mp10) REVERT: A 931 GLU cc_start: 0.8079 (tt0) cc_final: 0.7787 (mt-10) REVERT: A 974 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8004 (mtpp) REVERT: A 1007 LYS cc_start: 0.8126 (tttt) cc_final: 0.7841 (tttt) REVERT: A 1033 GLU cc_start: 0.7583 (tt0) cc_final: 0.7351 (tp30) REVERT: A 1110 GLN cc_start: 0.8083 (mp10) cc_final: 0.7616 (mp10) REVERT: A 1118 LYS cc_start: 0.4524 (tmtt) cc_final: 0.2555 (mttm) REVERT: A 1122 GLU cc_start: 0.6850 (tt0) cc_final: 0.5799 (tt0) REVERT: A 1143 GLU cc_start: 0.7031 (tt0) cc_final: 0.6710 (mt-10) outliers start: 28 outliers final: 23 residues processed: 238 average time/residue: 0.2196 time to fit residues: 68.8462 Evaluate side-chains 240 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1063 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 35 optimal weight: 0.0030 chunk 75 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.146695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120206 restraints weight = 11888.543| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.79 r_work: 0.3304 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8300 Z= 0.116 Angle : 0.511 8.926 11258 Z= 0.265 Chirality : 0.039 0.229 1354 Planarity : 0.004 0.058 1379 Dihedral : 9.632 175.523 1127 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.40 % Allowed : 17.89 % Favored : 78.71 % 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: 2.37 (0.26), residues: 1015 helix: 2.07 (0.19), residues: 730 sheet: 0.74 (0.70), residues: 55 loop : 0.28 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 278 HIS 0.004 0.001 HIS A1120 PHE 0.009 0.001 PHE A 201 TYR 0.008 0.001 TYR A 309 ARG 0.004 0.000 ARG A1169 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 578) hydrogen bonds : angle 3.93372 ( 1704) covalent geometry : bond 0.00255 ( 8300) covalent geometry : angle 0.51064 (11258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8091 (mm) cc_final: 0.7804 (mt) REVERT: A 120 VAL cc_start: 0.8003 (t) cc_final: 0.7438 (p) REVERT: A 124 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 140 GLN cc_start: 0.8243 (mp-120) cc_final: 0.7819 (mp10) REVERT: A 155 ASP cc_start: 0.8344 (t0) cc_final: 0.8040 (t0) REVERT: A 161 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7768 (mtt180) REVERT: A 187 ASN cc_start: 0.7874 (m-40) cc_final: 0.7488 (m-40) REVERT: A 355 MET cc_start: 0.8447 (tmm) cc_final: 0.7933 (tmm) REVERT: A 366 MET cc_start: 0.8273 (mtp) cc_final: 0.7994 (mtp) REVERT: A 443 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7710 (tp30) REVERT: A 450 VAL cc_start: 0.8346 (m) cc_final: 0.8109 (p) REVERT: A 511 MET cc_start: 0.8133 (tmm) cc_final: 0.7759 (tmm) REVERT: A 588 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7737 (ttpp) REVERT: A 633 LYS cc_start: 0.8354 (mttt) cc_final: 0.8121 (mmtm) REVERT: A 634 SER cc_start: 0.8067 (m) cc_final: 0.7801 (p) REVERT: A 643 TRP cc_start: 0.7595 (t60) cc_final: 0.7321 (t-100) REVERT: A 646 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7481 (ttp-170) REVERT: A 684 ILE cc_start: 0.7258 (mm) cc_final: 0.6832 (pt) REVERT: A 697 MET cc_start: 0.5706 (tpp) cc_final: 0.5443 (tpp) REVERT: A 841 LYS cc_start: 0.7887 (tptt) cc_final: 0.7554 (mptt) REVERT: A 850 VAL cc_start: 0.8673 (t) cc_final: 0.8368 (m) REVERT: A 877 GLN cc_start: 0.8623 (tt0) cc_final: 0.8196 (tt0) REVERT: A 900 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7458 (mp10) REVERT: A 931 GLU cc_start: 0.8082 (tt0) cc_final: 0.7777 (mt-10) REVERT: A 974 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7994 (mtpp) REVERT: A 1007 LYS cc_start: 0.8124 (tttt) cc_final: 0.7831 (tttt) REVERT: A 1033 GLU cc_start: 0.7546 (tt0) cc_final: 0.7338 (tp30) REVERT: A 1104 MET cc_start: 0.7735 (mmm) cc_final: 0.7499 (tpt) REVERT: A 1118 LYS cc_start: 0.4544 (tmtt) cc_final: 0.2539 (mttm) REVERT: A 1122 GLU cc_start: 0.6976 (tt0) cc_final: 0.6027 (tt0) REVERT: A 1123 ARG cc_start: 0.7671 (mmt180) cc_final: 0.6773 (mmt-90) REVERT: A 1143 GLU cc_start: 0.7002 (tt0) cc_final: 0.6633 (tt0) outliers start: 30 outliers final: 25 residues processed: 234 average time/residue: 0.2278 time to fit residues: 70.2491 Evaluate side-chains 245 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1063 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118013 restraints weight = 11983.284| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.82 r_work: 0.3296 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8300 Z= 0.147 Angle : 0.526 9.187 11258 Z= 0.273 Chirality : 0.040 0.239 1354 Planarity : 0.004 0.055 1379 Dihedral : 9.643 175.164 1127 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.17 % Allowed : 17.89 % Favored : 78.94 % 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: 2.31 (0.26), residues: 1015 helix: 2.01 (0.19), residues: 730 sheet: 0.95 (0.71), residues: 53 loop : 0.20 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 278 HIS 0.003 0.001 HIS A1120 PHE 0.015 0.001 PHE A 972 TYR 0.011 0.001 TYR A 309 ARG 0.004 0.000 ARG A1169 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 578) hydrogen bonds : angle 3.98238 ( 1704) covalent geometry : bond 0.00336 ( 8300) covalent geometry : angle 0.52599 (11258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.834 Fit side-chains REVERT: A 108 ILE cc_start: 0.8100 (mm) cc_final: 0.7814 (mt) REVERT: A 120 VAL cc_start: 0.8013 (t) cc_final: 0.7525 (p) REVERT: A 124 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 140 GLN cc_start: 0.8286 (mp-120) cc_final: 0.7972 (mp10) REVERT: A 155 ASP cc_start: 0.8355 (t0) cc_final: 0.8007 (t0) REVERT: A 161 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7769 (mtt180) REVERT: A 187 ASN cc_start: 0.7863 (m-40) cc_final: 0.7481 (m-40) REVERT: A 355 MET cc_start: 0.8463 (tmm) cc_final: 0.7903 (tmm) REVERT: A 366 MET cc_start: 0.8302 (mtp) cc_final: 0.8034 (mtp) REVERT: A 443 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7728 (tp30) REVERT: A 450 VAL cc_start: 0.8378 (m) cc_final: 0.8124 (p) REVERT: A 511 MET cc_start: 0.8177 (tmm) cc_final: 0.7788 (tmm) REVERT: A 588 LYS cc_start: 0.8014 (ttpp) cc_final: 0.7752 (ttpp) REVERT: A 633 LYS cc_start: 0.8357 (mttt) cc_final: 0.8125 (mmtm) REVERT: A 634 SER cc_start: 0.8059 (m) cc_final: 0.7804 (p) REVERT: A 643 TRP cc_start: 0.7630 (t60) cc_final: 0.7289 (t-100) REVERT: A 684 ILE cc_start: 0.7268 (mm) cc_final: 0.6848 (pt) REVERT: A 697 MET cc_start: 0.5714 (tpp) cc_final: 0.5470 (tpp) REVERT: A 877 GLN cc_start: 0.8627 (tt0) cc_final: 0.8174 (tt0) REVERT: A 900 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7458 (mp10) REVERT: A 931 GLU cc_start: 0.8077 (tt0) cc_final: 0.7756 (mt-10) REVERT: A 974 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7998 (mtpp) REVERT: A 986 GLU cc_start: 0.6905 (tp30) cc_final: 0.6639 (tm-30) REVERT: A 1007 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7805 (tttt) REVERT: A 1118 LYS cc_start: 0.4085 (tmtt) cc_final: 0.2390 (mttm) REVERT: A 1122 GLU cc_start: 0.7031 (tt0) cc_final: 0.6590 (mt-10) REVERT: A 1123 ARG cc_start: 0.7733 (mmt180) cc_final: 0.6970 (mmt-90) REVERT: A 1143 GLU cc_start: 0.6971 (tt0) cc_final: 0.6485 (mt-10) REVERT: A 1182 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6313 (mp0) outliers start: 28 outliers final: 27 residues processed: 232 average time/residue: 0.2240 time to fit residues: 68.1616 Evaluate side-chains 244 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1063 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119396 restraints weight = 11733.468| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.80 r_work: 0.3299 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8300 Z= 0.144 Angle : 0.525 8.889 11258 Z= 0.273 Chirality : 0.040 0.240 1354 Planarity : 0.004 0.054 1379 Dihedral : 9.638 174.703 1127 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.17 % Allowed : 17.67 % Favored : 79.16 % 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: 2.27 (0.26), residues: 1015 helix: 1.98 (0.19), residues: 730 sheet: 0.91 (0.70), residues: 53 loop : 0.22 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 278 HIS 0.003 0.001 HIS A1120 PHE 0.014 0.001 PHE A 163 TYR 0.011 0.001 TYR A 309 ARG 0.004 0.000 ARG A1169 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 578) hydrogen bonds : angle 3.99457 ( 1704) covalent geometry : bond 0.00330 ( 8300) covalent geometry : angle 0.52532 (11258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8091 (mm) cc_final: 0.7815 (mt) REVERT: A 120 VAL cc_start: 0.8018 (t) cc_final: 0.7536 (p) REVERT: A 124 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7340 (mt-10) REVERT: A 140 GLN cc_start: 0.8306 (mp-120) cc_final: 0.7969 (mp10) REVERT: A 155 ASP cc_start: 0.8356 (t0) cc_final: 0.8004 (t0) REVERT: A 161 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7737 (mtt180) REVERT: A 187 ASN cc_start: 0.7854 (m-40) cc_final: 0.7475 (m-40) REVERT: A 355 MET cc_start: 0.8456 (tmm) cc_final: 0.7898 (tmm) REVERT: A 366 MET cc_start: 0.8310 (mtp) cc_final: 0.8041 (mtp) REVERT: A 443 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7686 (tp30) REVERT: A 450 VAL cc_start: 0.8367 (m) cc_final: 0.8116 (p) REVERT: A 474 ILE cc_start: 0.8365 (tp) cc_final: 0.8155 (tt) REVERT: A 511 MET cc_start: 0.8163 (tmm) cc_final: 0.7781 (tmm) REVERT: A 588 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7768 (ttpp) REVERT: A 629 ASP cc_start: 0.7894 (p0) cc_final: 0.7646 (m-30) REVERT: A 633 LYS cc_start: 0.8333 (mttt) cc_final: 0.8123 (mmtm) REVERT: A 634 SER cc_start: 0.8097 (m) cc_final: 0.7790 (p) REVERT: A 643 TRP cc_start: 0.7592 (t60) cc_final: 0.7260 (t-100) REVERT: A 684 ILE cc_start: 0.7262 (mm) cc_final: 0.6849 (pt) REVERT: A 697 MET cc_start: 0.5751 (tpp) cc_final: 0.5522 (tpp) REVERT: A 900 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7442 (mp10) REVERT: A 931 GLU cc_start: 0.8084 (tt0) cc_final: 0.7758 (mt-10) REVERT: A 974 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8013 (mtpp) REVERT: A 986 GLU cc_start: 0.6914 (tp30) cc_final: 0.6627 (tm-30) REVERT: A 1007 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7779 (tttt) REVERT: A 1118 LYS cc_start: 0.4079 (tmtt) cc_final: 0.2196 (mttm) REVERT: A 1122 GLU cc_start: 0.7000 (tt0) cc_final: 0.6071 (tt0) REVERT: A 1143 GLU cc_start: 0.6949 (tt0) cc_final: 0.6433 (tt0) REVERT: A 1182 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6329 (mp0) outliers start: 28 outliers final: 25 residues processed: 231 average time/residue: 0.2216 time to fit residues: 67.0585 Evaluate side-chains 240 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1063 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.0060 chunk 60 optimal weight: 2.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 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 = 0.3828 r_free = 0.3828 target = 0.147234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120418 restraints weight = 11868.922| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.81 r_work: 0.3313 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8300 Z= 0.114 Angle : 0.510 8.828 11258 Z= 0.264 Chirality : 0.039 0.230 1354 Planarity : 0.004 0.071 1379 Dihedral : 9.622 174.979 1127 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.06 % Allowed : 17.89 % Favored : 79.05 % 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: 2.43 (0.26), residues: 1015 helix: 2.10 (0.19), residues: 731 sheet: 0.76 (0.69), residues: 55 loop : 0.32 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 278 HIS 0.004 0.001 HIS A1120 PHE 0.036 0.001 PHE A 163 TYR 0.007 0.001 TYR A 309 ARG 0.004 0.000 ARG A1169 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 578) hydrogen bonds : angle 3.90922 ( 1704) covalent geometry : bond 0.00254 ( 8300) covalent geometry : angle 0.50993 (11258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4895.37 seconds wall clock time: 85 minutes 8.39 seconds (5108.39 seconds total)