Starting phenix.real_space_refine on Thu Mar 13 02:50:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f42_50181/03_2025/9f42_50181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f42_50181/03_2025/9f42_50181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f42_50181/03_2025/9f42_50181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f42_50181/03_2025/9f42_50181.map" model { file = "/net/cci-nas-00/data/ceres_data/9f42_50181/03_2025/9f42_50181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f42_50181/03_2025/9f42_50181.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5413 2.51 5 N 1462 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8465 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 6.92, per 1000 atoms: 0.82 Number of scatterers: 8465 At special positions: 0 Unit cell: (103.49, 144.1, 82.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1533 8.00 N 1462 7.00 C 5413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 923.5 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 47.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'E' and resid 19 through 25 removed outlier: 4.112A pdb=" N ASP E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 94 through 112 Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 179 through 186 Processing helix chain 'E' and resid 198 through 219 removed outlier: 3.581A pdb=" N ILE E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 269 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 287 removed outlier: 6.452A pdb=" N CYS E 283 " --> pdb=" O MET E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 307 through 328 Processing helix chain 'E' and resid 329 through 338 removed outlier: 3.649A pdb=" N ARG E 338 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 removed outlier: 3.868A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 392 removed outlier: 3.676A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN E 392 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 398 Processing helix chain 'E' and resid 407 through 422 removed outlier: 3.887A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.754A pdb=" N LEU E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER E 442 " --> pdb=" O GLN E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 458 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 480 through 482 No H-bonds generated for 'chain 'E' and resid 480 through 482' Processing helix chain 'E' and resid 486 through 502 removed outlier: 4.809A pdb=" N LEU E 490 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 512 removed outlier: 4.564A pdb=" N ASP E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 523 removed outlier: 4.038A pdb=" N TYR E 517 " --> pdb=" O ASN E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 557 through 565 Processing helix chain 'E' and resid 570 through 585 removed outlier: 3.538A pdb=" N TRP E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 598 Processing helix chain 'E' and resid 599 through 605 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'E' and resid 612 through 628 Processing helix chain 'E' and resid 634 through 649 Processing helix chain 'E' and resid 656 through 674 Processing helix chain 'E' and resid 674 through 685 removed outlier: 3.758A pdb=" N PHE E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 820 Processing helix chain 'E' and resid 823 through 839 removed outlier: 3.522A pdb=" N ILE E 837 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR E 839 " --> pdb=" O ASN E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 958 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 982 through 1008 Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 123 removed outlier: 7.548A pdb=" N VAL E 58 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS E 120 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL E 60 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER E 122 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU E 62 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG E 145 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER E 59 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL E 146 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL E 193 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE E 148 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP E 195 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR E 150 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 163 through 167 Processing sheet with id=AA3, first strand: chain 'E' and resid 1015 through 1016 removed outlier: 3.929A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER E1329 " --> pdb=" O ASP E1015 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E1306 " --> pdb=" O GLY E1319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 3.626A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE E1046 " --> pdb=" O TYR E1059 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR E1059 " --> pdb=" O ILE E1046 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE E1048 " --> pdb=" O LEU E1057 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 1070 through 1076 removed outlier: 4.091A pdb=" N ALA E1092 " --> pdb=" O THR E1088 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE E1093 " --> pdb=" O ALA E1111 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA E1111 " --> pdb=" O ILE E1093 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E1095 " --> pdb=" O VAL E1109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 1127 through 1131 removed outlier: 5.019A pdb=" N GLY E1142 " --> pdb=" O ILE E1146 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE E1146 " --> pdb=" O GLY E1142 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL E1147 " --> pdb=" O ASP E1160 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP E1160 " --> pdb=" O VAL E1147 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE E1149 " --> pdb=" O VAL E1158 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET E1156 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 1169 through 1173 removed outlier: 6.846A pdb=" N ILE E1190 " --> pdb=" O THR E1206 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR E1206 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E1192 " --> pdb=" O VAL E1204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 1214 through 1218 removed outlier: 7.124A pdb=" N VAL E1230 " --> pdb=" O VAL E1215 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA E1217 " --> pdb=" O VAL E1228 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL E1228 " --> pdb=" O ALA E1217 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER E1231 " --> pdb=" O ASP E1235 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP E1235 " --> pdb=" O SER E1231 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP E1240 " --> pdb=" O SER E1246 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER E1246 " --> pdb=" O ASP E1240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 1259 through 1260 removed outlier: 3.721A pdb=" N ASN E1288 " --> pdb=" O ILE E1279 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2763 1.34 - 1.46: 1717 1.46 - 1.58: 4101 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 8666 Sorted by residual: bond pdb=" C SER E 188 " pdb=" N PRO E 189 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.57e-01 bond pdb=" CA ILE E1304 " pdb=" CB ILE E1304 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.33e-01 bond pdb=" C PHE G 401 " pdb=" N PHE G 402 " ideal model delta sigma weight residual 1.333 1.344 -0.011 1.30e-02 5.92e+03 7.18e-01 bond pdb=" N CYS E 81 " pdb=" CA CYS E 81 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.75e-01 bond pdb=" CG1 ILE E 319 " pdb=" CD1 ILE E 319 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.25e-01 ... (remaining 8661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11628 1.55 - 3.11: 125 3.11 - 4.66: 24 4.66 - 6.22: 9 6.22 - 7.77: 1 Bond angle restraints: 11787 Sorted by residual: angle pdb=" C PRO E 80 " pdb=" N CYS E 81 " pdb=" CA CYS E 81 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.57e+00 angle pdb=" CA LEU E 390 " pdb=" CB LEU E 390 " pdb=" CG LEU E 390 " ideal model delta sigma weight residual 116.30 124.07 -7.77 3.50e+00 8.16e-02 4.93e+00 angle pdb=" C CYS E 81 " pdb=" CA CYS E 81 " pdb=" CB CYS E 81 " ideal model delta sigma weight residual 110.42 114.56 -4.14 1.99e+00 2.53e-01 4.34e+00 angle pdb=" CA LEU E1013 " pdb=" CB LEU E1013 " pdb=" CG LEU E1013 " ideal model delta sigma weight residual 116.30 122.29 -5.99 3.50e+00 8.16e-02 2.93e+00 angle pdb=" CA TRP E 576 " pdb=" CB TRP E 576 " pdb=" CG TRP E 576 " ideal model delta sigma weight residual 113.60 110.41 3.19 1.90e+00 2.77e-01 2.82e+00 ... (remaining 11782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 4815 16.78 - 33.55: 290 33.55 - 50.33: 76 50.33 - 67.10: 17 67.10 - 83.88: 7 Dihedral angle restraints: 5205 sinusoidal: 2092 harmonic: 3113 Sorted by residual: dihedral pdb=" CA PHE E1060 " pdb=" C PHE E1060 " pdb=" N HIS E1061 " pdb=" CA HIS E1061 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASN E1022 " pdb=" CB ASN E1022 " pdb=" CG ASN E1022 " pdb=" OD1 ASN E1022 " ideal model delta sinusoidal sigma weight residual -90.00 -155.06 65.06 2 2.00e+01 2.50e-03 9.87e+00 dihedral pdb=" CB GLU E 675 " pdb=" CG GLU E 675 " pdb=" CD GLU E 675 " pdb=" OE1 GLU E 675 " ideal model delta sinusoidal sigma weight residual 0.00 -83.88 83.88 1 3.00e+01 1.11e-03 9.53e+00 ... (remaining 5202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 763 0.026 - 0.052: 340 0.052 - 0.077: 125 0.077 - 0.103: 61 0.103 - 0.129: 43 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA ILE E1279 " pdb=" N ILE E1279 " pdb=" C ILE E1279 " pdb=" CB ILE E1279 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE E 974 " pdb=" N ILE E 974 " pdb=" C ILE E 974 " pdb=" CB ILE E 974 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE E1190 " pdb=" N ILE E1190 " pdb=" C ILE E1190 " pdb=" CB ILE E1190 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1329 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 298 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO E 299 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 299 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 299 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E1313 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO E1314 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E1314 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E1314 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E1161 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO E1162 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO E1162 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E1162 " -0.015 5.00e-02 4.00e+02 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 394 2.73 - 3.27: 8616 3.27 - 3.82: 14326 3.82 - 4.36: 16867 4.36 - 4.90: 29330 Nonbonded interactions: 69533 Sorted by model distance: nonbonded pdb=" OG1 THR E1088 " pdb=" OD1 ASP E1090 " model vdw 2.189 3.040 nonbonded pdb=" NH2 ARG E 660 " pdb=" O ALA E1111 " model vdw 2.196 3.120 nonbonded pdb=" O VAL E 418 " pdb=" OG1 THR E 421 " model vdw 2.228 3.040 nonbonded pdb=" NH1 ARG E 50 " pdb=" OD2 ASP E 508 " model vdw 2.290 3.120 nonbonded pdb=" O LEU E 267 " pdb=" ND2 ASN E 349 " model vdw 2.341 3.120 ... (remaining 69528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 59.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.002 0.028 8666 Z= 0.147 Angle : 0.479 7.774 11787 Z= 0.244 Chirality : 0.040 0.129 1332 Planarity : 0.004 0.038 1503 Dihedral : 12.229 83.878 3175 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 7.90 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 1047 helix: 1.75 (0.24), residues: 464 sheet: -1.24 (0.41), residues: 160 loop : -0.84 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 576 HIS 0.003 0.001 HIS E 531 PHE 0.008 0.001 PHE E 518 TYR 0.011 0.001 TYR E 517 ARG 0.009 0.000 ARG G 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.893 Fit side-chains REVERT: E 24 TRP cc_start: 0.8192 (m100) cc_final: 0.7908 (m100) REVERT: E 97 LYS cc_start: 0.7945 (tptp) cc_final: 0.6645 (mttp) REVERT: E 100 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7016 (tp30) REVERT: E 140 ASN cc_start: 0.7453 (t0) cc_final: 0.7076 (m110) REVERT: E 185 TRP cc_start: 0.6298 (m-10) cc_final: 0.5835 (m-10) REVERT: E 254 MET cc_start: 0.6905 (tpt) cc_final: 0.6332 (ttt) REVERT: E 301 ARG cc_start: 0.7539 (ptp-170) cc_final: 0.7311 (mtm110) REVERT: E 311 GLU cc_start: 0.7235 (tp30) cc_final: 0.7030 (tp30) REVERT: E 390 LEU cc_start: 0.8195 (pp) cc_final: 0.7494 (mt) REVERT: E 396 ILE cc_start: 0.7753 (mm) cc_final: 0.7546 (mt) REVERT: E 479 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8185 (mt) REVERT: E 503 SER cc_start: 0.8851 (p) cc_final: 0.8540 (t) REVERT: E 828 ASP cc_start: 0.7239 (m-30) cc_final: 0.6728 (m-30) REVERT: E 992 PHE cc_start: 0.8036 (m-10) cc_final: 0.7798 (m-80) REVERT: E 1243 MET cc_start: 0.6475 (tpp) cc_final: 0.6255 (tpp) outliers start: 17 outliers final: 4 residues processed: 174 average time/residue: 0.2580 time to fit residues: 61.5547 Evaluate side-chains 135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 527 MET Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1207 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 0.0470 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 GLN E 105 ASN E 153 HIS E 405 HIS ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1003 GLN ** E1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.205980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.171452 restraints weight = 9384.229| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.31 r_work: 0.3679 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8666 Z= 0.224 Angle : 0.553 15.047 11787 Z= 0.276 Chirality : 0.044 0.144 1332 Planarity : 0.004 0.041 1503 Dihedral : 5.132 55.110 1155 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.99 % Allowed : 10.03 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1047 helix: 1.57 (0.24), residues: 472 sheet: -1.51 (0.40), residues: 158 loop : -0.92 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E1049 HIS 0.004 0.001 HIS E 531 PHE 0.010 0.002 PHE E 518 TYR 0.018 0.001 TYR E 475 ARG 0.011 0.000 ARG E1237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.862 Fit side-chains REVERT: E 97 LYS cc_start: 0.7856 (tptp) cc_final: 0.6815 (mttp) REVERT: E 100 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6991 (tp30) REVERT: E 128 ASP cc_start: 0.7247 (m-30) cc_final: 0.6903 (p0) REVERT: E 140 ASN cc_start: 0.7454 (t0) cc_final: 0.7157 (m110) REVERT: E 164 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7545 (m) REVERT: E 182 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7768 (tt) REVERT: E 186 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6301 (mmt) REVERT: E 204 LYS cc_start: 0.7263 (mptt) cc_final: 0.6843 (tmmt) REVERT: E 254 MET cc_start: 0.7300 (tpt) cc_final: 0.6644 (ttt) REVERT: E 281 GLN cc_start: 0.7962 (mm110) cc_final: 0.7735 (mm-40) REVERT: E 390 LEU cc_start: 0.8140 (pp) cc_final: 0.7613 (mt) REVERT: E 479 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7971 (mt) REVERT: E 483 SER cc_start: 0.8291 (m) cc_final: 0.8005 (p) REVERT: E 503 SER cc_start: 0.8917 (p) cc_final: 0.8639 (t) REVERT: E 557 ASN cc_start: 0.6625 (t0) cc_final: 0.6288 (t0) REVERT: E 828 ASP cc_start: 0.7108 (m-30) cc_final: 0.6534 (m-30) REVERT: E 992 PHE cc_start: 0.8080 (m-10) cc_final: 0.7863 (m-80) REVERT: E 1004 GLN cc_start: 0.7004 (mt0) cc_final: 0.6676 (mt0) REVERT: E 1022 ASN cc_start: 0.2328 (OUTLIER) cc_final: 0.1986 (m-40) REVERT: E 1073 MET cc_start: 0.8200 (mtp) cc_final: 0.7357 (ttm) REVERT: E 1154 ARG cc_start: 0.7234 (mtp-110) cc_final: 0.6932 (mtp-110) REVERT: E 1238 ILE cc_start: 0.5026 (mt) cc_final: 0.4775 (mm) REVERT: E 1243 MET cc_start: 0.6714 (tpp) cc_final: 0.6329 (tpp) REVERT: G 405 ASP cc_start: 0.8814 (m-30) cc_final: 0.8569 (m-30) outliers start: 28 outliers final: 18 residues processed: 176 average time/residue: 0.2200 time to fit residues: 52.8769 Evaluate side-chains 165 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 527 MET Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1025 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1141 SER Chi-restraints excluded: chain E residue 1146 ILE Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1306 CYS Chi-restraints excluded: chain E residue 1330 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 69 optimal weight: 0.0570 chunk 57 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 32 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN E 405 HIS ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1003 GLN ** E1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.204654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.169700 restraints weight = 9516.576| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.41 r_work: 0.3656 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8666 Z= 0.199 Angle : 0.515 10.354 11787 Z= 0.258 Chirality : 0.043 0.139 1332 Planarity : 0.004 0.042 1503 Dihedral : 5.020 55.619 1155 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.95 % Allowed : 11.31 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1047 helix: 1.62 (0.24), residues: 473 sheet: -1.43 (0.40), residues: 158 loop : -0.90 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E1049 HIS 0.004 0.001 HIS E 531 PHE 0.009 0.001 PHE E 588 TYR 0.014 0.001 TYR E 475 ARG 0.004 0.000 ARG E1203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.590 Fit side-chains REVERT: E 64 LEU cc_start: 0.7960 (mp) cc_final: 0.7700 (mp) REVERT: E 97 LYS cc_start: 0.7893 (tptp) cc_final: 0.6889 (mttp) REVERT: E 100 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6976 (tp30) REVERT: E 128 ASP cc_start: 0.7243 (m-30) cc_final: 0.6889 (p0) REVERT: E 140 ASN cc_start: 0.7453 (t0) cc_final: 0.7205 (m110) REVERT: E 164 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7222 (p) REVERT: E 182 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7796 (tt) REVERT: E 186 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6500 (mmt) REVERT: E 204 LYS cc_start: 0.7217 (mptt) cc_final: 0.6933 (tmmt) REVERT: E 254 MET cc_start: 0.7416 (tpt) cc_final: 0.6758 (ttt) REVERT: E 375 MET cc_start: 0.8598 (pmm) cc_final: 0.7713 (pmm) REVERT: E 390 LEU cc_start: 0.8106 (pp) cc_final: 0.7611 (mt) REVERT: E 479 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8111 (mt) REVERT: E 483 SER cc_start: 0.8292 (m) cc_final: 0.7974 (p) REVERT: E 503 SER cc_start: 0.8864 (p) cc_final: 0.8614 (t) REVERT: E 557 ASN cc_start: 0.6974 (t0) cc_final: 0.6403 (t0) REVERT: E 565 GLN cc_start: 0.7025 (mt0) cc_final: 0.6716 (mt0) REVERT: E 603 LYS cc_start: 0.7650 (ttmt) cc_final: 0.7319 (mtpt) REVERT: E 641 ASP cc_start: 0.6847 (m-30) cc_final: 0.6060 (m-30) REVERT: E 828 ASP cc_start: 0.7147 (m-30) cc_final: 0.6641 (m-30) REVERT: E 992 PHE cc_start: 0.8075 (m-10) cc_final: 0.7840 (m-80) REVERT: E 993 LEU cc_start: 0.8220 (mp) cc_final: 0.7864 (mp) REVERT: E 1022 ASN cc_start: 0.2030 (OUTLIER) cc_final: 0.1580 (m-40) REVERT: E 1145 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7821 (mmt180) REVERT: E 1154 ARG cc_start: 0.7333 (mtp-110) cc_final: 0.7000 (mtp-110) REVERT: E 1190 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7014 (mt) REVERT: E 1243 MET cc_start: 0.6875 (tpp) cc_final: 0.6443 (tpp) REVERT: G 403 MET cc_start: 0.8707 (ttm) cc_final: 0.8192 (ttm) outliers start: 37 outliers final: 20 residues processed: 170 average time/residue: 0.2675 time to fit residues: 62.9740 Evaluate side-chains 169 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 527 MET Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 673 GLN Chi-restraints excluded: chain E residue 839 TYR Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1025 VAL Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1146 ILE Chi-restraints excluded: chain E residue 1190 ILE Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1306 CYS Chi-restraints excluded: chain E residue 1330 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 93 optimal weight: 0.1980 chunk 88 optimal weight: 0.0040 chunk 92 optimal weight: 0.2980 chunk 103 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 overall best weight: 0.1770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN E 405 HIS E 956 GLN ** E1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.204701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.169943 restraints weight = 9474.421| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.39 r_work: 0.3660 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8666 Z= 0.167 Angle : 0.491 8.436 11787 Z= 0.246 Chirality : 0.042 0.137 1332 Planarity : 0.004 0.040 1503 Dihedral : 4.826 48.234 1155 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.74 % Allowed : 12.17 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1047 helix: 1.77 (0.24), residues: 471 sheet: -1.31 (0.42), residues: 157 loop : -0.88 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E1049 HIS 0.003 0.001 HIS E 531 PHE 0.009 0.001 PHE E 588 TYR 0.014 0.001 TYR E 475 ARG 0.003 0.000 ARG E 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.803 Fit side-chains REVERT: E 64 LEU cc_start: 0.8027 (mp) cc_final: 0.7800 (mp) REVERT: E 97 LYS cc_start: 0.7941 (tptp) cc_final: 0.6917 (mttp) REVERT: E 100 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6955 (tp30) REVERT: E 128 ASP cc_start: 0.7305 (m-30) cc_final: 0.6916 (p0) REVERT: E 182 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7815 (tt) REVERT: E 186 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6542 (mmt) REVERT: E 204 LYS cc_start: 0.7574 (mptt) cc_final: 0.7259 (tmmt) REVERT: E 254 MET cc_start: 0.7622 (tpt) cc_final: 0.7010 (ttt) REVERT: E 301 ARG cc_start: 0.8002 (ptp90) cc_final: 0.7775 (ptp90) REVERT: E 390 LEU cc_start: 0.7960 (pp) cc_final: 0.7622 (mt) REVERT: E 397 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7959 (mp) REVERT: E 479 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8087 (mt) REVERT: E 483 SER cc_start: 0.8143 (m) cc_final: 0.7830 (p) REVERT: E 503 SER cc_start: 0.8838 (p) cc_final: 0.8619 (t) REVERT: E 641 ASP cc_start: 0.6958 (m-30) cc_final: 0.6154 (m-30) REVERT: E 828 ASP cc_start: 0.7206 (m-30) cc_final: 0.6703 (m-30) REVERT: E 992 PHE cc_start: 0.7981 (m-10) cc_final: 0.7738 (m-80) REVERT: E 993 LEU cc_start: 0.8140 (mp) cc_final: 0.7728 (mp) REVERT: E 1022 ASN cc_start: 0.2052 (OUTLIER) cc_final: 0.1613 (m-40) REVERT: E 1243 MET cc_start: 0.6803 (tpp) cc_final: 0.6457 (tpp) outliers start: 35 outliers final: 22 residues processed: 160 average time/residue: 0.2136 time to fit residues: 46.5272 Evaluate side-chains 164 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 673 GLN Chi-restraints excluded: chain E residue 956 GLN Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1141 SER Chi-restraints excluded: chain E residue 1146 ILE Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1306 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 85 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 GLN E 105 ASN E 405 HIS E 565 GLN E 956 GLN E1233 ASN E1312 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.194409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.159760 restraints weight = 9434.701| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.36 r_work: 0.3551 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8666 Z= 0.329 Angle : 0.585 8.553 11787 Z= 0.299 Chirality : 0.046 0.199 1332 Planarity : 0.005 0.041 1503 Dihedral : 5.046 56.741 1152 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.38 % Allowed : 11.63 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 1047 helix: 1.54 (0.24), residues: 469 sheet: -1.66 (0.40), residues: 156 loop : -0.96 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E1049 HIS 0.004 0.001 HIS E 531 PHE 0.015 0.002 PHE E1048 TYR 0.012 0.002 TYR E 475 ARG 0.006 0.001 ARG E 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.854 Fit side-chains REVERT: E 64 LEU cc_start: 0.8138 (mp) cc_final: 0.7907 (mp) REVERT: E 97 LYS cc_start: 0.8060 (tptp) cc_final: 0.7114 (mttp) REVERT: E 100 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7035 (tp30) REVERT: E 128 ASP cc_start: 0.7441 (m-30) cc_final: 0.7076 (p0) REVERT: E 139 ARG cc_start: 0.6620 (mtm-85) cc_final: 0.6131 (ttp-110) REVERT: E 182 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7708 (tp) REVERT: E 186 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7145 (mmt) REVERT: E 254 MET cc_start: 0.7892 (tpt) cc_final: 0.7336 (ttt) REVERT: E 389 CYS cc_start: 0.7915 (t) cc_final: 0.6502 (m) REVERT: E 390 LEU cc_start: 0.7966 (pp) cc_final: 0.7550 (mt) REVERT: E 479 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8261 (mt) REVERT: E 483 SER cc_start: 0.8358 (m) cc_final: 0.8064 (p) REVERT: E 503 SER cc_start: 0.9009 (p) cc_final: 0.8791 (t) REVERT: E 557 ASN cc_start: 0.6873 (t0) cc_final: 0.6352 (t0) REVERT: E 565 GLN cc_start: 0.7179 (mt0) cc_final: 0.6947 (mt0) REVERT: E 603 LYS cc_start: 0.8254 (ttmt) cc_final: 0.8014 (mtpt) REVERT: E 641 ASP cc_start: 0.7250 (m-30) cc_final: 0.6469 (m-30) REVERT: E 828 ASP cc_start: 0.7293 (m-30) cc_final: 0.6808 (m-30) REVERT: E 965 ARG cc_start: 0.8732 (ttm170) cc_final: 0.8486 (ttm-80) REVERT: E 992 PHE cc_start: 0.8073 (m-10) cc_final: 0.7859 (m-80) REVERT: E 1022 ASN cc_start: 0.2823 (OUTLIER) cc_final: 0.2333 (m-40) REVERT: E 1144 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7856 (m) REVERT: E 1193 TYR cc_start: 0.6739 (m-80) cc_final: 0.6333 (m-80) REVERT: E 1243 MET cc_start: 0.6556 (tpp) cc_final: 0.6262 (tpp) REVERT: G 403 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8292 (ttm) outliers start: 41 outliers final: 24 residues processed: 179 average time/residue: 0.2144 time to fit residues: 52.1429 Evaluate side-chains 173 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 673 GLN Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1042 ASP Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1141 SER Chi-restraints excluded: chain E residue 1144 VAL Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1306 CYS Chi-restraints excluded: chain E residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 85 optimal weight: 0.0870 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 15 optimal weight: 0.0000 chunk 61 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 overall best weight: 0.0898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN E 161 ASN E 405 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.199486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.164750 restraints weight = 9381.903| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.38 r_work: 0.3605 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8666 Z= 0.151 Angle : 0.501 7.959 11787 Z= 0.252 Chirality : 0.042 0.154 1332 Planarity : 0.004 0.039 1503 Dihedral : 4.859 57.294 1152 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.06 % Allowed : 12.70 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1047 helix: 1.77 (0.24), residues: 470 sheet: -1.74 (0.39), residues: 162 loop : -0.86 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E1049 HIS 0.003 0.001 HIS E 515 PHE 0.009 0.001 PHE E 588 TYR 0.014 0.001 TYR E 475 ARG 0.006 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.997 Fit side-chains REVERT: E 64 LEU cc_start: 0.8075 (mp) cc_final: 0.7866 (mp) REVERT: E 97 LYS cc_start: 0.8051 (tptp) cc_final: 0.7100 (mttp) REVERT: E 100 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7059 (tp30) REVERT: E 128 ASP cc_start: 0.7342 (m-30) cc_final: 0.7041 (p0) REVERT: E 139 ARG cc_start: 0.6549 (mtm-85) cc_final: 0.6127 (ttp-110) REVERT: E 182 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7621 (tp) REVERT: E 185 TRP cc_start: 0.7406 (m-10) cc_final: 0.7066 (m-10) REVERT: E 186 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6840 (mmt) REVERT: E 390 LEU cc_start: 0.7860 (pp) cc_final: 0.7502 (mt) REVERT: E 479 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8138 (mt) REVERT: E 483 SER cc_start: 0.8238 (m) cc_final: 0.7961 (p) REVERT: E 503 SER cc_start: 0.8944 (p) cc_final: 0.8729 (t) REVERT: E 565 GLN cc_start: 0.6909 (mt0) cc_final: 0.6669 (mt0) REVERT: E 598 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: E 828 ASP cc_start: 0.7305 (m-30) cc_final: 0.6815 (m-30) REVERT: E 965 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8411 (ttm-80) REVERT: E 992 PHE cc_start: 0.8048 (m-10) cc_final: 0.7831 (m-80) REVERT: E 1022 ASN cc_start: 0.2413 (OUTLIER) cc_final: 0.1954 (m-40) REVERT: E 1052 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6510 (mm-30) REVERT: E 1127 MET cc_start: 0.8152 (ttt) cc_final: 0.7834 (ttt) REVERT: E 1144 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.7990 (p) REVERT: E 1243 MET cc_start: 0.6660 (tpp) cc_final: 0.6293 (tpp) REVERT: E 1306 CYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6283 (p) REVERT: G 403 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8426 (ttm) outliers start: 38 outliers final: 20 residues processed: 167 average time/residue: 0.2071 time to fit residues: 47.5682 Evaluate side-chains 159 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 646 MET Chi-restraints excluded: chain E residue 673 GLN Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1144 VAL Chi-restraints excluded: chain E residue 1146 ILE Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1306 CYS Chi-restraints excluded: chain E residue 1309 PHE Chi-restraints excluded: chain E residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN E 405 HIS E 956 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.195922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.161105 restraints weight = 9475.505| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.39 r_work: 0.3562 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8666 Z= 0.216 Angle : 0.537 12.921 11787 Z= 0.265 Chirality : 0.043 0.140 1332 Planarity : 0.004 0.041 1503 Dihedral : 4.836 56.943 1152 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.95 % Allowed : 13.98 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.27), residues: 1047 helix: 1.78 (0.24), residues: 468 sheet: -1.95 (0.38), residues: 166 loop : -0.79 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E1049 HIS 0.003 0.001 HIS E 531 PHE 0.011 0.001 PHE E1048 TYR 0.012 0.001 TYR E 475 ARG 0.004 0.000 ARG E1203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.914 Fit side-chains REVERT: E 64 LEU cc_start: 0.8105 (mp) cc_final: 0.7902 (mp) REVERT: E 97 LYS cc_start: 0.8013 (tptp) cc_final: 0.7061 (mttp) REVERT: E 100 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7079 (tp30) REVERT: E 128 ASP cc_start: 0.7317 (m-30) cc_final: 0.6947 (p0) REVERT: E 139 ARG cc_start: 0.6743 (mtm-85) cc_final: 0.6133 (ttp-110) REVERT: E 182 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7684 (tp) REVERT: E 186 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7029 (mmt) REVERT: E 375 MET cc_start: 0.8538 (pmm) cc_final: 0.7766 (pmm) REVERT: E 390 LEU cc_start: 0.7862 (pp) cc_final: 0.7519 (mt) REVERT: E 479 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8206 (mt) REVERT: E 483 SER cc_start: 0.8246 (m) cc_final: 0.7990 (p) REVERT: E 503 SER cc_start: 0.8987 (p) cc_final: 0.8752 (t) REVERT: E 598 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: E 828 ASP cc_start: 0.7318 (m-30) cc_final: 0.6861 (m-30) REVERT: E 965 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8415 (ttm-80) REVERT: E 979 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6166 (m-30) REVERT: E 1022 ASN cc_start: 0.2517 (OUTLIER) cc_final: 0.1937 (m-40) REVERT: E 1052 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6351 (mm-30) REVERT: E 1127 MET cc_start: 0.8164 (ttt) cc_final: 0.7910 (ttt) REVERT: E 1132 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7466 (mt-10) REVERT: E 1144 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8124 (p) REVERT: E 1243 MET cc_start: 0.6694 (tpp) cc_final: 0.6307 (tpp) REVERT: E 1256 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6490 (tt) REVERT: E 1306 CYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6580 (p) REVERT: G 403 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8369 (ttm) outliers start: 37 outliers final: 22 residues processed: 159 average time/residue: 0.1956 time to fit residues: 43.4641 Evaluate side-chains 165 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 673 GLN Chi-restraints excluded: chain E residue 956 GLN Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1141 SER Chi-restraints excluded: chain E residue 1144 VAL Chi-restraints excluded: chain E residue 1190 ILE Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1256 LEU Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1306 CYS Chi-restraints excluded: chain E residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN E 405 HIS E 565 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.195264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.160586 restraints weight = 9516.416| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.39 r_work: 0.3557 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8666 Z= 0.225 Angle : 0.538 11.700 11787 Z= 0.265 Chirality : 0.043 0.139 1332 Planarity : 0.004 0.041 1503 Dihedral : 4.829 53.982 1152 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.95 % Allowed : 14.09 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.27), residues: 1047 helix: 1.77 (0.24), residues: 468 sheet: -1.91 (0.40), residues: 157 loop : -0.86 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E1049 HIS 0.004 0.001 HIS E 531 PHE 0.009 0.001 PHE E 350 TYR 0.013 0.001 TYR E 475 ARG 0.007 0.000 ARG E 985 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.863 Fit side-chains REVERT: E 97 LYS cc_start: 0.8028 (tptp) cc_final: 0.7064 (mttm) REVERT: E 100 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7100 (tp30) REVERT: E 128 ASP cc_start: 0.7299 (m-30) cc_final: 0.6945 (p0) REVERT: E 139 ARG cc_start: 0.6776 (mtm-85) cc_final: 0.6164 (ttp-110) REVERT: E 143 GLU cc_start: 0.6975 (pm20) cc_final: 0.6708 (pm20) REVERT: E 182 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7673 (tp) REVERT: E 186 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7208 (mmt) REVERT: E 375 MET cc_start: 0.8533 (pmm) cc_final: 0.7762 (pmm) REVERT: E 390 LEU cc_start: 0.7872 (pp) cc_final: 0.7535 (mt) REVERT: E 479 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8209 (mt) REVERT: E 483 SER cc_start: 0.8260 (m) cc_final: 0.8005 (p) REVERT: E 503 SER cc_start: 0.8997 (p) cc_final: 0.8750 (t) REVERT: E 598 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: E 658 MET cc_start: 0.8393 (ptp) cc_final: 0.8144 (ptp) REVERT: E 673 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6405 (tp40) REVERT: E 828 ASP cc_start: 0.7362 (m-30) cc_final: 0.6877 (m-30) REVERT: E 965 ARG cc_start: 0.8654 (ttm170) cc_final: 0.8422 (ttm-80) REVERT: E 1022 ASN cc_start: 0.2457 (OUTLIER) cc_final: 0.1907 (m-40) REVERT: E 1052 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6421 (mm-30) REVERT: E 1127 MET cc_start: 0.8184 (ttt) cc_final: 0.7900 (ttt) REVERT: E 1144 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8143 (p) REVERT: E 1243 MET cc_start: 0.6340 (tpp) cc_final: 0.6038 (tpp) REVERT: E 1306 CYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6607 (p) REVERT: G 403 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8376 (ttm) outliers start: 37 outliers final: 26 residues processed: 161 average time/residue: 0.2002 time to fit residues: 45.0540 Evaluate side-chains 169 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 673 GLN Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1141 SER Chi-restraints excluded: chain E residue 1144 VAL Chi-restraints excluded: chain E residue 1146 ILE Chi-restraints excluded: chain E residue 1190 ILE Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1306 CYS Chi-restraints excluded: chain E residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 17 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 12 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN E 565 GLN E 956 GLN 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 = 0.170218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136641 restraints weight = 9661.974| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.28 r_work: 0.3344 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8666 Z= 0.297 Angle : 0.574 11.520 11787 Z= 0.285 Chirality : 0.044 0.140 1332 Planarity : 0.004 0.040 1503 Dihedral : 4.904 47.710 1152 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.06 % Allowed : 14.51 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1047 helix: 1.65 (0.24), residues: 462 sheet: -2.12 (0.37), residues: 172 loop : -0.82 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E1049 HIS 0.004 0.001 HIS E 531 PHE 0.012 0.002 PHE E1048 TYR 0.013 0.002 TYR E 475 ARG 0.007 0.000 ARG E 985 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.928 Fit side-chains REVERT: E 97 LYS cc_start: 0.7972 (tptp) cc_final: 0.6999 (mttm) REVERT: E 100 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7104 (tp30) REVERT: E 105 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7706 (m-40) REVERT: E 139 ARG cc_start: 0.6612 (mtm-85) cc_final: 0.6111 (ttp-110) REVERT: E 143 GLU cc_start: 0.6968 (pm20) cc_final: 0.6736 (pm20) REVERT: E 182 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7707 (tp) REVERT: E 186 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7316 (mmt) REVERT: E 375 MET cc_start: 0.8454 (pmm) cc_final: 0.7684 (pmm) REVERT: E 390 LEU cc_start: 0.7890 (pp) cc_final: 0.7521 (mt) REVERT: E 479 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8128 (mt) REVERT: E 483 SER cc_start: 0.8261 (m) cc_final: 0.7989 (p) REVERT: E 503 SER cc_start: 0.8967 (p) cc_final: 0.8670 (t) REVERT: E 593 TRP cc_start: 0.6858 (m-10) cc_final: 0.6371 (m-10) REVERT: E 598 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: E 658 MET cc_start: 0.8337 (ptp) cc_final: 0.8114 (ptp) REVERT: E 828 ASP cc_start: 0.7343 (m-30) cc_final: 0.6842 (m-30) REVERT: E 965 ARG cc_start: 0.8578 (ttm170) cc_final: 0.8336 (ttm-80) REVERT: E 1022 ASN cc_start: 0.2686 (OUTLIER) cc_final: 0.2152 (m-40) REVERT: E 1052 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6337 (mm-30) REVERT: E 1127 MET cc_start: 0.8260 (ttt) cc_final: 0.7940 (ttt) REVERT: E 1144 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8153 (p) REVERT: E 1243 MET cc_start: 0.6344 (tpp) cc_final: 0.6021 (tpp) REVERT: E 1306 CYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6765 (p) REVERT: G 403 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8278 (ttm) outliers start: 38 outliers final: 27 residues processed: 153 average time/residue: 0.2124 time to fit residues: 44.8207 Evaluate side-chains 166 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 673 GLN Chi-restraints excluded: chain E residue 956 GLN Chi-restraints excluded: chain E residue 980 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1141 SER Chi-restraints excluded: chain E residue 1144 VAL Chi-restraints excluded: chain E residue 1146 ILE Chi-restraints excluded: chain E residue 1190 ILE Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1306 CYS Chi-restraints excluded: chain E residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 0.0970 chunk 36 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN E 956 GLN ** E1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.170863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.137015 restraints weight = 9423.526| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.30 r_work: 0.3354 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8666 Z= 0.236 Angle : 0.553 11.165 11787 Z= 0.276 Chirality : 0.043 0.139 1332 Planarity : 0.004 0.041 1503 Dihedral : 4.846 45.497 1152 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.16 % Allowed : 14.41 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 1047 helix: 1.69 (0.24), residues: 462 sheet: -2.12 (0.37), residues: 173 loop : -0.87 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP E1049 HIS 0.003 0.001 HIS E 531 PHE 0.010 0.001 PHE E1048 TYR 0.016 0.001 TYR E 839 ARG 0.008 0.000 ARG E1203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.945 Fit side-chains REVERT: E 97 LYS cc_start: 0.7959 (tptp) cc_final: 0.7023 (mttp) REVERT: E 100 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7081 (tp30) REVERT: E 139 ARG cc_start: 0.6556 (mtm-85) cc_final: 0.6077 (ttp-110) REVERT: E 143 GLU cc_start: 0.6980 (pm20) cc_final: 0.6756 (pm20) REVERT: E 182 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7773 (tp) REVERT: E 186 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7294 (mmt) REVERT: E 375 MET cc_start: 0.8437 (pmm) cc_final: 0.7668 (pmm) REVERT: E 378 MET cc_start: 0.8174 (tpp) cc_final: 0.7646 (tpp) REVERT: E 390 LEU cc_start: 0.7842 (pp) cc_final: 0.7458 (mt) REVERT: E 479 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8124 (mt) REVERT: E 483 SER cc_start: 0.8262 (m) cc_final: 0.7998 (p) REVERT: E 503 SER cc_start: 0.9008 (p) cc_final: 0.8689 (t) REVERT: E 593 TRP cc_start: 0.6845 (m-10) cc_final: 0.6380 (m-10) REVERT: E 598 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: E 658 MET cc_start: 0.8348 (ptp) cc_final: 0.8134 (ptp) REVERT: E 673 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6488 (tp40) REVERT: E 828 ASP cc_start: 0.7330 (m-30) cc_final: 0.6844 (m-30) REVERT: E 965 ARG cc_start: 0.8551 (ttm170) cc_final: 0.8321 (ttm-80) REVERT: E 1022 ASN cc_start: 0.2714 (OUTLIER) cc_final: 0.2161 (m-40) REVERT: E 1052 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6315 (mm-30) REVERT: E 1127 MET cc_start: 0.8230 (ttt) cc_final: 0.7896 (ttt) REVERT: E 1144 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8231 (p) REVERT: E 1243 MET cc_start: 0.6229 (tpp) cc_final: 0.5919 (tpp) REVERT: G 403 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8248 (ttm) outliers start: 39 outliers final: 24 residues processed: 157 average time/residue: 0.2147 time to fit residues: 46.4742 Evaluate side-chains 162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain E residue 673 GLN Chi-restraints excluded: chain E residue 980 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1051 TRP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1141 SER Chi-restraints excluded: chain E residue 1144 VAL Chi-restraints excluded: chain E residue 1146 ILE Chi-restraints excluded: chain E residue 1190 ILE Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain E residue 1259 LEU Chi-restraints excluded: chain E residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 0.4980 chunk 86 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 3 optimal weight: 0.0000 chunk 62 optimal weight: 0.1980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 565 GLN ** E1159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.168408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.134694 restraints weight = 9630.539| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.31 r_work: 0.3403 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8666 Z= 0.265 Angle : 0.567 10.988 11787 Z= 0.283 Chirality : 0.044 0.149 1332 Planarity : 0.004 0.039 1503 Dihedral : 4.887 45.337 1152 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.20 % Allowed : 15.37 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1047 helix: 1.67 (0.24), residues: 463 sheet: -2.21 (0.36), residues: 168 loop : -0.88 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E1049 HIS 0.004 0.001 HIS E 531 PHE 0.013 0.001 PHE E1048 TYR 0.014 0.002 TYR E 475 ARG 0.008 0.001 ARG E1203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4592.85 seconds wall clock time: 81 minutes 28.52 seconds (4888.52 seconds total)