Starting phenix.real_space_refine on Fri Oct 10 17:53:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdv_17622/10_2025/8pdv_17622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdv_17622/10_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_17622/10_2025/8pdv_17622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdv_17622/10_2025/8pdv_17622.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdv_17622/10_2025/8pdv_17622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdv_17622/10_2025/8pdv_17622.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.85, per 1000 atoms: 0.23 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: 0.81 Conformation dependent library (CDL) restraints added in 256.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.17 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: 1.17 Time building geometry restraints manager: 1.03 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.610 ------------------------------------------------------------------------------- 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 : 3.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 733 TYR 0.010 0.001 TYR A 309 PHE 0.017 0.001 PHE A 201 TRP 0.009 0.001 TRP A 278 HIS 0.002 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8300) covalent geometry : angle 0.59426 (11258) hydrogen bonds : bond 0.18955 ( 578) hydrogen bonds : angle 6.74787 ( 1704) *********************** 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 : 0.342 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: 0.6680 (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: 0.6829 (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: 0.7358 (ttp-170) REVERT: A 647 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7425 (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: 0.8093 (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: 0.7374 (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: 0.7297 (m-80) REVERT: A 1003 SER cc_start: 0.8647 (t) cc_final: 0.8265 (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: 0.6621 (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: 0.6627 (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: 0.0981 time to fit residues: 33.9791 Evaluate side-chains 223 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.143812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117523 restraints weight = 12061.536| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.81 r_work: 0.3308 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8300 Z= 0.130 Angle : 0.533 8.000 11258 Z= 0.281 Chirality : 0.040 0.178 1354 Planarity : 0.004 0.049 1379 Dihedral : 9.635 168.177 1127 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.81 % Allowed : 11.44 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.27), residues: 1015 helix: 1.87 (0.19), residues: 731 sheet: 0.61 (0.69), residues: 51 loop : 0.51 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1169 TYR 0.015 0.001 TYR A 743 PHE 0.012 0.001 PHE A 352 TRP 0.014 0.001 TRP A 278 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8300) covalent geometry : angle 0.53349 (11258) hydrogen bonds : bond 0.05051 ( 578) hydrogen bonds : angle 4.46061 ( 1704) *********************** 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 242 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 84 SER cc_start: 0.8357 (p) cc_final: 0.7992 (t) REVERT: A 124 GLU cc_start: 0.7790 (tt0) cc_final: 0.7352 (tp30) REVERT: A 169 LEU cc_start: 0.8525 (tp) cc_final: 0.8301 (tp) REVERT: A 187 ASN cc_start: 0.7875 (m-40) cc_final: 0.7468 (m-40) REVERT: A 344 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7938 (mm-30) REVERT: A 354 GLU cc_start: 0.8343 (tt0) cc_final: 0.8015 (mt-10) REVERT: A 355 MET cc_start: 0.8376 (tmm) cc_final: 0.7818 (tmm) REVERT: A 371 VAL cc_start: 0.8511 (p) cc_final: 0.8304 (t) REVERT: A 383 MET cc_start: 0.8408 (mmm) cc_final: 0.8123 (mmm) REVERT: A 443 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7707 (tp30) REVERT: A 503 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 511 MET cc_start: 0.8262 (tmm) cc_final: 0.7908 (tmm) REVERT: A 579 MET cc_start: 0.6986 (tpt) cc_final: 0.6759 (tpt) REVERT: A 588 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7677 (ttpp) REVERT: A 628 VAL cc_start: 0.7848 (m) cc_final: 0.7525 (t) REVERT: A 629 ASP cc_start: 0.7881 (p0) cc_final: 0.7638 (p0) REVERT: A 633 LYS cc_start: 0.8397 (mttt) cc_final: 0.8146 (mmtm) REVERT: A 634 SER cc_start: 0.8145 (m) cc_final: 0.7805 (p) REVERT: A 646 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.7616 (ttp-170) REVERT: A 684 ILE cc_start: 0.7327 (mm) cc_final: 0.6984 (pt) REVERT: A 697 MET cc_start: 0.5556 (tpp) cc_final: 0.5183 (tpp) REVERT: A 847 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7226 (mm-30) REVERT: A 853 ILE cc_start: 0.8001 (mt) cc_final: 0.7673 (tp) REVERT: A 862 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7682 (tppt) REVERT: A 866 GLU cc_start: 0.7453 (tp30) cc_final: 0.7087 (tp30) REVERT: A 870 ILE cc_start: 0.8481 (mt) cc_final: 0.7911 (mt) REVERT: A 876 LEU cc_start: 0.8564 (mt) cc_final: 0.8310 (mm) REVERT: A 900 GLN cc_start: 0.7763 (mm110) cc_final: 0.7525 (mm-40) REVERT: A 974 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8083 (mtpp) REVERT: A 1003 SER cc_start: 0.8870 (t) cc_final: 0.8652 (t) REVERT: A 1058 THR cc_start: 0.8400 (m) cc_final: 0.7978 (p) REVERT: A 1118 LYS cc_start: 0.5285 (tmtt) cc_final: 0.3226 (tppt) REVERT: A 1122 GLU cc_start: 0.7693 (tp30) cc_final: 0.7408 (tp30) REVERT: A 1143 GLU cc_start: 0.7107 (tt0) cc_final: 0.6699 (tt0) REVERT: A 1154 ASN cc_start: 0.7587 (t0) cc_final: 0.7108 (t0) REVERT: A 1182 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6343 (mp0) REVERT: A 1186 LEU cc_start: 0.8782 (tp) cc_final: 0.8565 (tp) outliers start: 16 outliers final: 6 residues processed: 233 average time/residue: 0.0982 time to fit residues: 30.1991 Evaluate side-chains 219 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 640 ILE 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 33 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 886 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117808 restraints weight = 11985.997| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.80 r_work: 0.3302 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2590 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= 0.156 Angle : 0.518 8.026 11258 Z= 0.271 Chirality : 0.039 0.204 1354 Planarity : 0.004 0.053 1379 Dihedral : 9.672 174.132 1127 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.04 % Allowed : 14.50 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.26), residues: 1015 helix: 1.87 (0.19), residues: 732 sheet: 0.81 (0.68), residues: 51 loop : 0.40 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1169 TYR 0.012 0.001 TYR A 309 PHE 0.016 0.002 PHE A1136 TRP 0.018 0.001 TRP A 278 HIS 0.004 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8300) covalent geometry : angle 0.51812 (11258) hydrogen bonds : bond 0.04779 ( 578) hydrogen bonds : angle 4.25206 ( 1704) *********************** 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 241 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8320 (p) cc_final: 0.7984 (t) REVERT: A 120 VAL cc_start: 0.8144 (t) cc_final: 0.7756 (p) REVERT: A 161 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7796 (mtt180) REVERT: A 187 ASN cc_start: 0.7931 (m-40) cc_final: 0.7514 (m-40) REVERT: A 256 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 354 GLU cc_start: 0.8331 (tt0) cc_final: 0.8009 (mt-10) REVERT: A 355 MET cc_start: 0.8465 (tmm) cc_final: 0.7864 (tmm) REVERT: A 383 MET cc_start: 0.8463 (mmm) cc_final: 0.8237 (mmm) REVERT: A 443 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7683 (tp30) REVERT: A 511 MET cc_start: 0.8229 (tmm) cc_final: 0.7859 (tmm) REVERT: A 531 GLU cc_start: 0.7327 (tp30) cc_final: 0.7098 (tp30) REVERT: A 532 ILE cc_start: 0.8187 (mm) cc_final: 0.7546 (mt) REVERT: A 588 LYS cc_start: 0.7924 (ttpp) cc_final: 0.7699 (ttpp) REVERT: A 628 VAL cc_start: 0.7873 (m) cc_final: 0.7667 (t) REVERT: A 629 ASP cc_start: 0.7904 (p0) cc_final: 0.7670 (p0) REVERT: A 633 LYS cc_start: 0.8399 (mttt) cc_final: 0.8149 (mmtm) REVERT: A 634 SER cc_start: 0.8118 (m) cc_final: 0.7816 (p) REVERT: A 646 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7607 (ttp-170) REVERT: A 684 ILE cc_start: 0.7405 (mm) cc_final: 0.6983 (pt) REVERT: A 697 MET cc_start: 0.5598 (tpp) cc_final: 0.5300 (tpp) REVERT: A 847 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 862 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7907 (tppt) REVERT: A 876 LEU cc_start: 0.8495 (mt) cc_final: 0.8290 (mm) REVERT: A 900 GLN cc_start: 0.7727 (mm110) cc_final: 0.7512 (mm-40) REVERT: A 974 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8078 (mtpp) REVERT: A 994 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6688 (tp30) REVERT: A 1003 SER cc_start: 0.8784 (t) cc_final: 0.8553 (t) REVERT: A 1033 GLU cc_start: 0.7522 (tt0) cc_final: 0.7240 (tt0) REVERT: A 1118 LYS cc_start: 0.5590 (tmtt) cc_final: 0.3256 (tppt) REVERT: A 1122 GLU cc_start: 0.7713 (tp30) cc_final: 0.7504 (tt0) REVERT: A 1154 ASN cc_start: 0.7509 (t0) cc_final: 0.7077 (t0) REVERT: A 1182 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6354 (mp0) REVERT: A 1186 LEU cc_start: 0.8770 (tp) cc_final: 0.8552 (tp) outliers start: 18 outliers final: 14 residues processed: 233 average time/residue: 0.1038 time to fit residues: 32.0513 Evaluate side-chains 234 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 186 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1002 VAL 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 52 optimal weight: 0.0070 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116920 restraints weight = 11980.793| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.82 r_work: 0.3304 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8300 Z= 0.145 Angle : 0.502 6.895 11258 Z= 0.264 Chirality : 0.039 0.219 1354 Planarity : 0.004 0.054 1379 Dihedral : 9.672 174.607 1127 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.28 % Allowed : 15.18 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.26), residues: 1015 helix: 1.88 (0.19), residues: 731 sheet: 1.01 (0.70), residues: 51 loop : 0.40 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1169 TYR 0.011 0.001 TYR A 309 PHE 0.015 0.001 PHE A 575 TRP 0.036 0.002 TRP A 643 HIS 0.005 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8300) covalent geometry : angle 0.50158 (11258) hydrogen bonds : bond 0.04386 ( 578) hydrogen bonds : angle 4.12354 ( 1704) *********************** 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 248 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 SER cc_start: 0.8280 (p) cc_final: 0.7943 (t) REVERT: A 108 ILE cc_start: 0.8151 (mm) cc_final: 0.7860 (mt) REVERT: A 120 VAL cc_start: 0.8104 (t) cc_final: 0.7750 (p) REVERT: A 124 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7384 (tp30) REVERT: A 160 MET cc_start: 0.8089 (mmm) cc_final: 0.7784 (mmm) REVERT: A 161 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7737 (mtt180) REVERT: A 187 ASN cc_start: 0.7902 (m-40) cc_final: 0.7511 (m-40) REVERT: A 354 GLU cc_start: 0.8334 (tt0) cc_final: 0.8098 (tt0) REVERT: A 355 MET cc_start: 0.8485 (tmm) cc_final: 0.7875 (tmm) REVERT: A 383 MET cc_start: 0.8515 (mmm) cc_final: 0.8251 (mmm) REVERT: A 443 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7637 (tp30) REVERT: A 511 MET cc_start: 0.8181 (tmm) cc_final: 0.7822 (tmm) REVERT: A 532 ILE cc_start: 0.8223 (mm) cc_final: 0.7487 (mt) REVERT: A 588 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7702 (ttpp) REVERT: A 628 VAL cc_start: 0.7899 (m) cc_final: 0.7677 (t) REVERT: A 633 LYS cc_start: 0.8389 (mttt) cc_final: 0.8141 (mmtm) REVERT: A 634 SER cc_start: 0.8122 (m) cc_final: 0.7823 (p) REVERT: A 646 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7477 (ttp-170) REVERT: A 684 ILE cc_start: 0.7397 (mm) cc_final: 0.6987 (pt) REVERT: A 697 MET cc_start: 0.5614 (tpp) cc_final: 0.5342 (tpp) REVERT: A 900 GLN cc_start: 0.7763 (mm110) cc_final: 0.7562 (mm-40) REVERT: A 974 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8023 (mtpp) REVERT: A 994 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6665 (tp30) REVERT: A 1003 SER cc_start: 0.8775 (t) cc_final: 0.8526 (t) REVERT: A 1033 GLU cc_start: 0.7506 (tt0) cc_final: 0.7166 (tt0) REVERT: A 1104 MET cc_start: 0.8017 (tpp) cc_final: 0.7664 (tpt) REVERT: A 1118 LYS cc_start: 0.5128 (tmtt) cc_final: 0.2816 (tppt) REVERT: A 1122 GLU cc_start: 0.7800 (tp30) cc_final: 0.7495 (tt0) REVERT: A 1182 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6283 (mp0) REVERT: A 1186 LEU cc_start: 0.8764 (tp) cc_final: 0.8510 (tp) outliers start: 29 outliers final: 22 residues processed: 232 average time/residue: 0.0949 time to fit residues: 29.2240 Evaluate side-chains 238 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 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 867 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 961 SER Chi-restraints excluded: chain A residue 1002 VAL 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 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.145182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118472 restraints weight = 11774.304| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.81 r_work: 0.3315 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3085 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= 0.121 Angle : 0.484 7.939 11258 Z= 0.254 Chirality : 0.039 0.224 1354 Planarity : 0.004 0.048 1379 Dihedral : 9.643 175.122 1127 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.62 % Allowed : 16.08 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.26), residues: 1015 helix: 2.00 (0.19), residues: 733 sheet: 1.21 (0.73), residues: 51 loop : 0.29 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1169 TYR 0.009 0.001 TYR A 309 PHE 0.011 0.001 PHE A 575 TRP 0.031 0.001 TRP A 643 HIS 0.004 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8300) covalent geometry : angle 0.48411 (11258) hydrogen bonds : bond 0.04028 ( 578) hydrogen bonds : angle 3.99092 ( 1704) *********************** 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 256 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8053 (t) cc_final: 0.7687 (p) REVERT: A 124 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7329 (tp30) REVERT: A 155 ASP cc_start: 0.8387 (t0) cc_final: 0.8094 (t0) REVERT: A 160 MET cc_start: 0.8089 (mmm) cc_final: 0.7774 (mmm) REVERT: A 161 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7739 (mtt180) REVERT: A 187 ASN cc_start: 0.7860 (m-40) cc_final: 0.7461 (m-40) REVERT: A 256 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 355 MET cc_start: 0.8454 (tmm) cc_final: 0.7918 (tmm) REVERT: A 366 MET cc_start: 0.8280 (mtp) cc_final: 0.7996 (mtp) REVERT: A 443 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7630 (tp30) REVERT: A 511 MET cc_start: 0.8145 (tmm) cc_final: 0.7759 (tmm) REVERT: A 532 ILE cc_start: 0.8158 (mm) cc_final: 0.7796 (mt) REVERT: A 588 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7763 (ttpp) REVERT: A 596 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8122 (ttmt) REVERT: A 633 LYS cc_start: 0.8364 (mttt) cc_final: 0.8110 (mmtm) REVERT: A 634 SER cc_start: 0.8114 (m) cc_final: 0.7772 (p) REVERT: A 646 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.7448 (ttp-170) REVERT: A 684 ILE cc_start: 0.7339 (mm) cc_final: 0.6937 (pt) REVERT: A 697 MET cc_start: 0.5614 (tpp) cc_final: 0.5344 (tpp) REVERT: A 812 ARG cc_start: 0.7732 (ptm160) cc_final: 0.7455 (ptm160) REVERT: A 847 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 876 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 900 GLN cc_start: 0.7736 (mm110) cc_final: 0.7533 (mm-40) REVERT: A 960 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8196 (t) REVERT: A 974 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8006 (mtpp) REVERT: A 1003 SER cc_start: 0.8773 (t) cc_final: 0.8549 (t) REVERT: A 1033 GLU cc_start: 0.7515 (tt0) cc_final: 0.7238 (tt0) REVERT: A 1110 GLN cc_start: 0.7876 (mp10) cc_final: 0.7408 (mp10) REVERT: A 1118 LYS cc_start: 0.4816 (tmtt) cc_final: 0.2810 (mttm) REVERT: A 1123 ARG cc_start: 0.7647 (mmt180) cc_final: 0.6985 (mmp-170) REVERT: A 1182 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6324 (mp0) REVERT: A 1186 LEU cc_start: 0.8765 (tp) cc_final: 0.8550 (tp) outliers start: 32 outliers final: 24 residues processed: 241 average time/residue: 0.0991 time to fit residues: 31.8344 Evaluate side-chains 242 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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 651 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 960 VAL 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 1063 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 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.143953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117231 restraints weight = 11697.683| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.78 r_work: 0.3290 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8300 Z= 0.209 Angle : 0.553 8.930 11258 Z= 0.284 Chirality : 0.042 0.238 1354 Planarity : 0.004 0.061 1379 Dihedral : 9.710 175.185 1127 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.85 % Allowed : 16.42 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.26), residues: 1015 helix: 1.77 (0.19), residues: 732 sheet: 1.18 (0.72), residues: 51 loop : 0.26 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1169 TYR 0.015 0.002 TYR A 309 PHE 0.017 0.002 PHE A 575 TRP 0.018 0.002 TRP A 278 HIS 0.005 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 8300) covalent geometry : angle 0.55311 (11258) hydrogen bonds : bond 0.04648 ( 578) hydrogen bonds : angle 4.17881 ( 1704) *********************** 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 260 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8152 (mm) cc_final: 0.7859 (mt) REVERT: A 120 VAL cc_start: 0.8118 (t) cc_final: 0.7764 (p) REVERT: A 124 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 155 ASP cc_start: 0.8346 (t0) cc_final: 0.8067 (t0) REVERT: A 161 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7710 (mtt180) REVERT: A 187 ASN cc_start: 0.7892 (m-40) cc_final: 0.7533 (m-40) REVERT: A 256 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 355 MET cc_start: 0.8494 (tmm) cc_final: 0.7879 (tmm) REVERT: A 366 MET cc_start: 0.8322 (mtp) cc_final: 0.8079 (mtp) REVERT: A 383 MET cc_start: 0.8372 (mmm) cc_final: 0.8140 (mmm) REVERT: A 443 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7776 (tp30) REVERT: A 511 MET cc_start: 0.8210 (tmm) cc_final: 0.7815 (tmm) REVERT: A 588 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7787 (ttpp) REVERT: A 596 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8116 (ttmt) REVERT: A 633 LYS cc_start: 0.8407 (mttt) cc_final: 0.8153 (mmtm) REVERT: A 634 SER cc_start: 0.8117 (m) cc_final: 0.7826 (p) REVERT: A 646 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7408 (ttp-170) REVERT: A 678 MET cc_start: 0.5781 (mmm) cc_final: 0.5309 (mmm) REVERT: A 684 ILE cc_start: 0.7369 (mm) cc_final: 0.6948 (pt) REVERT: A 697 MET cc_start: 0.5682 (tpp) cc_final: 0.5417 (tpp) REVERT: A 974 LYS cc_start: 0.8357 (ttmt) cc_final: 0.8016 (mtpp) REVERT: A 1003 SER cc_start: 0.8829 (t) cc_final: 0.8606 (t) REVERT: A 1033 GLU cc_start: 0.7496 (tt0) cc_final: 0.7284 (tt0) REVERT: A 1110 GLN cc_start: 0.8039 (mp10) cc_final: 0.7592 (mp10) REVERT: A 1118 LYS cc_start: 0.4361 (tmtt) cc_final: 0.2442 (mttm) REVERT: A 1122 GLU cc_start: 0.6250 (tt0) cc_final: 0.5907 (tt0) REVERT: A 1182 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6356 (mp0) REVERT: A 1186 LEU cc_start: 0.8788 (tp) cc_final: 0.8561 (tp) outliers start: 34 outliers final: 27 residues processed: 243 average time/residue: 0.0952 time to fit residues: 30.6709 Evaluate side-chains 245 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 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 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 1062 THR Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.144828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118225 restraints weight = 11833.401| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.80 r_work: 0.3307 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3329 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= 0.138 Angle : 0.522 8.415 11258 Z= 0.268 Chirality : 0.040 0.229 1354 Planarity : 0.004 0.052 1379 Dihedral : 9.655 174.289 1127 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.17 % Allowed : 18.01 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.26), residues: 1015 helix: 1.86 (0.19), residues: 734 sheet: 0.95 (0.69), residues: 53 loop : 0.23 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1169 TYR 0.010 0.001 TYR A 309 PHE 0.012 0.001 PHE A 575 TRP 0.035 0.002 TRP A 643 HIS 0.004 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8300) covalent geometry : angle 0.52207 (11258) hydrogen bonds : bond 0.04153 ( 578) hydrogen bonds : angle 4.05623 ( 1704) *********************** 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 247 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8116 (mm) cc_final: 0.7839 (mt) REVERT: A 120 VAL cc_start: 0.8073 (t) cc_final: 0.7710 (p) REVERT: A 124 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 155 ASP cc_start: 0.8298 (t0) cc_final: 0.7987 (t0) REVERT: A 161 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7745 (mtt180) REVERT: A 187 ASN cc_start: 0.7876 (m-40) cc_final: 0.7503 (m-40) REVERT: A 256 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 355 MET cc_start: 0.8476 (tmm) cc_final: 0.7882 (tmm) REVERT: A 366 MET cc_start: 0.8313 (mtp) cc_final: 0.8070 (mtp) REVERT: A 443 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7771 (tp30) REVERT: A 474 ILE cc_start: 0.8340 (tp) cc_final: 0.8116 (tt) REVERT: A 511 MET cc_start: 0.8152 (tmm) cc_final: 0.7765 (tmm) REVERT: A 588 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7743 (ttpp) REVERT: A 596 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8079 (ttmt) REVERT: A 633 LYS cc_start: 0.8367 (mttt) cc_final: 0.8136 (mmtm) REVERT: A 634 SER cc_start: 0.8113 (m) cc_final: 0.7817 (p) REVERT: A 646 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7426 (ttp-170) REVERT: A 684 ILE cc_start: 0.7314 (mm) cc_final: 0.6887 (pt) REVERT: A 697 MET cc_start: 0.5690 (tpp) cc_final: 0.5418 (tpp) REVERT: A 974 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8036 (mtpp) REVERT: A 994 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6734 (tp30) REVERT: A 1003 SER cc_start: 0.8897 (t) cc_final: 0.8632 (t) REVERT: A 1107 MET cc_start: 0.7118 (mtp) cc_final: 0.6865 (mtm) REVERT: A 1110 GLN cc_start: 0.8046 (mp10) cc_final: 0.7579 (mp10) REVERT: A 1118 LYS cc_start: 0.4347 (tmtt) cc_final: 0.2453 (mttm) REVERT: A 1123 ARG cc_start: 0.7777 (mmt180) cc_final: 0.7220 (mmp-170) REVERT: A 1143 GLU cc_start: 0.7007 (tt0) cc_final: 0.6653 (mt-10) outliers start: 28 outliers final: 23 residues processed: 231 average time/residue: 0.0982 time to fit residues: 30.0511 Evaluate side-chains 238 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 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 651 LEU Chi-restraints excluded: chain A residue 916 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 1062 THR 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 81 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.145620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118811 restraints weight = 11818.848| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.80 r_work: 0.3309 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8300 Z= 0.133 Angle : 0.510 6.962 11258 Z= 0.264 Chirality : 0.040 0.232 1354 Planarity : 0.004 0.051 1379 Dihedral : 9.645 174.860 1127 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.28 % Allowed : 18.23 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.26), residues: 1015 helix: 1.90 (0.19), residues: 733 sheet: 1.07 (0.70), residues: 53 loop : 0.29 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.010 0.001 TYR A 309 PHE 0.026 0.001 PHE A 163 TRP 0.016 0.001 TRP A 278 HIS 0.004 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8300) covalent geometry : angle 0.51030 (11258) hydrogen bonds : bond 0.04061 ( 578) hydrogen bonds : angle 4.00177 ( 1704) *********************** 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 248 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.320 Fit side-chains REVERT: A 108 ILE cc_start: 0.8087 (mm) cc_final: 0.7806 (mt) REVERT: A 120 VAL cc_start: 0.8080 (t) cc_final: 0.7722 (p) REVERT: A 124 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 140 GLN cc_start: 0.8217 (mp-120) cc_final: 0.7799 (mp10) REVERT: A 155 ASP cc_start: 0.8343 (t0) cc_final: 0.8104 (t0) REVERT: A 161 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7709 (mtt180) REVERT: A 187 ASN cc_start: 0.7861 (m-40) cc_final: 0.7495 (m-40) REVERT: A 256 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 355 MET cc_start: 0.8464 (tmm) cc_final: 0.7867 (tmm) REVERT: A 366 MET cc_start: 0.8324 (mtp) cc_final: 0.8067 (mtp) REVERT: A 443 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7740 (tp30) REVERT: A 450 VAL cc_start: 0.8388 (m) cc_final: 0.8141 (p) REVERT: A 474 ILE cc_start: 0.8354 (tp) cc_final: 0.8139 (tt) REVERT: A 511 MET cc_start: 0.8175 (tmm) cc_final: 0.7782 (tmm) REVERT: A 588 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7744 (ttpp) REVERT: A 633 LYS cc_start: 0.8339 (mttt) cc_final: 0.8105 (mmtm) REVERT: A 634 SER cc_start: 0.8111 (m) cc_final: 0.7802 (p) REVERT: A 646 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7443 (ttp-170) REVERT: A 684 ILE cc_start: 0.7297 (mm) cc_final: 0.6873 (pt) REVERT: A 697 MET cc_start: 0.5691 (tpp) cc_final: 0.5435 (tpp) REVERT: A 854 ILE cc_start: 0.7879 (pt) cc_final: 0.7628 (pt) REVERT: A 857 MET cc_start: 0.8145 (ptt) cc_final: 0.7832 (ppp) REVERT: A 931 GLU cc_start: 0.8107 (tt0) cc_final: 0.7783 (mt-10) REVERT: A 974 LYS cc_start: 0.8337 (ttmt) cc_final: 0.8039 (mtpp) REVERT: A 1003 SER cc_start: 0.8874 (t) cc_final: 0.8631 (t) REVERT: A 1118 LYS cc_start: 0.4236 (tmtt) cc_final: 0.2810 (mttm) REVERT: A 1122 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6070 (mt-10) REVERT: A 1143 GLU cc_start: 0.6985 (tt0) cc_final: 0.6577 (tt0) outliers start: 29 outliers final: 27 residues processed: 233 average time/residue: 0.0958 time to fit residues: 29.7616 Evaluate side-chains 243 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 377 LEU 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 629 ASP Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 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 1062 THR 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 4 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 65 optimal weight: 0.0060 chunk 97 optimal weight: 0.0040 chunk 89 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 overall best weight: 0.2408 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.147425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120530 restraints weight = 11671.437| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.80 r_work: 0.3319 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8300 Z= 0.107 Angle : 0.513 10.830 11258 Z= 0.265 Chirality : 0.039 0.230 1354 Planarity : 0.004 0.070 1379 Dihedral : 9.622 175.564 1127 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.83 % Allowed : 18.80 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.26), residues: 1015 helix: 2.07 (0.19), residues: 731 sheet: 0.84 (0.70), residues: 55 loop : 0.42 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1169 TYR 0.007 0.001 TYR A1066 PHE 0.031 0.001 PHE A 163 TRP 0.014 0.001 TRP A 278 HIS 0.004 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8300) covalent geometry : angle 0.51270 (11258) hydrogen bonds : bond 0.03677 ( 578) hydrogen bonds : angle 3.91778 ( 1704) *********************** 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 243 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.308 Fit side-chains REVERT: A 108 ILE cc_start: 0.8068 (mm) cc_final: 0.7796 (mt) REVERT: A 120 VAL cc_start: 0.8052 (t) cc_final: 0.7706 (p) REVERT: A 124 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 140 GLN cc_start: 0.8263 (mp-120) cc_final: 0.7921 (mp10) REVERT: A 155 ASP cc_start: 0.8346 (t0) cc_final: 0.8069 (t0) REVERT: A 161 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7712 (mtt180) REVERT: A 187 ASN cc_start: 0.7837 (m-40) cc_final: 0.7454 (m-40) REVERT: A 355 MET cc_start: 0.8421 (tmm) cc_final: 0.7928 (tmm) REVERT: A 366 MET cc_start: 0.8285 (mtp) cc_final: 0.8006 (mtt) REVERT: A 450 VAL cc_start: 0.8359 (m) cc_final: 0.8115 (p) REVERT: A 511 MET cc_start: 0.8159 (tmm) cc_final: 0.7765 (tmm) REVERT: A 588 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7753 (ttpp) REVERT: A 633 LYS cc_start: 0.8273 (mttt) cc_final: 0.8067 (mmtm) REVERT: A 634 SER cc_start: 0.8064 (m) cc_final: 0.7816 (p) REVERT: A 646 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7439 (ttp-170) REVERT: A 684 ILE cc_start: 0.7245 (mm) cc_final: 0.6829 (pt) REVERT: A 697 MET cc_start: 0.5708 (tpp) cc_final: 0.5456 (tpp) REVERT: A 812 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7356 (mtp85) REVERT: A 854 ILE cc_start: 0.7807 (pt) cc_final: 0.7572 (pt) REVERT: A 857 MET cc_start: 0.8133 (ptt) cc_final: 0.7817 (ppp) REVERT: A 900 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7480 (mp10) REVERT: A 931 GLU cc_start: 0.8087 (tt0) cc_final: 0.7768 (mt-10) REVERT: A 974 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8050 (mtpp) REVERT: A 1003 SER cc_start: 0.8855 (t) cc_final: 0.8589 (t) REVERT: A 1104 MET cc_start: 0.7737 (mmm) cc_final: 0.7485 (tpt) REVERT: A 1118 LYS cc_start: 0.4289 (tmtt) cc_final: 0.2734 (mttt) REVERT: A 1122 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5998 (mt-10) REVERT: A 1123 ARG cc_start: 0.7565 (mmt180) cc_final: 0.7355 (mmt180) REVERT: A 1143 GLU cc_start: 0.6941 (tt0) cc_final: 0.6539 (tt0) outliers start: 25 outliers final: 22 residues processed: 228 average time/residue: 0.0951 time to fit residues: 28.9265 Evaluate side-chains 236 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 377 LEU 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 916 LEU Chi-restraints excluded: chain A residue 921 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 1062 THR 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 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.145523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118925 restraints weight = 11748.166| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.82 r_work: 0.3317 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3558 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= 0.161 Angle : 0.548 9.789 11258 Z= 0.282 Chirality : 0.040 0.252 1354 Planarity : 0.004 0.067 1379 Dihedral : 9.646 175.666 1127 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.72 % Allowed : 19.14 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.26), residues: 1015 helix: 1.96 (0.19), residues: 730 sheet: 0.95 (0.71), residues: 53 loop : 0.36 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1169 TYR 0.014 0.001 TYR A 309 PHE 0.014 0.002 PHE A 163 TRP 0.032 0.002 TRP A 643 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8300) covalent geometry : angle 0.54832 (11258) hydrogen bonds : bond 0.04166 ( 578) hydrogen bonds : angle 4.01810 ( 1704) ********************** 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 242 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.310 Fit side-chains REVERT: A 108 ILE cc_start: 0.8077 (mm) cc_final: 0.7798 (mt) REVERT: A 120 VAL cc_start: 0.8075 (t) cc_final: 0.7733 (p) REVERT: A 124 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 140 GLN cc_start: 0.8230 (mp-120) cc_final: 0.7856 (mp10) REVERT: A 155 ASP cc_start: 0.8369 (t0) cc_final: 0.8058 (t0) REVERT: A 161 ARG cc_start: 0.7981 (mtm180) cc_final: 0.7725 (mtt180) REVERT: A 187 ASN cc_start: 0.7835 (m-40) cc_final: 0.7467 (m-40) REVERT: A 355 MET cc_start: 0.8432 (tmm) cc_final: 0.7856 (tmm) REVERT: A 366 MET cc_start: 0.8263 (mtp) cc_final: 0.7986 (mtt) REVERT: A 443 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7562 (tp30) REVERT: A 450 VAL cc_start: 0.8381 (m) cc_final: 0.8119 (p) REVERT: A 474 ILE cc_start: 0.8370 (tp) cc_final: 0.8142 (tt) REVERT: A 511 MET cc_start: 0.8168 (tmm) cc_final: 0.7764 (tmm) REVERT: A 588 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7814 (ttpp) REVERT: A 633 LYS cc_start: 0.8286 (mttt) cc_final: 0.8073 (mmtm) REVERT: A 634 SER cc_start: 0.8174 (m) cc_final: 0.7855 (p) REVERT: A 646 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7430 (ttp-170) REVERT: A 684 ILE cc_start: 0.7269 (mm) cc_final: 0.6861 (pt) REVERT: A 697 MET cc_start: 0.5730 (tpp) cc_final: 0.5502 (tpp) REVERT: A 812 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.7302 (ttm110) REVERT: A 854 ILE cc_start: 0.7816 (pt) cc_final: 0.7568 (pt) REVERT: A 857 MET cc_start: 0.8067 (ptt) cc_final: 0.7731 (ppp) REVERT: A 865 ARG cc_start: 0.6992 (tmm-80) cc_final: 0.6780 (tmm-80) REVERT: A 931 GLU cc_start: 0.8116 (tt0) cc_final: 0.7786 (mt-10) REVERT: A 974 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8074 (mtpp) REVERT: A 986 GLU cc_start: 0.6767 (tp30) cc_final: 0.6541 (tm-30) REVERT: A 1003 SER cc_start: 0.8884 (t) cc_final: 0.8636 (t) REVERT: A 1118 LYS cc_start: 0.3944 (tmtt) cc_final: 0.2619 (mttm) REVERT: A 1122 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6318 (mt-10) REVERT: A 1143 GLU cc_start: 0.6903 (tt0) cc_final: 0.6469 (mt-10) REVERT: A 1182 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6271 (mp0) outliers start: 24 outliers final: 23 residues processed: 229 average time/residue: 0.1013 time to fit residues: 30.8149 Evaluate side-chains 239 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 377 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 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 1062 THR 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 69 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119726 restraints weight = 11771.603| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.79 r_work: 0.3316 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8300 Z= 0.133 Angle : 0.523 9.877 11258 Z= 0.271 Chirality : 0.039 0.239 1354 Planarity : 0.004 0.065 1379 Dihedral : 9.624 174.857 1127 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.60 % Allowed : 18.80 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.26), residues: 1015 helix: 1.99 (0.19), residues: 730 sheet: 0.99 (0.71), residues: 53 loop : 0.37 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1169 TYR 0.010 0.001 TYR A 309 PHE 0.013 0.001 PHE A 972 TRP 0.025 0.002 TRP A 643 HIS 0.004 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8300) covalent geometry : angle 0.52253 (11258) hydrogen bonds : bond 0.03928 ( 578) hydrogen bonds : angle 3.96074 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.93 seconds wall clock time: 42 minutes 38.30 seconds (2558.30 seconds total)