Starting phenix.real_space_refine on Wed Aug 5 02:52:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uv2_64521/08_2026/9uv2_64521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uv2_64521/08_2026/9uv2_64521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uv2_64521/08_2026/9uv2_64521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uv2_64521/08_2026/9uv2_64521.map" model { file = "/net/cci-nas-00/data/ceres_data/9uv2_64521/08_2026/9uv2_64521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uv2_64521/08_2026/9uv2_64521.cif" } resolution = 2.83 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5252 2.51 5 N 1326 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8042 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3263 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "A" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3263 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 758 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "D" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 758 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Time building chain proxies: 2.10, per 1000 atoms: 0.26 Number of scatterers: 8042 At special positions: 0 Unit cell: (69.7, 98.4, 97.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1410 8.00 N 1326 7.00 C 5252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 506.7 milliseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 2 sheets defined 69.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 removed outlier: 3.536A pdb=" N THR B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 50 Processing helix chain 'B' and resid 56 through 75 Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 130 Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 183 through 208 Processing helix chain 'B' and resid 213 through 236 removed outlier: 3.865A pdb=" N SER B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 262 removed outlier: 3.776A pdb=" N VAL B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.508A pdb=" N ASN B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 320 removed outlier: 4.124A pdb=" N ALA B 318 " --> pdb=" O GLY B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.503A pdb=" N ARG B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.788A pdb=" N VAL B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 453 through 460 Processing helix chain 'A' and resid 8 through 24 removed outlier: 3.872A pdb=" N LEU A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 50 removed outlier: 3.625A pdb=" N THR A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 74 removed outlier: 3.524A pdb=" N ILE A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.585A pdb=" N ASN A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 removed outlier: 3.598A pdb=" N PHE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 208 Processing helix chain 'A' and resid 213 through 236 removed outlier: 3.742A pdb=" N SER A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 263 removed outlier: 3.730A pdb=" N VAL A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.715A pdb=" N ALA A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.871A pdb=" N ALA A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.673A pdb=" N VAL A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.570A pdb=" N LYS A 416 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 452 through 460 removed outlier: 3.940A pdb=" N ALA A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 423 through 426 Processing helix chain 'C' and resid 427 through 443 Processing helix chain 'C' and resid 450 through 462 Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.526A pdb=" N ALA C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 499 removed outlier: 3.699A pdb=" N PHE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 492 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 421 through 444 removed outlier: 3.935A pdb=" N TYR D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 462 Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.506A pdb=" N ALA D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 497 removed outlier: 3.764A pdb=" N PHE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 504 removed outlier: 3.580A pdb=" N MET D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 369 through 371 removed outlier: 6.267A pdb=" N VAL B 309 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLY B 343 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 311 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 388 " --> pdb=" O THR B 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 371 removed outlier: 3.514A pdb=" N THR A 384 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A 385 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 423 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 387 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 420 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 447 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 422 " --> pdb=" O LEU A 447 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.99 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: 2527 1.34 - 1.46: 1236 1.46 - 1.58: 4341 1.58 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 8206 Sorted by residual: bond pdb=" CG PRO A 115 " pdb=" CD PRO A 115 " ideal model delta sigma weight residual 1.503 1.539 -0.036 3.40e-02 8.65e+02 1.13e+00 bond pdb=" CB GLU A 442 " pdb=" CG GLU A 442 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CA ASN B 104 " pdb=" CB ASN B 104 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.75e-02 3.27e+03 8.32e-01 bond pdb=" CA GLY D 438 " pdb=" C GLY D 438 " ideal model delta sigma weight residual 1.514 1.501 0.013 1.41e-02 5.03e+03 7.94e-01 bond pdb=" N MET C 416 " pdb=" CA MET C 416 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.68e-01 ... (remaining 8201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 10973 1.98 - 3.95: 151 3.95 - 5.93: 22 5.93 - 7.91: 2 7.91 - 9.88: 2 Bond angle restraints: 11150 Sorted by residual: angle pdb=" N LYS B 452 " pdb=" CA LYS B 452 " pdb=" C LYS B 452 " ideal model delta sigma weight residual 114.75 108.41 6.34 1.26e+00 6.30e-01 2.53e+01 angle pdb=" C MET A 113 " pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 121.80 131.68 -9.88 2.44e+00 1.68e-01 1.64e+01 angle pdb=" N ALA A 451 " pdb=" CA ALA A 451 " pdb=" C ALA A 451 " ideal model delta sigma weight residual 114.75 109.67 5.08 1.26e+00 6.30e-01 1.62e+01 angle pdb=" N GLY C 426 " pdb=" CA GLY C 426 " pdb=" C GLY C 426 " ideal model delta sigma weight residual 113.18 105.14 8.04 2.37e+00 1.78e-01 1.15e+01 angle pdb=" N THR C 500 " pdb=" CA THR C 500 " pdb=" C THR C 500 " ideal model delta sigma weight residual 114.16 109.15 5.01 1.48e+00 4.57e-01 1.15e+01 ... (remaining 11145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4075 17.85 - 35.70: 524 35.70 - 53.55: 155 53.55 - 71.40: 30 71.40 - 89.25: 10 Dihedral angle restraints: 4794 sinusoidal: 1754 harmonic: 3040 Sorted by residual: dihedral pdb=" CA VAL C 499 " pdb=" C VAL C 499 " pdb=" N THR C 500 " pdb=" CA THR C 500 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ALA A 8 " pdb=" C ALA A 8 " pdb=" N ALA A 9 " pdb=" CA ALA A 9 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA ASP A 450 " pdb=" C ASP A 450 " pdb=" N ALA A 451 " pdb=" CA ALA A 451 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 4791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 745 0.027 - 0.054: 381 0.054 - 0.081: 146 0.081 - 0.107: 65 0.107 - 0.134: 15 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA ASN B 104 " pdb=" N ASN B 104 " pdb=" C ASN B 104 " pdb=" CB ASN B 104 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASN A 104 " pdb=" N ASN A 104 " pdb=" C ASN A 104 " pdb=" CB ASN A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL B 364 " pdb=" N VAL B 364 " pdb=" C VAL B 364 " pdb=" CB VAL B 364 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1349 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 8 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" C ALA A 8 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA A 8 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA A 9 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 114 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 115 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 214 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO B 215 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " 0.036 5.00e-02 4.00e+02 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1317 2.76 - 3.29: 8198 3.29 - 3.83: 14443 3.83 - 4.36: 17326 4.36 - 4.90: 29403 Nonbonded interactions: 70687 Sorted by model distance: nonbonded pdb=" O ALA A 167 " pdb=" OG SER A 171 " model vdw 2.223 3.040 nonbonded pdb=" O HIS B 204 " pdb=" OG SER B 208 " model vdw 2.260 3.040 nonbonded pdb=" O SER B 426 " pdb=" OG SER B 426 " model vdw 2.264 3.040 nonbonded pdb=" O THR A 295 " pdb=" OG1 THR A 299 " model vdw 2.268 3.040 nonbonded pdb=" OG SER B 223 " pdb=" O GLY B 249 " model vdw 2.284 3.040 ... (remaining 70682 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 3.700 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 0.003 0.036 8206 Z= 0.132 Angle : 0.604 9.882 11150 Z= 0.359 Chirality : 0.040 0.134 1352 Planarity : 0.005 0.064 1382 Dihedral : 18.022 89.249 2838 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.97 % Favored : 95.65 % Rotamer: Outliers : 4.94 % Allowed : 30.24 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 1058 helix: 0.19 (0.20), residues: 716 sheet: -0.09 (0.76), residues: 46 loop : -0.89 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 265 TYR 0.007 0.001 TYR D 440 PHE 0.010 0.001 PHE B 178 TRP 0.010 0.001 TRP D 415 HIS 0.003 0.000 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 8206) covalent geometry : angle 0.60351 / 0.36 (11150) hydrogen bonds : bond 0.14958 / 10.46 ( 526) hydrogen bonds : angle 6.41040 / 4.42 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.180 Fit side-chains REVERT: B 56 ASN cc_start: 0.5686 (m-40) cc_final: 0.5389 (t0) REVERT: B 264 ASN cc_start: 0.7687 (t0) cc_final: 0.7473 (t0) REVERT: A 27 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7520 (t-90) REVERT: A 293 GLU cc_start: 0.7214 (tt0) cc_final: 0.6830 (tm-30) REVERT: A 304 LYS cc_start: 0.8393 (pttp) cc_final: 0.7769 (ptpt) REVERT: A 460 LYS cc_start: 0.8199 (tttt) cc_final: 0.7968 (ttpt) outliers start: 42 outliers final: 35 residues processed: 168 average time/residue: 0.4117 time to fit residues: 74.7141 Evaluate side-chains 158 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 445 HIS C 458 ASN ** C 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115443 restraints weight = 8758.952| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.51 r_work: 0.3157 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8206 Z= 0.150 Angle : 0.568 10.027 11150 Z= 0.299 Chirality : 0.042 0.142 1352 Planarity : 0.005 0.060 1382 Dihedral : 8.123 60.079 1163 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.25 % Favored : 95.37 % Rotamer: Outliers : 6.12 % Allowed : 26.24 % Favored : 67.65 % 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: 0.03 (0.26), residues: 1058 helix: 0.45 (0.19), residues: 722 sheet: 0.00 (0.78), residues: 46 loop : -0.80 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 265 TYR 0.010 0.001 TYR B 366 PHE 0.014 0.001 PHE B 178 TRP 0.007 0.001 TRP D 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8206) covalent geometry : angle 0.56798 / 0.30 (11150) hydrogen bonds : bond 0.03861 / 2.68 ( 526) hydrogen bonds : angle 4.47633 / 3.21 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: B 264 ASN cc_start: 0.8211 (t0) cc_final: 0.7953 (t0) REVERT: B 361 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6172 (mm-30) REVERT: A 293 GLU cc_start: 0.7208 (tt0) cc_final: 0.6802 (tm-30) REVERT: A 460 LYS cc_start: 0.8283 (tttt) cc_final: 0.8037 (ttpt) REVERT: C 502 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.5128 (ptt180) outliers start: 52 outliers final: 26 residues processed: 170 average time/residue: 0.4309 time to fit residues: 78.6290 Evaluate side-chains 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 ASN B 445 HIS A 443 ASN D 492 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113928 restraints weight = 8694.445| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.48 r_work: 0.3007 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8206 Z= 0.158 Angle : 0.559 9.948 11150 Z= 0.295 Chirality : 0.042 0.149 1352 Planarity : 0.005 0.059 1382 Dihedral : 7.241 59.191 1137 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.54 % Favored : 95.09 % Rotamer: Outliers : 6.00 % Allowed : 25.76 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.26), residues: 1058 helix: 0.63 (0.19), residues: 712 sheet: 0.25 (0.80), residues: 46 loop : -0.98 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 265 TYR 0.011 0.001 TYR B 366 PHE 0.013 0.001 PHE B 178 TRP 0.008 0.001 TRP D 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8206) covalent geometry : angle 0.55937 / 0.30 (11150) hydrogen bonds : bond 0.03793 / 2.64 ( 526) hydrogen bonds : angle 4.35185 / 3.14 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.326 Fit side-chains REVERT: B 180 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.6083 (mtm-85) REVERT: B 361 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6211 (mm-30) REVERT: B 383 ASP cc_start: 0.7688 (m-30) cc_final: 0.7247 (t0) REVERT: A 27 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7593 (t-90) REVERT: A 293 GLU cc_start: 0.7235 (tt0) cc_final: 0.6747 (tm-30) REVERT: A 460 LYS cc_start: 0.8276 (tttt) cc_final: 0.7993 (ttpt) REVERT: C 502 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.5312 (ptt180) REVERT: D 422 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7556 (tppt) outliers start: 51 outliers final: 26 residues processed: 161 average time/residue: 0.4882 time to fit residues: 84.1124 Evaluate side-chains 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 ASN B 445 HIS C 509 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112031 restraints weight = 8908.295| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.49 r_work: 0.3087 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8206 Z= 0.175 Angle : 0.574 9.848 11150 Z= 0.300 Chirality : 0.042 0.146 1352 Planarity : 0.005 0.059 1382 Dihedral : 6.884 58.561 1131 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.54 % Favored : 95.09 % Rotamer: Outliers : 6.35 % Allowed : 25.76 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.13 (0.26), residues: 1058 helix: 0.53 (0.19), residues: 734 sheet: 0.14 (0.82), residues: 46 loop : -0.86 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 350 TYR 0.012 0.001 TYR B 366 PHE 0.012 0.001 PHE B 178 TRP 0.008 0.001 TRP D 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 8206) covalent geometry : angle 0.57397 / 0.30 (11150) hydrogen bonds : bond 0.03837 / 2.67 ( 526) hydrogen bonds : angle 4.35744 / 3.16 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 0.294 Fit side-chains REVERT: B 361 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6386 (mm-30) REVERT: B 383 ASP cc_start: 0.7771 (m-30) cc_final: 0.7389 (t0) REVERT: B 445 HIS cc_start: 0.6979 (OUTLIER) cc_final: 0.5728 (m-70) REVERT: A 27 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7755 (t-90) REVERT: A 293 GLU cc_start: 0.7223 (tt0) cc_final: 0.6849 (tm-30) REVERT: A 302 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 341 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7170 (mtp180) REVERT: A 374 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: C 502 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.5761 (ptt180) REVERT: D 422 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7613 (tppt) outliers start: 54 outliers final: 28 residues processed: 165 average time/residue: 0.4624 time to fit residues: 81.9567 Evaluate side-chains 156 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 445 HIS A 27 HIS A 34 ASN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112080 restraints weight = 8809.226| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.51 r_work: 0.3143 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8206 Z= 0.142 Angle : 0.552 10.376 11150 Z= 0.288 Chirality : 0.041 0.136 1352 Planarity : 0.005 0.059 1382 Dihedral : 6.683 55.517 1127 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.44 % Favored : 95.18 % Rotamer: Outliers : 6.00 % Allowed : 26.00 % Favored : 68.00 % 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: 0.31 (0.27), residues: 1058 helix: 0.68 (0.19), residues: 734 sheet: -0.27 (0.70), residues: 60 loop : -0.75 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.010 0.001 TYR B 366 PHE 0.011 0.001 PHE B 178 TRP 0.009 0.001 TRP D 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 8206) covalent geometry : angle 0.55196 / 0.29 (11150) hydrogen bonds : bond 0.03631 / 2.52 ( 526) hydrogen bonds : angle 4.23365 / 3.07 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.293 Fit side-chains REVERT: B 264 ASN cc_start: 0.8391 (t0) cc_final: 0.8010 (t0) REVERT: B 361 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6479 (mm-30) REVERT: B 383 ASP cc_start: 0.7743 (m-30) cc_final: 0.7346 (t0) REVERT: A 1 MET cc_start: 0.3770 (tpt) cc_final: 0.3483 (tpt) REVERT: A 156 MET cc_start: 0.7877 (mpp) cc_final: 0.7464 (mtt) REVERT: A 293 GLU cc_start: 0.7166 (tt0) cc_final: 0.6805 (tm-30) REVERT: A 302 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 341 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7148 (mtp180) REVERT: C 411 ILE cc_start: 0.4176 (OUTLIER) cc_final: 0.3489 (pt) REVERT: C 502 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.5484 (ptt180) REVERT: D 422 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7591 (tppt) outliers start: 51 outliers final: 28 residues processed: 163 average time/residue: 0.4553 time to fit residues: 79.9707 Evaluate side-chains 151 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN B 445 HIS ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112896 restraints weight = 8738.233| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.51 r_work: 0.3105 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8206 Z= 0.138 Angle : 0.556 10.674 11150 Z= 0.287 Chirality : 0.041 0.145 1352 Planarity : 0.005 0.059 1382 Dihedral : 6.320 55.316 1124 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.25 % Favored : 95.37 % Rotamer: Outliers : 5.65 % Allowed : 26.00 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.41 (0.27), residues: 1058 helix: 0.75 (0.19), residues: 734 sheet: -0.25 (0.70), residues: 60 loop : -0.68 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.009 0.001 TYR B 366 PHE 0.011 0.001 PHE B 178 TRP 0.009 0.001 TRP D 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8206) covalent geometry : angle 0.55568 / 0.29 (11150) hydrogen bonds : bond 0.03582 / 2.48 ( 526) hydrogen bonds : angle 4.19073 / 3.04 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 162 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7459 (tptp) REVERT: B 292 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6782 (ptm-80) REVERT: B 361 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6326 (mm-30) REVERT: B 383 ASP cc_start: 0.7714 (m-30) cc_final: 0.7303 (t0) REVERT: B 445 HIS cc_start: 0.6858 (OUTLIER) cc_final: 0.5821 (m-70) REVERT: A 156 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7424 (mtt) REVERT: A 293 GLU cc_start: 0.7171 (tt0) cc_final: 0.6732 (tm-30) REVERT: A 302 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7818 (mp) REVERT: A 361 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: C 411 ILE cc_start: 0.4142 (OUTLIER) cc_final: 0.3537 (pt) REVERT: C 454 MET cc_start: 0.8405 (mtp) cc_final: 0.8184 (mtp) REVERT: C 502 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.5481 (ptt180) REVERT: D 422 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7571 (tppt) outliers start: 48 outliers final: 28 residues processed: 157 average time/residue: 0.4816 time to fit residues: 81.1070 Evaluate side-chains 159 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN B 445 HIS ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113228 restraints weight = 8771.473| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.50 r_work: 0.3110 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8206 Z= 0.151 Angle : 0.559 11.417 11150 Z= 0.289 Chirality : 0.042 0.145 1352 Planarity : 0.005 0.059 1382 Dihedral : 6.232 55.806 1124 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.44 % Favored : 95.27 % Rotamer: Outliers : 5.06 % Allowed : 26.71 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.27), residues: 1058 helix: 0.73 (0.19), residues: 736 sheet: -0.27 (0.70), residues: 60 loop : -0.62 (0.44), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.011 0.001 TYR B 366 PHE 0.012 0.001 PHE B 178 TRP 0.008 0.001 TRP D 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8206) covalent geometry : angle 0.55858 / 0.29 (11150) hydrogen bonds : bond 0.03640 / 2.52 ( 526) hydrogen bonds : angle 4.20247 / 3.05 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 162 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7457 (tptp) REVERT: B 361 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6372 (mm-30) REVERT: B 383 ASP cc_start: 0.7730 (m-30) cc_final: 0.7315 (t0) REVERT: B 447 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6391 (tt) REVERT: A 156 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7433 (mtt) REVERT: A 293 GLU cc_start: 0.7179 (tt0) cc_final: 0.6739 (tm-30) REVERT: A 302 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7811 (mp) REVERT: C 411 ILE cc_start: 0.4164 (OUTLIER) cc_final: 0.3565 (pt) REVERT: C 454 MET cc_start: 0.8399 (mtp) cc_final: 0.8162 (mtp) REVERT: C 502 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.5552 (ptt180) REVERT: D 422 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7572 (tppt) outliers start: 43 outliers final: 27 residues processed: 158 average time/residue: 0.4571 time to fit residues: 77.7549 Evaluate side-chains 155 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN B 445 HIS ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114194 restraints weight = 8725.384| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.52 r_work: 0.3182 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8206 Z= 0.140 Angle : 0.561 11.512 11150 Z= 0.287 Chirality : 0.041 0.147 1352 Planarity : 0.004 0.059 1382 Dihedral : 6.081 56.268 1124 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.63 % Favored : 95.09 % Rotamer: Outliers : 4.71 % Allowed : 26.94 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.48 (0.27), residues: 1058 helix: 0.80 (0.19), residues: 734 sheet: -0.28 (0.69), residues: 60 loop : -0.64 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 265 TYR 0.010 0.001 TYR B 366 PHE 0.011 0.001 PHE B 178 TRP 0.009 0.001 TRP D 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 8206) covalent geometry : angle 0.56087 / 0.29 (11150) hydrogen bonds : bond 0.03570 / 2.48 ( 526) hydrogen bonds : angle 4.14578 / 3.02 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 162 LYS cc_start: 0.7741 (tmtt) cc_final: 0.7453 (tptp) REVERT: B 361 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6353 (mm-30) REVERT: B 383 ASP cc_start: 0.7710 (m-30) cc_final: 0.7304 (t0) REVERT: B 387 VAL cc_start: 0.8267 (t) cc_final: 0.8017 (m) REVERT: A 156 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7401 (mtt) REVERT: A 293 GLU cc_start: 0.7188 (tt0) cc_final: 0.6783 (tm-30) REVERT: A 299 THR cc_start: 0.8533 (m) cc_final: 0.8331 (m) REVERT: A 302 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 341 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7130 (mtp180) REVERT: A 361 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: A 381 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7437 (t0) REVERT: C 411 ILE cc_start: 0.4100 (OUTLIER) cc_final: 0.3546 (pt) REVERT: C 454 MET cc_start: 0.8349 (mtp) cc_final: 0.8123 (mtp) REVERT: C 502 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.5500 (ptt180) REVERT: D 422 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7569 (tppt) outliers start: 40 outliers final: 28 residues processed: 155 average time/residue: 0.4733 time to fit residues: 78.9134 Evaluate side-chains 158 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113600 restraints weight = 8764.728| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.52 r_work: 0.3170 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8206 Z= 0.150 Angle : 0.562 12.036 11150 Z= 0.290 Chirality : 0.042 0.150 1352 Planarity : 0.004 0.058 1382 Dihedral : 6.059 56.818 1124 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.91 % Favored : 94.80 % Rotamer: Outliers : 4.82 % Allowed : 27.06 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.46 (0.27), residues: 1058 helix: 0.76 (0.19), residues: 736 sheet: -0.34 (0.68), residues: 60 loop : -0.55 (0.44), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 350 TYR 0.011 0.001 TYR B 366 PHE 0.012 0.001 PHE B 178 TRP 0.008 0.001 TRP D 415 HIS 0.005 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8206) covalent geometry : angle 0.56198 / 0.29 (11150) hydrogen bonds : bond 0.03648 / 2.53 ( 526) hydrogen bonds : angle 4.17341 / 3.04 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 162 LYS cc_start: 0.7773 (tmtt) cc_final: 0.7479 (tptp) REVERT: B 292 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6929 (ptp-110) REVERT: B 361 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6450 (mm-30) REVERT: B 383 ASP cc_start: 0.7722 (m-30) cc_final: 0.7323 (t0) REVERT: A 1 MET cc_start: 0.3813 (tpt) cc_final: 0.3469 (tpt) REVERT: A 156 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7418 (mtt) REVERT: A 293 GLU cc_start: 0.7202 (tt0) cc_final: 0.6816 (tm-30) REVERT: A 299 THR cc_start: 0.8549 (m) cc_final: 0.8342 (m) REVERT: A 302 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 341 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7127 (mtp180) REVERT: A 361 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: A 381 ASP cc_start: 0.7989 (m-30) cc_final: 0.7471 (t0) REVERT: C 411 ILE cc_start: 0.4104 (OUTLIER) cc_final: 0.3548 (pt) REVERT: C 454 MET cc_start: 0.8373 (mtp) cc_final: 0.8128 (mtp) REVERT: C 502 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.5641 (ptt180) REVERT: D 422 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7579 (tppt) REVERT: D 470 LEU cc_start: 0.7522 (mt) cc_final: 0.7100 (mp) outliers start: 41 outliers final: 29 residues processed: 154 average time/residue: 0.4902 time to fit residues: 80.9361 Evaluate side-chains 158 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 43 optimal weight: 0.0070 chunk 8 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN B 445 HIS ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS C 458 ASN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.147004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115800 restraints weight = 8685.199| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.77 r_work: 0.3149 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8206 Z= 0.121 Angle : 0.556 12.100 11150 Z= 0.282 Chirality : 0.040 0.140 1352 Planarity : 0.004 0.059 1382 Dihedral : 5.851 57.740 1122 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.35 % Favored : 95.37 % Rotamer: Outliers : 4.47 % Allowed : 27.88 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.67 (0.27), residues: 1058 helix: 0.94 (0.20), residues: 734 sheet: -0.27 (0.68), residues: 60 loop : -0.54 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 265 TYR 0.008 0.001 TYR B 366 PHE 0.009 0.001 PHE B 50 TRP 0.010 0.001 TRP D 415 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8206) covalent geometry : angle 0.55612 / 0.28 (11150) hydrogen bonds : bond 0.03416 / 2.37 ( 526) hydrogen bonds : angle 4.02874 / 2.94 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: B 27 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7746 (t-90) REVERT: B 162 LYS cc_start: 0.7160 (tmtt) cc_final: 0.6908 (tptp) REVERT: B 269 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7576 (p) REVERT: B 292 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6651 (ptp-110) REVERT: B 361 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6356 (mm-30) REVERT: B 383 ASP cc_start: 0.7325 (m-30) cc_final: 0.6856 (t0) REVERT: A 293 GLU cc_start: 0.7098 (tt0) cc_final: 0.6646 (tm-30) REVERT: A 299 THR cc_start: 0.8268 (m) cc_final: 0.8047 (m) REVERT: A 302 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7274 (mp) REVERT: A 341 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6621 (mtp180) REVERT: A 361 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: A 381 ASP cc_start: 0.7868 (m-30) cc_final: 0.7216 (t0) REVERT: A 460 LYS cc_start: 0.8110 (tttt) cc_final: 0.7801 (ttpt) REVERT: C 411 ILE cc_start: 0.3780 (OUTLIER) cc_final: 0.3405 (pt) REVERT: C 502 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.4834 (ptt180) REVERT: D 470 LEU cc_start: 0.6988 (mt) cc_final: 0.6561 (mp) outliers start: 38 outliers final: 24 residues processed: 152 average time/residue: 0.4394 time to fit residues: 71.9887 Evaluate side-chains 155 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain C residue 502 ARG Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 490 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 ASN B 445 HIS ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS C 458 ASN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112638 restraints weight = 8707.904| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.78 r_work: 0.2971 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8206 Z= 0.149 Angle : 0.570 12.251 11150 Z= 0.292 Chirality : 0.041 0.151 1352 Planarity : 0.004 0.059 1382 Dihedral : 5.608 58.023 1118 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.54 % Favored : 95.18 % Rotamer: Outliers : 4.24 % Allowed : 28.47 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.59 (0.27), residues: 1058 helix: 0.87 (0.19), residues: 734 sheet: -0.16 (0.67), residues: 60 loop : -0.57 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 265 TYR 0.010 0.001 TYR B 366 PHE 0.011 0.001 PHE B 178 TRP 0.007 0.001 TRP D 415 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8206) covalent geometry : angle 0.56962 / 0.29 (11150) hydrogen bonds : bond 0.03621 / 2.51 ( 526) hydrogen bonds : angle 4.12261 / 3.00 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2806.41 seconds wall clock time: 48 minutes 39.54 seconds (2919.54 seconds total)