Starting phenix.real_space_refine on Tue Feb 3 20:37:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kou_62480/02_2026/9kou_62480.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kou_62480/02_2026/9kou_62480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kou_62480/02_2026/9kou_62480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kou_62480/02_2026/9kou_62480.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kou_62480/02_2026/9kou_62480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kou_62480/02_2026/9kou_62480.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 56 5.16 5 C 4414 2.51 5 N 1068 2.21 5 O 1133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6672 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3331 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Chain: "B" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3336 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.29, per 1000 atoms: 0.19 Number of scatterers: 6672 At special positions: 0 Unit cell: (79.18, 68.48, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 1 15.00 O 1133 8.00 N 1068 7.00 C 4414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 163.0 milliseconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 22 through 45 removed outlier: 4.247A pdb=" N MET A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 Processing helix chain 'A' and resid 72 through 97 removed outlier: 4.990A pdb=" N ALA A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 122 removed outlier: 3.594A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 148 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.830A pdb=" N SER A 159 " --> pdb=" O THR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 175 through 199 removed outlier: 4.028A pdb=" N GLY A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 removed outlier: 5.253A pdb=" N TYR A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 removed outlier: 3.756A pdb=" N ALA A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 242 " --> pdb=" O TYR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 299 through 322 Processing helix chain 'A' and resid 341 through 359 Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.574A pdb=" N GLY A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 377 through 398 removed outlier: 3.540A pdb=" N GLN A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 405 through 422 removed outlier: 3.819A pdb=" N PHE A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 removed outlier: 5.251A pdb=" N THR A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE A 429 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.675A pdb=" N ASN A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 494 removed outlier: 4.060A pdb=" N PHE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 44 removed outlier: 4.101A pdb=" N ALA B 28 " --> pdb=" O TYR B 24 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLY B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 72 through 97 removed outlier: 5.102A pdb=" N ALA B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 121 removed outlier: 4.471A pdb=" N ALA B 118 " --> pdb=" O MET B 114 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 150 removed outlier: 3.577A pdb=" N ILE B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 143 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.561A pdb=" N ALA B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 200 removed outlier: 3.626A pdb=" N VAL B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 213 removed outlier: 3.673A pdb=" N ARG B 213 " --> pdb=" O ASP B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 213' Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.605A pdb=" N LEU B 226 " --> pdb=" O TRP B 222 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 3.889A pdb=" N ALA B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 242 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 322 removed outlier: 6.084A pdb=" N LEU B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 341 through 371 removed outlier: 3.665A pdb=" N GLU B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.550A pdb=" N MET B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 398 removed outlier: 3.863A pdb=" N GLN B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 407 through 423 Processing helix chain 'B' and resid 424 through 427 Processing helix chain 'B' and resid 429 through 434 removed outlier: 4.195A pdb=" N ALA B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 461 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.541A pdb=" N LEU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 494 removed outlier: 4.157A pdb=" N PHE B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1329 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: 0.69 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1975 1.34 - 1.46: 1697 1.46 - 1.58: 3067 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 6843 Sorted by residual: bond pdb=" CB PRO A 363 " pdb=" CG PRO A 363 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.07e+00 bond pdb=" CA PHE B 494 " pdb=" CB PHE B 494 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.21e-02 6.83e+03 1.83e+00 bond pdb=" CB VAL A 221 " pdb=" CG1 VAL A 221 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 bond pdb=" CG ASP B 314 " pdb=" OD1 ASP B 314 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.40e+00 bond pdb=" CB LEU A 153 " pdb=" CG LEU A 153 " ideal model delta sigma weight residual 1.530 1.507 0.023 2.00e-02 2.50e+03 1.33e+00 ... (remaining 6838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 9139 3.43 - 6.86: 91 6.86 - 10.29: 14 10.29 - 13.72: 2 13.72 - 17.15: 1 Bond angle restraints: 9247 Sorted by residual: angle pdb=" N VAL B 106 " pdb=" CA VAL B 106 " pdb=" C VAL B 106 " ideal model delta sigma weight residual 112.43 107.03 5.40 9.20e-01 1.18e+00 3.45e+01 angle pdb=" CA LEU B 398 " pdb=" CB LEU B 398 " pdb=" CG LEU B 398 " ideal model delta sigma weight residual 116.30 133.45 -17.15 3.50e+00 8.16e-02 2.40e+01 angle pdb=" CA MET B 388 " pdb=" CB MET B 388 " pdb=" CG MET B 388 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 angle pdb=" CB LEU A 153 " pdb=" CG LEU A 153 " pdb=" CD2 LEU A 153 " ideal model delta sigma weight residual 110.70 98.73 11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CA PRO A 363 " pdb=" N PRO A 363 " pdb=" CD PRO A 363 " ideal model delta sigma weight residual 112.00 106.49 5.51 1.40e+00 5.10e-01 1.55e+01 ... (remaining 9242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3320 17.99 - 35.99: 481 35.99 - 53.98: 123 53.98 - 71.98: 14 71.98 - 89.97: 1 Dihedral angle restraints: 3939 sinusoidal: 1486 harmonic: 2453 Sorted by residual: dihedral pdb=" CA MET B 387 " pdb=" C MET B 387 " pdb=" N MET B 388 " pdb=" CA MET B 388 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR B 41 " pdb=" C TYR B 41 " pdb=" N ASP B 42 " pdb=" CA ASP B 42 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET A 331 " pdb=" C MET A 331 " pdb=" N GLY A 332 " pdb=" CA GLY A 332 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 851 0.057 - 0.114: 173 0.114 - 0.171: 15 0.171 - 0.228: 2 0.228 - 0.285: 1 Chirality restraints: 1042 Sorted by residual: chirality pdb=" CG LEU A 153 " pdb=" CB LEU A 153 " pdb=" CD1 LEU A 153 " pdb=" CD2 LEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB THR A 307 " pdb=" CA THR A 307 " pdb=" OG1 THR A 307 " pdb=" CG2 THR A 307 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA PHE B 494 " pdb=" N PHE B 494 " pdb=" C PHE B 494 " pdb=" CB PHE B 494 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 1039 not shown) Planarity restraints: 1130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 362 " 0.060 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 363 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 491 " -0.019 2.00e-02 2.50e+03 2.22e-02 8.65e+00 pdb=" CG PHE B 491 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 491 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 491 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 491 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 491 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 491 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 494 " -0.024 2.00e-02 2.50e+03 2.22e-02 8.64e+00 pdb=" CG PHE B 494 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE B 494 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 494 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 494 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 494 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 494 " -0.001 2.00e-02 2.50e+03 ... (remaining 1127 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2712 2.89 - 3.39: 7070 3.39 - 3.89: 11267 3.89 - 4.40: 12608 4.40 - 4.90: 21262 Nonbonded interactions: 54919 Sorted by model distance: nonbonded pdb=" O ASN B 200 " pdb=" OD1 ASN B 200 " model vdw 2.387 3.040 nonbonded pdb=" O TRP B 310 " pdb=" OD1 ASP B 314 " model vdw 2.457 3.040 nonbonded pdb=" O PHE B 196 " pdb=" OD1 ASN B 200 " model vdw 2.473 3.040 nonbonded pdb=" O TYR B 468 " pdb=" OD1 ASN B 469 " model vdw 2.517 3.040 nonbonded pdb=" N ASP A 400 " pdb=" OD1 ASP A 400 " model vdw 2.521 3.120 ... (remaining 54914 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 499) selection = (chain 'B' and (resid 23 through 244 or resid 293 through 499)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6843 Z= 0.168 Angle : 0.836 17.152 9247 Z= 0.425 Chirality : 0.045 0.285 1042 Planarity : 0.005 0.088 1130 Dihedral : 17.381 89.973 2381 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.01 % Allowed : 34.01 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.29), residues: 853 helix: 0.32 (0.21), residues: 653 sheet: None (None), residues: 0 loop : -2.21 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 103 TYR 0.019 0.001 TYR A 399 PHE 0.052 0.002 PHE B 491 TRP 0.025 0.002 TRP A 239 HIS 0.002 0.000 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6843) covalent geometry : angle 0.83558 ( 9247) hydrogen bonds : bond 0.10835 ( 449) hydrogen bonds : angle 6.02154 ( 1329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.161 Fit side-chains REVERT: A 78 MET cc_start: 0.8136 (mmm) cc_final: 0.7891 (mmm) REVERT: A 165 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6179 (ptmm) REVERT: A 379 MET cc_start: 0.8022 (ppp) cc_final: 0.7810 (ppp) REVERT: A 422 PHE cc_start: 0.7495 (t80) cc_final: 0.7238 (t80) REVERT: A 471 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7610 (tp40) REVERT: A 477 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7556 (tttt) REVERT: B 88 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7624 (tp) REVERT: B 291 LEU cc_start: 0.7863 (mt) cc_final: 0.7565 (mp) REVERT: B 388 MET cc_start: 0.6036 (mmt) cc_final: 0.5687 (mmt) outliers start: 7 outliers final: 3 residues processed: 161 average time/residue: 0.0507 time to fit residues: 11.4618 Evaluate side-chains 154 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 443 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 HIS B 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.179942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148542 restraints weight = 9454.751| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.36 r_work: 0.3744 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6843 Z= 0.153 Angle : 0.686 14.038 9247 Z= 0.346 Chirality : 0.042 0.162 1042 Planarity : 0.004 0.045 1130 Dihedral : 5.011 38.834 934 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.20 % Allowed : 29.67 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.29), residues: 853 helix: 0.33 (0.21), residues: 653 sheet: None (None), residues: 0 loop : -2.00 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 167 TYR 0.016 0.001 TYR B 378 PHE 0.020 0.001 PHE B 494 TRP 0.021 0.002 TRP A 222 HIS 0.002 0.000 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6843) covalent geometry : angle 0.68623 ( 9247) hydrogen bonds : bond 0.03918 ( 449) hydrogen bonds : angle 4.73110 ( 1329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.8195 (mmm) cc_final: 0.7892 (mmm) REVERT: A 107 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: A 165 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.5843 (ptmm) REVERT: A 379 MET cc_start: 0.7913 (ppp) cc_final: 0.7684 (ppp) REVERT: A 401 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6176 (t80) REVERT: A 471 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7527 (tp40) REVERT: A 477 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7599 (tttm) REVERT: B 42 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: B 107 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.6856 (t80) REVERT: B 201 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7272 (ptpp) REVERT: B 234 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 291 LEU cc_start: 0.7866 (mt) cc_final: 0.7617 (mp) REVERT: B 294 GLU cc_start: 0.6009 (tt0) cc_final: 0.4997 (pt0) REVERT: B 447 ILE cc_start: 0.8269 (tp) cc_final: 0.7860 (mt) outliers start: 29 outliers final: 12 residues processed: 178 average time/residue: 0.0556 time to fit residues: 13.9814 Evaluate side-chains 164 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 415 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.181301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149505 restraints weight = 9337.524| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.37 r_work: 0.3744 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6843 Z= 0.143 Angle : 0.688 14.282 9247 Z= 0.340 Chirality : 0.042 0.207 1042 Planarity : 0.004 0.039 1130 Dihedral : 4.656 35.668 927 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.33 % Allowed : 30.39 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.29), residues: 853 helix: 0.38 (0.21), residues: 653 sheet: None (None), residues: 0 loop : -2.12 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 167 TYR 0.015 0.001 TYR B 378 PHE 0.038 0.001 PHE B 494 TRP 0.021 0.002 TRP A 222 HIS 0.001 0.000 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6843) covalent geometry : angle 0.68778 ( 9247) hydrogen bonds : bond 0.03691 ( 449) hydrogen bonds : angle 4.49876 ( 1329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.7074 (pmm) cc_final: 0.6762 (ttm) REVERT: A 78 MET cc_start: 0.8097 (mmm) cc_final: 0.7782 (mmm) REVERT: A 107 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: A 153 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7221 (tp) REVERT: A 379 MET cc_start: 0.7895 (ppp) cc_final: 0.7692 (ppp) REVERT: A 471 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7466 (tp40) REVERT: A 477 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7604 (tttm) REVERT: B 42 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: B 52 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7918 (mp) REVERT: B 107 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.6811 (t80) REVERT: B 234 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 291 LEU cc_start: 0.7895 (mt) cc_final: 0.7201 (tt) REVERT: B 294 GLU cc_start: 0.6086 (tt0) cc_final: 0.5067 (pt0) REVERT: B 447 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7812 (mt) outliers start: 23 outliers final: 14 residues processed: 170 average time/residue: 0.0571 time to fit residues: 13.7795 Evaluate side-chains 166 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.0030 chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.181195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.149353 restraints weight = 9435.697| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.38 r_work: 0.3739 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6843 Z= 0.141 Angle : 0.671 14.782 9247 Z= 0.333 Chirality : 0.041 0.198 1042 Planarity : 0.003 0.029 1130 Dihedral : 4.414 19.304 923 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.07 % Allowed : 27.79 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.29), residues: 853 helix: 0.42 (0.21), residues: 653 sheet: None (None), residues: 0 loop : -2.15 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.014 0.001 TYR B 378 PHE 0.040 0.001 PHE B 491 TRP 0.021 0.002 TRP A 222 HIS 0.002 0.000 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6843) covalent geometry : angle 0.67102 ( 9247) hydrogen bonds : bond 0.03605 ( 449) hydrogen bonds : angle 4.44940 ( 1329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.8071 (mmm) cc_final: 0.7758 (mmm) REVERT: A 107 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: A 113 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8495 (tt) REVERT: A 153 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7265 (tp) REVERT: A 165 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.5787 (ptmm) REVERT: A 190 MET cc_start: 0.6781 (tmm) cc_final: 0.6414 (ttp) REVERT: A 379 MET cc_start: 0.7928 (ppp) cc_final: 0.7683 (ppp) REVERT: A 425 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7642 (t0) REVERT: A 471 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7459 (tp40) REVERT: A 477 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7650 (tttm) REVERT: B 23 MET cc_start: 0.5716 (ppp) cc_final: 0.5296 (ppp) REVERT: B 42 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: B 52 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 78 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.5982 (tpt) REVERT: B 107 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.6431 (t80) REVERT: B 153 LEU cc_start: 0.8399 (pp) cc_final: 0.8056 (pt) REVERT: B 240 ARG cc_start: 0.7985 (tpp-160) cc_final: 0.7141 (ttm-80) REVERT: B 291 LEU cc_start: 0.8028 (mt) cc_final: 0.7397 (tt) REVERT: B 294 GLU cc_start: 0.6146 (tt0) cc_final: 0.5196 (pt0) REVERT: B 310 TRP cc_start: 0.7640 (t60) cc_final: 0.7431 (t60) REVERT: B 379 MET cc_start: 0.6331 (mmt) cc_final: 0.4681 (mmt) REVERT: B 447 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7840 (mt) REVERT: B 474 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8068 (p) outliers start: 35 outliers final: 19 residues processed: 183 average time/residue: 0.0556 time to fit residues: 14.5326 Evaluate side-chains 178 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.181800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149788 restraints weight = 9524.460| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.40 r_work: 0.3747 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6843 Z= 0.137 Angle : 0.686 15.396 9247 Z= 0.338 Chirality : 0.042 0.213 1042 Planarity : 0.003 0.029 1130 Dihedral : 4.384 19.284 923 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.92 % Allowed : 28.36 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.29), residues: 853 helix: 0.44 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -2.14 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.018 0.001 TYR A 238 PHE 0.029 0.001 PHE B 494 TRP 0.021 0.002 TRP A 222 HIS 0.001 0.000 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6843) covalent geometry : angle 0.68630 ( 9247) hydrogen bonds : bond 0.03554 ( 449) hydrogen bonds : angle 4.42322 ( 1329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.8080 (mmm) cc_final: 0.7756 (mmm) REVERT: A 107 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: A 113 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8509 (tt) REVERT: A 165 LYS cc_start: 0.6465 (OUTLIER) cc_final: 0.5757 (ptmm) REVERT: A 190 MET cc_start: 0.6780 (tmm) cc_final: 0.6416 (ttp) REVERT: A 379 MET cc_start: 0.7933 (ppp) cc_final: 0.7682 (ppp) REVERT: A 425 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7585 (t0) REVERT: A 471 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7462 (tp40) REVERT: A 477 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7737 (ttmm) REVERT: B 23 MET cc_start: 0.6129 (ppp) cc_final: 0.5396 (ppp) REVERT: B 42 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: B 52 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7889 (mp) REVERT: B 94 PHE cc_start: 0.6989 (m-10) cc_final: 0.6781 (m-10) REVERT: B 107 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.6811 (t80) REVERT: B 153 LEU cc_start: 0.8365 (pp) cc_final: 0.8013 (pt) REVERT: B 291 LEU cc_start: 0.8069 (mt) cc_final: 0.7446 (tt) REVERT: B 294 GLU cc_start: 0.6190 (tt0) cc_final: 0.5228 (pt0) REVERT: B 310 TRP cc_start: 0.7647 (t60) cc_final: 0.7306 (t60) REVERT: B 379 MET cc_start: 0.6346 (mmt) cc_final: 0.4602 (mmt) REVERT: B 447 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7881 (mt) REVERT: B 474 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.8060 (p) outliers start: 34 outliers final: 21 residues processed: 182 average time/residue: 0.0533 time to fit residues: 13.9533 Evaluate side-chains 180 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.181161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149498 restraints weight = 9448.844| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.38 r_work: 0.3745 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6843 Z= 0.138 Angle : 0.676 15.842 9247 Z= 0.332 Chirality : 0.041 0.203 1042 Planarity : 0.003 0.032 1130 Dihedral : 4.352 19.553 923 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.64 % Allowed : 28.36 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.29), residues: 853 helix: 0.45 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -2.15 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.016 0.001 TYR A 238 PHE 0.043 0.001 PHE B 491 TRP 0.020 0.002 TRP A 222 HIS 0.001 0.000 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6843) covalent geometry : angle 0.67557 ( 9247) hydrogen bonds : bond 0.03530 ( 449) hydrogen bonds : angle 4.39550 ( 1329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.8067 (mmm) cc_final: 0.7734 (mmm) REVERT: A 107 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: A 113 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8548 (tt) REVERT: A 165 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5742 (ptmm) REVERT: A 190 MET cc_start: 0.6787 (tmm) cc_final: 0.6429 (ttp) REVERT: A 379 MET cc_start: 0.7873 (ppp) cc_final: 0.7622 (ppp) REVERT: A 401 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.5728 (t80) REVERT: A 425 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7749 (t0) REVERT: A 471 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7473 (tp40) REVERT: A 477 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7732 (ttmm) REVERT: B 42 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.6980 (m-30) REVERT: B 52 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 107 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.6791 (t80) REVERT: B 153 LEU cc_start: 0.8393 (pp) cc_final: 0.8030 (pt) REVERT: B 291 LEU cc_start: 0.7937 (mt) cc_final: 0.7345 (tt) REVERT: B 294 GLU cc_start: 0.6288 (tt0) cc_final: 0.5256 (pt0) REVERT: B 310 TRP cc_start: 0.7657 (t60) cc_final: 0.7453 (t60) REVERT: B 379 MET cc_start: 0.6317 (mmt) cc_final: 0.4590 (mmt) REVERT: B 392 MET cc_start: 0.7961 (ttm) cc_final: 0.7317 (ttm) REVERT: B 447 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7874 (mt) REVERT: B 474 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7990 (t) outliers start: 39 outliers final: 26 residues processed: 186 average time/residue: 0.0511 time to fit residues: 13.6561 Evaluate side-chains 188 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.182628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150441 restraints weight = 9532.148| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.42 r_work: 0.3753 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6843 Z= 0.136 Angle : 0.704 15.941 9247 Z= 0.342 Chirality : 0.042 0.219 1042 Planarity : 0.003 0.030 1130 Dihedral : 4.379 19.181 923 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.07 % Allowed : 28.65 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.29), residues: 853 helix: 0.47 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.015 0.001 TYR A 238 PHE 0.030 0.001 PHE B 494 TRP 0.021 0.002 TRP A 222 HIS 0.002 0.000 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6843) covalent geometry : angle 0.70440 ( 9247) hydrogen bonds : bond 0.03533 ( 449) hydrogen bonds : angle 4.42104 ( 1329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.7005 (pmm) cc_final: 0.6609 (ttm) REVERT: A 78 MET cc_start: 0.8105 (mmm) cc_final: 0.7773 (mmm) REVERT: A 107 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: A 113 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 165 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5740 (ptmm) REVERT: A 190 MET cc_start: 0.6794 (tmm) cc_final: 0.6431 (ttp) REVERT: A 401 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5727 (t80) REVERT: A 425 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7748 (t0) REVERT: A 471 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7451 (tp40) REVERT: A 477 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7753 (ttmm) REVERT: B 42 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: B 52 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7915 (mp) REVERT: B 107 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.6831 (t80) REVERT: B 153 LEU cc_start: 0.8405 (pp) cc_final: 0.8055 (pt) REVERT: B 291 LEU cc_start: 0.7850 (mt) cc_final: 0.7296 (tt) REVERT: B 294 GLU cc_start: 0.6281 (tt0) cc_final: 0.5244 (pt0) REVERT: B 310 TRP cc_start: 0.7698 (t60) cc_final: 0.7472 (t60) REVERT: B 379 MET cc_start: 0.6407 (mmt) cc_final: 0.4758 (mmt) REVERT: B 392 MET cc_start: 0.7971 (ttm) cc_final: 0.7247 (ttm) REVERT: B 447 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7880 (mt) outliers start: 35 outliers final: 26 residues processed: 179 average time/residue: 0.0537 time to fit residues: 13.7749 Evaluate side-chains 183 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.182177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150142 restraints weight = 9430.028| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.39 r_work: 0.3756 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6843 Z= 0.138 Angle : 0.697 15.286 9247 Z= 0.341 Chirality : 0.042 0.201 1042 Planarity : 0.003 0.030 1130 Dihedral : 4.363 19.776 923 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.07 % Allowed : 28.08 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.29), residues: 853 helix: 0.46 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.015 0.001 TYR A 238 PHE 0.029 0.001 PHE B 494 TRP 0.020 0.002 TRP A 222 HIS 0.002 0.000 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6843) covalent geometry : angle 0.69677 ( 9247) hydrogen bonds : bond 0.03537 ( 449) hydrogen bonds : angle 4.43179 ( 1329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.7057 (pmm) cc_final: 0.6565 (ttm) REVERT: A 78 MET cc_start: 0.8098 (mmm) cc_final: 0.7755 (mmm) REVERT: A 107 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: A 113 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 190 MET cc_start: 0.6839 (tmm) cc_final: 0.6432 (ttp) REVERT: A 425 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7776 (t0) REVERT: A 464 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 471 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7450 (tp40) REVERT: A 477 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7759 (ttmm) REVERT: B 42 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: B 52 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 107 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 153 LEU cc_start: 0.8439 (pp) cc_final: 0.8078 (pt) REVERT: B 291 LEU cc_start: 0.7892 (mt) cc_final: 0.7336 (tt) REVERT: B 294 GLU cc_start: 0.6304 (tt0) cc_final: 0.5310 (pt0) REVERT: B 310 TRP cc_start: 0.7649 (t60) cc_final: 0.7405 (t60) REVERT: B 379 MET cc_start: 0.6241 (mmt) cc_final: 0.4623 (mmt) REVERT: B 447 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7877 (mt) REVERT: B 474 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7967 (t) outliers start: 35 outliers final: 26 residues processed: 183 average time/residue: 0.0473 time to fit residues: 12.6656 Evaluate side-chains 183 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.181620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149287 restraints weight = 9439.342| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.40 r_work: 0.3748 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6843 Z= 0.147 Angle : 0.707 15.060 9247 Z= 0.347 Chirality : 0.042 0.199 1042 Planarity : 0.003 0.031 1130 Dihedral : 4.378 20.244 923 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.35 % Allowed : 29.09 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.29), residues: 853 helix: 0.42 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.014 0.001 TYR B 378 PHE 0.029 0.001 PHE B 494 TRP 0.019 0.002 TRP A 222 HIS 0.002 0.000 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6843) covalent geometry : angle 0.70735 ( 9247) hydrogen bonds : bond 0.03629 ( 449) hydrogen bonds : angle 4.47829 ( 1329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.7086 (pmm) cc_final: 0.6600 (ttm) REVERT: A 78 MET cc_start: 0.8089 (mmm) cc_final: 0.7756 (mmm) REVERT: A 107 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: A 165 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.5765 (ptmm) REVERT: A 190 MET cc_start: 0.6841 (tmm) cc_final: 0.6464 (ttp) REVERT: A 379 MET cc_start: 0.7845 (ppp) cc_final: 0.7601 (ppp) REVERT: A 425 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7835 (t0) REVERT: A 464 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 471 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7432 (tp40) REVERT: A 477 LYS cc_start: 0.8064 (ttmt) cc_final: 0.7754 (ttmm) REVERT: B 42 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: B 52 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7960 (mp) REVERT: B 107 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.6945 (t80) REVERT: B 153 LEU cc_start: 0.8450 (pp) cc_final: 0.8084 (pt) REVERT: B 291 LEU cc_start: 0.7865 (mt) cc_final: 0.7311 (tt) REVERT: B 294 GLU cc_start: 0.6311 (tt0) cc_final: 0.5338 (pt0) REVERT: B 310 TRP cc_start: 0.7703 (t60) cc_final: 0.7441 (t60) REVERT: B 379 MET cc_start: 0.6294 (mmt) cc_final: 0.4700 (mmt) REVERT: B 392 MET cc_start: 0.7945 (ttm) cc_final: 0.7389 (ttm) REVERT: B 447 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7895 (mt) REVERT: B 474 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7979 (t) outliers start: 37 outliers final: 28 residues processed: 178 average time/residue: 0.0490 time to fit residues: 12.6688 Evaluate side-chains 183 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.179584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.147634 restraints weight = 9563.764| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.39 r_work: 0.3723 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6843 Z= 0.158 Angle : 0.706 14.972 9247 Z= 0.350 Chirality : 0.043 0.185 1042 Planarity : 0.003 0.031 1130 Dihedral : 4.447 20.836 923 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.21 % Allowed : 29.38 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.29), residues: 853 helix: 0.39 (0.21), residues: 651 sheet: None (None), residues: 0 loop : -2.15 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.015 0.001 TYR B 378 PHE 0.029 0.001 PHE B 494 TRP 0.019 0.002 TRP A 222 HIS 0.002 0.000 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6843) covalent geometry : angle 0.70560 ( 9247) hydrogen bonds : bond 0.03718 ( 449) hydrogen bonds : angle 4.53532 ( 1329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.7096 (pmm) cc_final: 0.6615 (ttm) REVERT: A 78 MET cc_start: 0.8141 (mmm) cc_final: 0.7792 (mmm) REVERT: A 107 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: A 165 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.5791 (ptmm) REVERT: A 190 MET cc_start: 0.6877 (tmm) cc_final: 0.6463 (ttp) REVERT: A 379 MET cc_start: 0.7939 (ppp) cc_final: 0.7696 (ppp) REVERT: A 425 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7608 (t0) REVERT: A 464 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 471 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7424 (tp40) REVERT: A 477 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7743 (ttmm) REVERT: B 52 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 97 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6799 (m-10) REVERT: B 107 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6930 (t80) REVERT: B 153 LEU cc_start: 0.8419 (pp) cc_final: 0.8071 (pt) REVERT: B 291 LEU cc_start: 0.7951 (mt) cc_final: 0.7364 (tt) REVERT: B 294 GLU cc_start: 0.6387 (tt0) cc_final: 0.5453 (pt0) REVERT: B 310 TRP cc_start: 0.7658 (t60) cc_final: 0.7419 (t60) REVERT: B 379 MET cc_start: 0.6299 (mmt) cc_final: 0.4703 (mmt) REVERT: B 447 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7883 (mt) REVERT: B 474 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7962 (t) outliers start: 36 outliers final: 27 residues processed: 179 average time/residue: 0.0498 time to fit residues: 12.9220 Evaluate side-chains 188 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 TYR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.180483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.147917 restraints weight = 9418.560| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.39 r_work: 0.3723 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6843 Z= 0.158 Angle : 0.717 14.793 9247 Z= 0.354 Chirality : 0.043 0.216 1042 Planarity : 0.003 0.031 1130 Dihedral : 4.462 20.798 923 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 5.21 % Allowed : 29.52 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.29), residues: 853 helix: 0.40 (0.21), residues: 645 sheet: None (None), residues: 0 loop : -2.29 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.015 0.001 TYR B 378 PHE 0.029 0.001 PHE B 494 TRP 0.019 0.002 TRP A 222 HIS 0.004 0.000 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6843) covalent geometry : angle 0.71696 ( 9247) hydrogen bonds : bond 0.03735 ( 449) hydrogen bonds : angle 4.54253 ( 1329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1297.73 seconds wall clock time: 22 minutes 56.85 seconds (1376.85 seconds total)