Starting phenix.real_space_refine on Wed Feb 12 09:19:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sep_25074/02_2025/7sep_25074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sep_25074/02_2025/7sep_25074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sep_25074/02_2025/7sep_25074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sep_25074/02_2025/7sep_25074.map" model { file = "/net/cci-nas-00/data/ceres_data/7sep_25074/02_2025/7sep_25074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sep_25074/02_2025/7sep_25074.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 15 5.16 5 C 4967 2.51 5 N 1261 2.21 5 O 1398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7641 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4343 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 496} Chain breaks: 4 Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3298 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 368} Chain breaks: 3 Time building chain proxies: 5.02, per 1000 atoms: 0.66 Number of scatterers: 7641 At special positions: 0 Unit cell: (78.155, 98.455, 127.89, 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 15 16.00 O 1398 8.00 N 1261 7.00 C 4967 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 40.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.928A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.731A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.907A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.981A pdb=" N GLY A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 270 " --> pdb=" O TRP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.520A pdb=" N THR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.839A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.561A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.779A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.515A pdb=" N GLN A 547 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.598A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.810A pdb=" N GLU B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 90' Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.557A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.293A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.052A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.504A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.953A pdb=" N TRP B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.219A pdb=" N LEU B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.540A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.679A pdb=" N THR B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.935A pdb=" N TRP B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.902A pdb=" N GLN B 428 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.843A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.592A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.571A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 459 removed outlier: 4.136A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 494 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 removed outlier: 4.020A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 110 Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 355 removed outlier: 7.964A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1784 1.33 - 1.45: 1570 1.45 - 1.57: 4465 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 7845 Sorted by residual: bond pdb=" N ASP A 237 " pdb=" CA ASP A 237 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.10e-02 8.26e+03 9.83e+00 bond pdb=" N HIS A 235 " pdb=" CA HIS A 235 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.18e-02 7.18e+03 9.42e+00 bond pdb=" N LEU A 234 " pdb=" CA LEU A 234 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.30e-02 5.92e+03 6.92e+00 bond pdb=" N TRP A 239 " pdb=" CA TRP A 239 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.26e-02 6.30e+03 5.84e+00 bond pdb=" N THR A 240 " pdb=" CA THR A 240 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.54e+00 ... (remaining 7840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 10351 1.70 - 3.40: 263 3.40 - 5.10: 31 5.10 - 6.80: 5 6.80 - 8.51: 2 Bond angle restraints: 10652 Sorted by residual: angle pdb=" C HIS A 235 " pdb=" CA HIS A 235 " pdb=" CB HIS A 235 " ideal model delta sigma weight residual 108.87 115.04 -6.17 1.55e+00 4.16e-01 1.59e+01 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 112.47 119.69 -7.22 2.06e+00 2.36e-01 1.23e+01 angle pdb=" CA THR A 240 " pdb=" C THR A 240 " pdb=" O THR A 240 " ideal model delta sigma weight residual 121.45 117.82 3.63 1.07e+00 8.73e-01 1.15e+01 angle pdb=" CA LYS A 238 " pdb=" C LYS A 238 " pdb=" O LYS A 238 " ideal model delta sigma weight residual 121.51 118.20 3.31 1.12e+00 7.97e-01 8.71e+00 angle pdb=" C HIS A 235 " pdb=" N PRO A 236 " pdb=" CA PRO A 236 " ideal model delta sigma weight residual 119.84 123.26 -3.42 1.25e+00 6.40e-01 7.48e+00 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 4317 16.64 - 33.27: 308 33.27 - 49.91: 78 49.91 - 66.54: 18 66.54 - 83.18: 4 Dihedral angle restraints: 4725 sinusoidal: 2009 harmonic: 2716 Sorted by residual: dihedral pdb=" CA LEU B 289 " pdb=" C LEU B 289 " pdb=" N THR B 290 " pdb=" CA THR B 290 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA PRO A 433 " pdb=" C PRO A 433 " pdb=" N ILE A 434 " pdb=" CA ILE A 434 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP B 185 " pdb=" C ASP B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 649 0.032 - 0.064: 326 0.064 - 0.096: 119 0.096 - 0.128: 54 0.128 - 0.160: 9 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CB ILE A 434 " pdb=" CA ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CG2 ILE A 434 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA PRO A 236 " pdb=" N PRO A 236 " pdb=" C PRO A 236 " pdb=" CB PRO A 236 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA PRO B 140 " pdb=" N PRO B 140 " pdb=" C PRO B 140 " pdb=" CB PRO B 140 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1154 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 421 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 239 " 0.024 2.00e-02 2.50e+03 1.25e-02 3.88e+00 pdb=" CG TRP A 239 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 239 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 239 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP A 239 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 239 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 239 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 239 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 411 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO B 412 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " 0.025 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 270 2.70 - 3.25: 7642 3.25 - 3.80: 11915 3.80 - 4.35: 13907 4.35 - 4.90: 23690 Nonbonded interactions: 57424 Sorted by model distance: nonbonded pdb=" N ASN A 545 " pdb=" OD1 ASN A 545 " model vdw 2.155 3.120 nonbonded pdb=" O SER A 162 " pdb=" OG1 THR A 165 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 354 " pdb=" OE1 GLU B 370 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR A 419 " pdb=" O PRO A 421 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR B 253 " pdb=" O GLU B 291 " model vdw 2.240 3.040 ... (remaining 57419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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 : 0.006 0.048 7845 Z= 0.383 Angle : 0.659 8.506 10652 Z= 0.378 Chirality : 0.046 0.160 1157 Planarity : 0.006 0.050 1335 Dihedral : 12.759 83.180 2969 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 8.22 % Allowed : 8.94 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.29), residues: 912 helix: 1.24 (0.31), residues: 297 sheet: -0.86 (0.42), residues: 150 loop : -0.73 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 239 HIS 0.006 0.001 HIS A 235 PHE 0.011 0.002 PHE A 124 TYR 0.019 0.002 TYR A 441 ARG 0.004 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 386 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7338 (pp20) REVERT: A 47 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6672 (tt) REVERT: A 48 SER cc_start: 0.8279 (t) cc_final: 0.7776 (p) REVERT: A 56 TYR cc_start: 0.7694 (m-80) cc_final: 0.7060 (m-80) REVERT: A 75 VAL cc_start: 0.7654 (t) cc_final: 0.7278 (m) REVERT: A 79 GLU cc_start: 0.6254 (pt0) cc_final: 0.5980 (pt0) REVERT: A 83 ARG cc_start: 0.7854 (mtt-85) cc_final: 0.5570 (mtp85) REVERT: A 86 ASP cc_start: 0.7125 (t70) cc_final: 0.6825 (t0) REVERT: A 87 PHE cc_start: 0.7684 (m-80) cc_final: 0.7420 (m-10) REVERT: A 101 LYS cc_start: 0.8415 (mttm) cc_final: 0.7687 (mtpp) REVERT: A 104 LYS cc_start: 0.8590 (tmtt) cc_final: 0.8273 (mtpp) REVERT: A 106 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7924 (t) REVERT: A 108 VAL cc_start: 0.8596 (t) cc_final: 0.8347 (p) REVERT: A 110 ASP cc_start: 0.6783 (p0) cc_final: 0.6557 (p0) REVERT: A 123 ASP cc_start: 0.8520 (p0) cc_final: 0.6693 (t0) REVERT: A 124 PHE cc_start: 0.8296 (t80) cc_final: 0.7982 (t80) REVERT: A 126 LYS cc_start: 0.8644 (mttm) cc_final: 0.8239 (mtmm) REVERT: A 142 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7104 (pt) REVERT: A 144 TYR cc_start: 0.6505 (m-80) cc_final: 0.6182 (m-80) REVERT: A 161 GLN cc_start: 0.8406 (tt0) cc_final: 0.7944 (tt0) REVERT: A 162 SER cc_start: 0.8719 (m) cc_final: 0.8488 (p) REVERT: A 169 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 172 LYS cc_start: 0.8858 (tttp) cc_final: 0.8497 (ttpt) REVERT: A 173 LYS cc_start: 0.8781 (tttt) cc_final: 0.8571 (tttt) REVERT: A 180 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 181 TYR cc_start: 0.7498 (m-80) cc_final: 0.7161 (m-80) REVERT: A 182 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 203 GLU cc_start: 0.7549 (tt0) cc_final: 0.7318 (tt0) REVERT: A 204 GLU cc_start: 0.7485 (tp30) cc_final: 0.7124 (tm-30) REVERT: A 206 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7441 (ttm-80) REVERT: A 208 HIS cc_start: 0.8153 (t-90) cc_final: 0.7823 (t-170) REVERT: A 217 PRO cc_start: 0.8027 (Cg_exo) cc_final: 0.7779 (Cg_endo) REVERT: A 232 TYR cc_start: 0.7930 (m-80) cc_final: 0.7689 (m-80) REVERT: A 233 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6798 (mt-10) REVERT: A 264 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 303 LEU cc_start: 0.8693 (mt) cc_final: 0.8293 (mt) REVERT: A 328 GLU cc_start: 0.7705 (tt0) cc_final: 0.7049 (tt0) REVERT: A 329 ILE cc_start: 0.8502 (mt) cc_final: 0.8224 (mt) REVERT: A 347 LYS cc_start: 0.8550 (mttt) cc_final: 0.8213 (mttm) REVERT: A 350 LYS cc_start: 0.8071 (tttt) cc_final: 0.7831 (ttpp) REVERT: A 354 TYR cc_start: 0.6330 (t80) cc_final: 0.6074 (t80) REVERT: A 357 MET cc_start: 0.5552 (tpt) cc_final: 0.5278 (tpt) REVERT: A 363 ASN cc_start: 0.7853 (t0) cc_final: 0.7543 (t0) REVERT: A 366 LYS cc_start: 0.8337 (tptm) cc_final: 0.7777 (ttmm) REVERT: A 370 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 374 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8004 (ttpp) REVERT: A 378 GLU cc_start: 0.7802 (tp30) cc_final: 0.7563 (tp30) REVERT: A 406 TRP cc_start: 0.7835 (p90) cc_final: 0.7296 (p90) REVERT: A 407 GLN cc_start: 0.7886 (mt0) cc_final: 0.7318 (mt0) REVERT: A 417 VAL cc_start: 0.8358 (t) cc_final: 0.8157 (m) REVERT: A 419 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7210 (p) REVERT: A 422 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 424 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.6899 (ttpp) REVERT: A 429 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8415 (mt) REVERT: A 454 LYS cc_start: 0.4669 (OUTLIER) cc_final: 0.4302 (mttp) REVERT: A 478 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 479 LEU cc_start: 0.8439 (tp) cc_final: 0.8133 (mm) REVERT: A 483 TYR cc_start: 0.7797 (t80) cc_final: 0.7421 (t80) REVERT: A 492 GLU cc_start: 0.6951 (mp0) cc_final: 0.6728 (mp0) REVERT: A 494 ASN cc_start: 0.7522 (m110) cc_final: 0.6997 (m110) REVERT: A 496 VAL cc_start: 0.8296 (t) cc_final: 0.7991 (m) REVERT: A 500 GLN cc_start: 0.7667 (pt0) cc_final: 0.7352 (pt0) REVERT: A 503 LEU cc_start: 0.8249 (tp) cc_final: 0.7822 (tp) REVERT: A 507 GLN cc_start: 0.8697 (pt0) cc_final: 0.8435 (pt0) REVERT: A 523 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 524 GLN cc_start: 0.7842 (tp40) cc_final: 0.7488 (mm-40) REVERT: A 529 GLU cc_start: 0.6989 (tp30) cc_final: 0.6757 (tp30) REVERT: A 540 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8002 (mmtt) REVERT: A 545 ASN cc_start: 0.4369 (OUTLIER) cc_final: 0.3365 (p0) REVERT: A 548 VAL cc_start: 0.2320 (t) cc_final: 0.1515 (m) REVERT: B 21 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.7964 (m) REVERT: B 22 LYS cc_start: 0.8263 (tttp) cc_final: 0.7859 (tttp) REVERT: B 27 THR cc_start: 0.8006 (p) cc_final: 0.7620 (p) REVERT: B 34 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 37 ILE cc_start: 0.8439 (mp) cc_final: 0.8164 (tt) REVERT: B 41 MET cc_start: 0.7683 (mtt) cc_final: 0.7457 (mtt) REVERT: B 42 GLU cc_start: 0.7023 (tt0) cc_final: 0.6649 (tt0) REVERT: B 57 ASN cc_start: 0.8083 (t0) cc_final: 0.7752 (t0) REVERT: B 77 PHE cc_start: 0.7999 (m-80) cc_final: 0.7720 (m-10) REVERT: B 82 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8148 (ttmt) REVERT: B 104 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7321 (ttmt) REVERT: B 131 THR cc_start: 0.7592 (m) cc_final: 0.7186 (p) REVERT: B 135 ILE cc_start: 0.8441 (mm) cc_final: 0.8108 (mm) REVERT: B 144 TYR cc_start: 0.8691 (m-80) cc_final: 0.8457 (m-80) REVERT: B 175 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.6753 (p0) REVERT: B 192 ASP cc_start: 0.8093 (t70) cc_final: 0.7671 (t70) REVERT: B 201 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7643 (mmtm) REVERT: B 204 GLU cc_start: 0.7985 (tp30) cc_final: 0.7568 (tp30) REVERT: B 256 ASP cc_start: 0.7366 (t70) cc_final: 0.6515 (t0) REVERT: B 257 ILE cc_start: 0.7823 (mt) cc_final: 0.7612 (mm) REVERT: B 260 LEU cc_start: 0.7595 (tp) cc_final: 0.7244 (mt) REVERT: B 263 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7704 (ttmp) REVERT: B 264 LEU cc_start: 0.8870 (tp) cc_final: 0.8615 (mm) REVERT: B 266 TRP cc_start: 0.7727 (t60) cc_final: 0.7383 (t60) REVERT: B 293 ILE cc_start: 0.6631 (mm) cc_final: 0.6382 (mm) REVERT: B 298 GLU cc_start: 0.8340 (pt0) cc_final: 0.7896 (tt0) REVERT: B 309 ILE cc_start: 0.8556 (mt) cc_final: 0.7979 (mt) REVERT: B 322 SER cc_start: 0.8746 (m) cc_final: 0.8239 (t) REVERT: B 328 GLU cc_start: 0.7067 (tt0) cc_final: 0.6850 (tt0) REVERT: B 347 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7930 (mttm) REVERT: B 350 LYS cc_start: 0.8203 (tptp) cc_final: 0.7920 (tppp) REVERT: B 356 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6509 (mmm160) REVERT: B 357 MET cc_start: 0.6218 (ptp) cc_final: 0.5984 (ptp) REVERT: B 391 LEU cc_start: 0.8518 (mt) cc_final: 0.8040 (mt) REVERT: B 396 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6903 (mt-10) REVERT: B 398 TRP cc_start: 0.8883 (t-100) cc_final: 0.8323 (t-100) outliers start: 69 outliers final: 28 residues processed: 426 average time/residue: 0.2239 time to fit residues: 122.6839 Evaluate side-chains 404 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 357 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 402 TRP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 480 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116073 restraints weight = 13906.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119951 restraints weight = 7083.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122398 restraints weight = 4251.501| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7845 Z= 0.227 Angle : 0.617 9.368 10652 Z= 0.319 Chirality : 0.045 0.172 1157 Planarity : 0.006 0.075 1335 Dihedral : 9.887 83.744 1090 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 7.87 % Allowed : 17.88 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.28), residues: 912 helix: 1.25 (0.30), residues: 311 sheet: -0.74 (0.41), residues: 141 loop : -0.63 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 239 HIS 0.003 0.001 HIS B 198 PHE 0.021 0.002 PHE A 227 TYR 0.025 0.002 TYR A 319 ARG 0.006 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 353 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7881 (p) REVERT: A 16 MET cc_start: 0.6048 (mmt) cc_final: 0.5639 (mmt) REVERT: A 29 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7010 (tm-30) REVERT: A 43 LYS cc_start: 0.8354 (tptp) cc_final: 0.8102 (tppt) REVERT: A 47 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6586 (tt) REVERT: A 50 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6816 (mm) REVERT: A 56 TYR cc_start: 0.7585 (m-80) cc_final: 0.7026 (m-80) REVERT: A 83 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.6688 (mtt90) REVERT: A 87 PHE cc_start: 0.7650 (m-80) cc_final: 0.7396 (m-10) REVERT: A 101 LYS cc_start: 0.8366 (mttm) cc_final: 0.7761 (mtpp) REVERT: A 104 LYS cc_start: 0.8556 (tmtt) cc_final: 0.8313 (mtpp) REVERT: A 126 LYS cc_start: 0.8589 (mttm) cc_final: 0.8071 (mtmm) REVERT: A 142 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7401 (pt) REVERT: A 162 SER cc_start: 0.8654 (m) cc_final: 0.8425 (p) REVERT: A 166 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8341 (tmtt) REVERT: A 169 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 173 LYS cc_start: 0.8705 (tttt) cc_final: 0.8492 (tttt) REVERT: A 180 ILE cc_start: 0.8578 (tp) cc_final: 0.8235 (mt) REVERT: A 181 TYR cc_start: 0.7530 (m-80) cc_final: 0.7215 (m-80) REVERT: A 182 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 203 GLU cc_start: 0.7331 (tt0) cc_final: 0.7100 (tt0) REVERT: A 204 GLU cc_start: 0.7388 (tp30) cc_final: 0.7021 (tm-30) REVERT: A 206 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7537 (ttm-80) REVERT: A 232 TYR cc_start: 0.8080 (m-80) cc_final: 0.7710 (m-80) REVERT: A 295 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7126 (pp) REVERT: A 328 GLU cc_start: 0.7463 (tt0) cc_final: 0.7006 (tt0) REVERT: A 329 ILE cc_start: 0.8415 (mt) cc_final: 0.8012 (mt) REVERT: A 330 GLN cc_start: 0.7738 (mp10) cc_final: 0.7439 (mp-120) REVERT: A 347 LYS cc_start: 0.8463 (mttt) cc_final: 0.8097 (mttp) REVERT: A 349 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8589 (mt) REVERT: A 350 LYS cc_start: 0.8486 (tttt) cc_final: 0.8230 (ttpp) REVERT: A 357 MET cc_start: 0.5556 (tpt) cc_final: 0.5250 (tpt) REVERT: A 366 LYS cc_start: 0.8304 (tptm) cc_final: 0.7790 (mtpp) REVERT: A 369 THR cc_start: 0.8126 (m) cc_final: 0.7921 (p) REVERT: A 370 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7297 (mt-10) REVERT: A 374 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8047 (ttpp) REVERT: A 378 GLU cc_start: 0.7848 (tp30) cc_final: 0.7646 (tp30) REVERT: A 405 TYR cc_start: 0.8164 (t80) cc_final: 0.7919 (t80) REVERT: A 406 TRP cc_start: 0.7792 (p90) cc_final: 0.7282 (p90) REVERT: A 407 GLN cc_start: 0.7680 (mt0) cc_final: 0.7298 (mt0) REVERT: A 422 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 476 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8048 (mttm) REVERT: A 478 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7212 (mm-30) REVERT: A 479 LEU cc_start: 0.8410 (tp) cc_final: 0.8081 (mm) REVERT: A 494 ASN cc_start: 0.7419 (m110) cc_final: 0.7131 (m110) REVERT: A 500 GLN cc_start: 0.7472 (pt0) cc_final: 0.7247 (pt0) REVERT: A 507 GLN cc_start: 0.8731 (pt0) cc_final: 0.8427 (pt0) REVERT: A 511 ASP cc_start: 0.6713 (m-30) cc_final: 0.6376 (m-30) REVERT: A 518 VAL cc_start: 0.8996 (t) cc_final: 0.8789 (p) REVERT: A 520 GLN cc_start: 0.7457 (tp40) cc_final: 0.6694 (tp-100) REVERT: A 523 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 524 GLN cc_start: 0.7654 (tp40) cc_final: 0.7261 (mm-40) REVERT: A 548 VAL cc_start: 0.2288 (OUTLIER) cc_final: 0.1431 (m) REVERT: B 21 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8214 (m) REVERT: B 22 LYS cc_start: 0.8088 (tttp) cc_final: 0.7654 (tttp) REVERT: B 34 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8170 (tt) REVERT: B 36 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7017 (mt-10) REVERT: B 41 MET cc_start: 0.7532 (mtt) cc_final: 0.7332 (mtt) REVERT: B 43 LYS cc_start: 0.8029 (tttp) cc_final: 0.7579 (tttp) REVERT: B 57 ASN cc_start: 0.8053 (t0) cc_final: 0.7821 (t0) REVERT: B 77 PHE cc_start: 0.7929 (m-80) cc_final: 0.7647 (m-10) REVERT: B 79 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7342 (mm-30) REVERT: B 82 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8142 (ttmm) REVERT: B 105 SER cc_start: 0.8007 (t) cc_final: 0.7779 (p) REVERT: B 128 THR cc_start: 0.7839 (p) cc_final: 0.7330 (t) REVERT: B 131 THR cc_start: 0.7817 (m) cc_final: 0.7309 (p) REVERT: B 167 ILE cc_start: 0.5154 (OUTLIER) cc_final: 0.4801 (tt) REVERT: B 178 ILE cc_start: 0.8441 (mt) cc_final: 0.8005 (tp) REVERT: B 248 GLU cc_start: 0.6728 (pm20) cc_final: 0.6240 (pm20) REVERT: B 256 ASP cc_start: 0.7033 (t70) cc_final: 0.6640 (t70) REVERT: B 263 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7728 (ttmp) REVERT: B 264 LEU cc_start: 0.8695 (tp) cc_final: 0.8445 (mm) REVERT: B 266 TRP cc_start: 0.7638 (t60) cc_final: 0.7060 (t60) REVERT: B 275 LYS cc_start: 0.8466 (mttm) cc_final: 0.8245 (mmtt) REVERT: B 298 GLU cc_start: 0.8436 (pt0) cc_final: 0.7867 (tt0) REVERT: B 309 ILE cc_start: 0.8332 (mt) cc_final: 0.7994 (mm) REVERT: B 322 SER cc_start: 0.8711 (m) cc_final: 0.8297 (p) REVERT: B 328 GLU cc_start: 0.7143 (tt0) cc_final: 0.6921 (tt0) REVERT: B 347 LYS cc_start: 0.8099 (mmtm) cc_final: 0.7873 (mttm) REVERT: B 374 LYS cc_start: 0.8178 (tttt) cc_final: 0.7822 (tptm) REVERT: B 391 LEU cc_start: 0.8449 (mt) cc_final: 0.8113 (mt) REVERT: B 396 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6648 (mt-10) REVERT: B 398 TRP cc_start: 0.8868 (t-100) cc_final: 0.8421 (t-100) REVERT: B 409 THR cc_start: 0.8229 (p) cc_final: 0.8012 (m) outliers start: 66 outliers final: 31 residues processed: 388 average time/residue: 0.2353 time to fit residues: 117.3764 Evaluate side-chains 385 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.0030 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 343 GLN A 367 GLN A 480 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 81 ASN B 197 GLN B 258 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 394 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115150 restraints weight = 14330.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119206 restraints weight = 7057.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121854 restraints weight = 4158.882| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7845 Z= 0.198 Angle : 0.588 9.062 10652 Z= 0.303 Chirality : 0.045 0.142 1157 Planarity : 0.005 0.056 1335 Dihedral : 8.391 86.962 1038 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 8.46 % Allowed : 20.14 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 912 helix: 1.24 (0.30), residues: 311 sheet: -0.79 (0.41), residues: 141 loop : -0.67 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 337 HIS 0.009 0.001 HIS B 235 PHE 0.023 0.002 PHE A 124 TYR 0.022 0.002 TYR A 319 ARG 0.006 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 341 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6776 (tm-30) REVERT: A 47 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6533 (tt) REVERT: A 50 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6582 (mp) REVERT: A 56 TYR cc_start: 0.7718 (m-80) cc_final: 0.7257 (m-80) REVERT: A 101 LYS cc_start: 0.8312 (mttm) cc_final: 0.7748 (mttm) REVERT: A 104 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8234 (mmmm) REVERT: A 110 ASP cc_start: 0.6546 (p0) cc_final: 0.6321 (p0) REVERT: A 126 LYS cc_start: 0.8532 (mttm) cc_final: 0.7843 (tptt) REVERT: A 142 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7372 (pt) REVERT: A 163 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8676 (m) REVERT: A 166 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8325 (tmtt) REVERT: A 169 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 172 LYS cc_start: 0.8814 (tttp) cc_final: 0.8593 (tttp) REVERT: A 173 LYS cc_start: 0.8712 (tttt) cc_final: 0.8347 (tppt) REVERT: A 180 ILE cc_start: 0.8473 (tp) cc_final: 0.8222 (mt) REVERT: A 181 TYR cc_start: 0.7607 (m-80) cc_final: 0.7307 (m-80) REVERT: A 182 GLN cc_start: 0.7094 (tm-30) cc_final: 0.6784 (tm-30) REVERT: A 203 GLU cc_start: 0.7334 (tt0) cc_final: 0.6951 (tt0) REVERT: A 204 GLU cc_start: 0.7425 (tp30) cc_final: 0.7016 (tm-30) REVERT: A 206 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7536 (ttm-80) REVERT: A 232 TYR cc_start: 0.7986 (m-80) cc_final: 0.7618 (m-80) REVERT: A 315 HIS cc_start: 0.7855 (m-70) cc_final: 0.7649 (m170) REVERT: A 329 ILE cc_start: 0.8392 (mt) cc_final: 0.8065 (mt) REVERT: A 330 GLN cc_start: 0.7695 (mp10) cc_final: 0.7346 (mp10) REVERT: A 347 LYS cc_start: 0.8403 (mttt) cc_final: 0.8022 (mttp) REVERT: A 349 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8603 (mt) REVERT: A 350 LYS cc_start: 0.8383 (tttt) cc_final: 0.8121 (ttpp) REVERT: A 357 MET cc_start: 0.5624 (tpt) cc_final: 0.5271 (tpt) REVERT: A 363 ASN cc_start: 0.7615 (t0) cc_final: 0.7271 (t0) REVERT: A 366 LYS cc_start: 0.8287 (tptm) cc_final: 0.7745 (mtpp) REVERT: A 369 THR cc_start: 0.8161 (m) cc_final: 0.7912 (p) REVERT: A 370 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7294 (mt-10) REVERT: A 374 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7978 (ttpp) REVERT: A 378 GLU cc_start: 0.7914 (tp30) cc_final: 0.7624 (tp30) REVERT: A 406 TRP cc_start: 0.7821 (p90) cc_final: 0.7091 (p90) REVERT: A 407 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: A 422 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 476 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7993 (mtpp) REVERT: A 478 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 479 LEU cc_start: 0.8418 (tp) cc_final: 0.8176 (mm) REVERT: A 483 TYR cc_start: 0.7915 (t80) cc_final: 0.6986 (t80) REVERT: A 494 ASN cc_start: 0.7394 (m110) cc_final: 0.7077 (m110) REVERT: A 500 GLN cc_start: 0.7554 (pt0) cc_final: 0.7226 (pt0) REVERT: A 503 LEU cc_start: 0.8042 (tp) cc_final: 0.7210 (tp) REVERT: A 507 GLN cc_start: 0.8705 (pt0) cc_final: 0.8097 (pt0) REVERT: A 511 ASP cc_start: 0.6524 (m-30) cc_final: 0.6271 (m-30) REVERT: A 520 GLN cc_start: 0.7579 (tp40) cc_final: 0.6383 (tp-100) REVERT: A 523 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7600 (mt-10) REVERT: A 535 TRP cc_start: 0.8601 (t60) cc_final: 0.8300 (t60) REVERT: A 540 LYS cc_start: 0.8218 (mmtt) cc_final: 0.8016 (mmmm) REVERT: A 545 ASN cc_start: 0.5079 (OUTLIER) cc_final: 0.4655 (p0) REVERT: A 548 VAL cc_start: 0.2117 (OUTLIER) cc_final: 0.1268 (m) REVERT: B 13 LYS cc_start: 0.7701 (mttm) cc_final: 0.7455 (mmtm) REVERT: B 21 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8257 (m) REVERT: B 36 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6996 (mt-10) REVERT: B 43 LYS cc_start: 0.8001 (tttp) cc_final: 0.7523 (tttp) REVERT: B 57 ASN cc_start: 0.8039 (t0) cc_final: 0.7800 (t0) REVERT: B 77 PHE cc_start: 0.7873 (m-80) cc_final: 0.7547 (m-10) REVERT: B 79 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7395 (mm-30) REVERT: B 82 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8046 (ttmm) REVERT: B 86 ASP cc_start: 0.7042 (p0) cc_final: 0.6111 (p0) REVERT: B 102 LYS cc_start: 0.8635 (mppt) cc_final: 0.8108 (mptt) REVERT: B 105 SER cc_start: 0.7939 (t) cc_final: 0.7703 (p) REVERT: B 128 THR cc_start: 0.7840 (p) cc_final: 0.7353 (t) REVERT: B 143 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6293 (ptt180) REVERT: B 167 ILE cc_start: 0.5072 (OUTLIER) cc_final: 0.4753 (tt) REVERT: B 178 ILE cc_start: 0.8396 (mt) cc_final: 0.7969 (tp) REVERT: B 248 GLU cc_start: 0.6723 (pm20) cc_final: 0.6268 (pm20) REVERT: B 256 ASP cc_start: 0.7247 (t70) cc_final: 0.6852 (t70) REVERT: B 260 LEU cc_start: 0.7749 (mt) cc_final: 0.7373 (mt) REVERT: B 263 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7716 (ttmp) REVERT: B 264 LEU cc_start: 0.8663 (tp) cc_final: 0.8448 (mm) REVERT: B 266 TRP cc_start: 0.7753 (t60) cc_final: 0.7156 (t60) REVERT: B 297 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: B 298 GLU cc_start: 0.8357 (pt0) cc_final: 0.7096 (tt0) REVERT: B 322 SER cc_start: 0.8733 (m) cc_final: 0.8317 (p) REVERT: B 328 GLU cc_start: 0.7284 (tt0) cc_final: 0.7046 (tt0) REVERT: B 347 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7806 (mttm) REVERT: B 374 LYS cc_start: 0.8172 (tttt) cc_final: 0.7824 (tptp) REVERT: B 378 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7130 (tp30) REVERT: B 388 LYS cc_start: 0.8014 (tttt) cc_final: 0.7672 (tttt) REVERT: B 391 LEU cc_start: 0.8466 (mt) cc_final: 0.7996 (mt) REVERT: B 396 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6705 (mt-10) REVERT: B 398 TRP cc_start: 0.8844 (t-100) cc_final: 0.8310 (t-100) outliers start: 71 outliers final: 36 residues processed: 371 average time/residue: 0.2184 time to fit residues: 105.3166 Evaluate side-chains 391 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 44 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 330 GLN ** 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 = 0.3726 r_free = 0.3726 target = 0.133381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116911 restraints weight = 14110.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120830 restraints weight = 7068.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123358 restraints weight = 4226.103| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7845 Z= 0.181 Angle : 0.580 9.496 10652 Z= 0.297 Chirality : 0.044 0.136 1157 Planarity : 0.005 0.052 1335 Dihedral : 8.050 86.234 1033 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 7.27 % Allowed : 21.10 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.28), residues: 912 helix: 1.34 (0.30), residues: 311 sheet: -0.74 (0.41), residues: 140 loop : -0.65 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 337 HIS 0.007 0.001 HIS A 208 PHE 0.022 0.002 PHE A 124 TYR 0.023 0.002 TYR A 319 ARG 0.004 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 351 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6063 (mmt) cc_final: 0.5795 (mmt) REVERT: A 29 GLU cc_start: 0.7615 (tm-30) cc_final: 0.6980 (tm-30) REVERT: A 43 LYS cc_start: 0.8290 (tptp) cc_final: 0.8079 (tppt) REVERT: A 47 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6310 (tt) REVERT: A 50 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.6503 (mt) REVERT: A 56 TYR cc_start: 0.7628 (m-80) cc_final: 0.7032 (m-80) REVERT: A 83 ARG cc_start: 0.7548 (mtt-85) cc_final: 0.7292 (mtt180) REVERT: A 97 PRO cc_start: 0.8437 (Cg_exo) cc_final: 0.8179 (Cg_endo) REVERT: A 101 LYS cc_start: 0.8346 (mttm) cc_final: 0.7787 (mttm) REVERT: A 104 LYS cc_start: 0.8607 (tmtt) cc_final: 0.8297 (mmtt) REVERT: A 123 ASP cc_start: 0.8504 (p0) cc_final: 0.7998 (p0) REVERT: A 126 LYS cc_start: 0.8419 (mttm) cc_final: 0.7829 (tptt) REVERT: A 142 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7388 (pt) REVERT: A 163 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8643 (m) REVERT: A 166 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8324 (tmtt) REVERT: A 169 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 172 LYS cc_start: 0.8731 (tttp) cc_final: 0.8520 (tttp) REVERT: A 173 LYS cc_start: 0.8606 (tttt) cc_final: 0.8280 (tttt) REVERT: A 180 ILE cc_start: 0.8483 (tp) cc_final: 0.8250 (mt) REVERT: A 181 TYR cc_start: 0.7627 (m-80) cc_final: 0.7357 (m-80) REVERT: A 182 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6704 (tm-30) REVERT: A 194 GLU cc_start: 0.7415 (tp30) cc_final: 0.7108 (tp30) REVERT: A 203 GLU cc_start: 0.7275 (tt0) cc_final: 0.6845 (tt0) REVERT: A 204 GLU cc_start: 0.7381 (tp30) cc_final: 0.7035 (tm-30) REVERT: A 206 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7641 (mtp85) REVERT: A 233 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 329 ILE cc_start: 0.8412 (mt) cc_final: 0.8083 (mt) REVERT: A 330 GLN cc_start: 0.7846 (mp10) cc_final: 0.7439 (mp10) REVERT: A 342 TYR cc_start: 0.8236 (p90) cc_final: 0.8034 (p90) REVERT: A 347 LYS cc_start: 0.8412 (mttt) cc_final: 0.8036 (mttp) REVERT: A 349 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8610 (mt) REVERT: A 350 LYS cc_start: 0.8391 (tttt) cc_final: 0.8143 (ttpp) REVERT: A 357 MET cc_start: 0.5578 (tpt) cc_final: 0.5230 (tpt) REVERT: A 363 ASN cc_start: 0.7698 (t0) cc_final: 0.7331 (t0) REVERT: A 366 LYS cc_start: 0.8281 (tptm) cc_final: 0.7681 (mtpp) REVERT: A 369 THR cc_start: 0.8210 (m) cc_final: 0.7962 (p) REVERT: A 370 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 374 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8056 (ttpp) REVERT: A 406 TRP cc_start: 0.7861 (p90) cc_final: 0.7174 (p90) REVERT: A 407 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7292 (mt0) REVERT: A 414 TRP cc_start: 0.8691 (p-90) cc_final: 0.8038 (p-90) REVERT: A 422 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7802 (mp) REVERT: A 478 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7084 (mm-30) REVERT: A 494 ASN cc_start: 0.7412 (m110) cc_final: 0.7100 (m110) REVERT: A 500 GLN cc_start: 0.7499 (pt0) cc_final: 0.7216 (pt0) REVERT: A 503 LEU cc_start: 0.8062 (tp) cc_final: 0.7077 (tp) REVERT: A 505 ILE cc_start: 0.8442 (mt) cc_final: 0.8151 (mm) REVERT: A 507 GLN cc_start: 0.8705 (pt0) cc_final: 0.8018 (pt0) REVERT: A 535 TRP cc_start: 0.8604 (t60) cc_final: 0.8394 (t60) REVERT: A 548 VAL cc_start: 0.2352 (OUTLIER) cc_final: 0.1485 (m) REVERT: B 21 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8211 (m) REVERT: B 34 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8123 (tt) REVERT: B 36 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6975 (mt-10) REVERT: B 43 LYS cc_start: 0.8015 (tttp) cc_final: 0.7539 (tttp) REVERT: B 57 ASN cc_start: 0.8000 (t0) cc_final: 0.7796 (t0) REVERT: B 77 PHE cc_start: 0.7939 (m-80) cc_final: 0.7558 (m-10) REVERT: B 79 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7328 (mm-30) REVERT: B 82 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8142 (ttmm) REVERT: B 86 ASP cc_start: 0.7034 (p0) cc_final: 0.6433 (p0) REVERT: B 102 LYS cc_start: 0.8644 (mppt) cc_final: 0.8118 (mptt) REVERT: B 105 SER cc_start: 0.8003 (t) cc_final: 0.7772 (p) REVERT: B 128 THR cc_start: 0.7814 (p) cc_final: 0.7360 (t) REVERT: B 143 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.6274 (ptt180) REVERT: B 167 ILE cc_start: 0.4955 (OUTLIER) cc_final: 0.4650 (tt) REVERT: B 178 ILE cc_start: 0.8387 (mt) cc_final: 0.7999 (tp) REVERT: B 248 GLU cc_start: 0.6624 (pm20) cc_final: 0.6230 (pm20) REVERT: B 256 ASP cc_start: 0.7123 (t70) cc_final: 0.6688 (t70) REVERT: B 260 LEU cc_start: 0.7693 (mt) cc_final: 0.7292 (mt) REVERT: B 263 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7639 (ttmp) REVERT: B 266 TRP cc_start: 0.7689 (t60) cc_final: 0.7135 (t60) REVERT: B 298 GLU cc_start: 0.8249 (pt0) cc_final: 0.7751 (tt0) REVERT: B 300 GLU cc_start: 0.7826 (tt0) cc_final: 0.7521 (tt0) REVERT: B 309 ILE cc_start: 0.8353 (mt) cc_final: 0.7959 (mm) REVERT: B 322 SER cc_start: 0.8690 (m) cc_final: 0.8301 (p) REVERT: B 328 GLU cc_start: 0.7266 (tt0) cc_final: 0.7004 (tt0) REVERT: B 339 TYR cc_start: 0.8228 (p90) cc_final: 0.7671 (p90) REVERT: B 347 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7857 (mttm) REVERT: B 353 LYS cc_start: 0.8332 (ptpp) cc_final: 0.7942 (ptpp) REVERT: B 374 LYS cc_start: 0.8177 (tttt) cc_final: 0.7816 (tptp) REVERT: B 388 LYS cc_start: 0.8064 (tttt) cc_final: 0.7730 (tttt) REVERT: B 391 LEU cc_start: 0.8494 (mt) cc_final: 0.8049 (mt) REVERT: B 396 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6655 (mt-10) REVERT: B 398 TRP cc_start: 0.8874 (t-100) cc_final: 0.8307 (t-100) outliers start: 61 outliers final: 32 residues processed: 378 average time/residue: 0.2258 time to fit residues: 109.9406 Evaluate side-chains 385 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 339 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.0570 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 480 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 81 ASN B 96 HIS B 182 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116884 restraints weight = 14253.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121052 restraints weight = 7003.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123762 restraints weight = 4139.250| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7845 Z= 0.181 Angle : 0.569 9.598 10652 Z= 0.291 Chirality : 0.044 0.137 1157 Planarity : 0.005 0.042 1335 Dihedral : 7.814 85.627 1031 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 7.63 % Allowed : 23.00 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.29), residues: 912 helix: 1.37 (0.31), residues: 310 sheet: -0.66 (0.41), residues: 140 loop : -0.67 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 337 HIS 0.005 0.001 HIS A 208 PHE 0.025 0.002 PHE A 171 TYR 0.028 0.002 TYR A 319 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 339 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.5984 (mmt) cc_final: 0.5678 (mmt) REVERT: A 47 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6165 (tt) REVERT: A 50 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6568 (mt) REVERT: A 56 TYR cc_start: 0.7655 (m-80) cc_final: 0.7056 (m-80) REVERT: A 83 ARG cc_start: 0.7364 (mtt-85) cc_final: 0.7104 (mtt180) REVERT: A 101 LYS cc_start: 0.8309 (mttm) cc_final: 0.7645 (mtpp) REVERT: A 123 ASP cc_start: 0.8548 (p0) cc_final: 0.8051 (p0) REVERT: A 125 ARG cc_start: 0.7728 (ptt180) cc_final: 0.7456 (ttt180) REVERT: A 126 LYS cc_start: 0.8446 (mttm) cc_final: 0.7780 (tptt) REVERT: A 142 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7318 (pt) REVERT: A 163 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8613 (m) REVERT: A 166 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8328 (tmtt) REVERT: A 169 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 172 LYS cc_start: 0.8794 (tttp) cc_final: 0.8570 (tttp) REVERT: A 173 LYS cc_start: 0.8672 (tttt) cc_final: 0.8435 (tttt) REVERT: A 180 ILE cc_start: 0.8452 (tp) cc_final: 0.8231 (mt) REVERT: A 181 TYR cc_start: 0.7651 (m-80) cc_final: 0.7331 (m-80) REVERT: A 182 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6709 (tm-30) REVERT: A 203 GLU cc_start: 0.7281 (tt0) cc_final: 0.6853 (tt0) REVERT: A 204 GLU cc_start: 0.7461 (tp30) cc_final: 0.7087 (tm-30) REVERT: A 206 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7677 (mtp85) REVERT: A 233 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6375 (mp0) REVERT: A 241 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8260 (t) REVERT: A 329 ILE cc_start: 0.8399 (mt) cc_final: 0.8034 (mt) REVERT: A 330 GLN cc_start: 0.7795 (mp10) cc_final: 0.7322 (mp10) REVERT: A 347 LYS cc_start: 0.8376 (mttt) cc_final: 0.8010 (mttp) REVERT: A 350 LYS cc_start: 0.8341 (tttt) cc_final: 0.8069 (ttpp) REVERT: A 357 MET cc_start: 0.5566 (tpt) cc_final: 0.5219 (tpt) REVERT: A 366 LYS cc_start: 0.8280 (tptm) cc_final: 0.7643 (mtpp) REVERT: A 369 THR cc_start: 0.8214 (m) cc_final: 0.7890 (p) REVERT: A 370 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 374 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7962 (ttpp) REVERT: A 406 TRP cc_start: 0.7860 (p90) cc_final: 0.7152 (p90) REVERT: A 407 GLN cc_start: 0.7872 (mt0) cc_final: 0.7362 (mt0) REVERT: A 422 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7787 (mp) REVERT: A 478 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 494 ASN cc_start: 0.7408 (m110) cc_final: 0.7022 (m110) REVERT: A 500 GLN cc_start: 0.7564 (pt0) cc_final: 0.7358 (pt0) REVERT: A 503 LEU cc_start: 0.8043 (tp) cc_final: 0.7119 (tp) REVERT: A 505 ILE cc_start: 0.8467 (mt) cc_final: 0.8204 (mm) REVERT: A 507 GLN cc_start: 0.8665 (pt0) cc_final: 0.8020 (pt0) REVERT: A 520 GLN cc_start: 0.6965 (tp40) cc_final: 0.6704 (tm-30) REVERT: A 545 ASN cc_start: 0.5030 (OUTLIER) cc_final: 0.4603 (p0) REVERT: A 548 VAL cc_start: 0.2158 (OUTLIER) cc_final: 0.1290 (m) REVERT: B 13 LYS cc_start: 0.7488 (mptt) cc_final: 0.7279 (mmtp) REVERT: B 21 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8217 (m) REVERT: B 36 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6980 (mt-10) REVERT: B 43 LYS cc_start: 0.8022 (tttp) cc_final: 0.7509 (tttp) REVERT: B 44 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 57 ASN cc_start: 0.8093 (t0) cc_final: 0.7834 (t0) REVERT: B 77 PHE cc_start: 0.7884 (m-80) cc_final: 0.7532 (m-10) REVERT: B 79 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7369 (mm-30) REVERT: B 82 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8198 (ttmm) REVERT: B 86 ASP cc_start: 0.7001 (p0) cc_final: 0.6374 (p0) REVERT: B 102 LYS cc_start: 0.8652 (mppt) cc_final: 0.8122 (mptt) REVERT: B 105 SER cc_start: 0.7919 (t) cc_final: 0.7664 (p) REVERT: B 128 THR cc_start: 0.7781 (p) cc_final: 0.7377 (t) REVERT: B 143 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6322 (ptt180) REVERT: B 167 ILE cc_start: 0.4921 (OUTLIER) cc_final: 0.4637 (tt) REVERT: B 178 ILE cc_start: 0.8406 (mt) cc_final: 0.7966 (tp) REVERT: B 192 ASP cc_start: 0.7991 (t0) cc_final: 0.7622 (m-30) REVERT: B 248 GLU cc_start: 0.6720 (pm20) cc_final: 0.6271 (pm20) REVERT: B 256 ASP cc_start: 0.7161 (t70) cc_final: 0.6343 (t70) REVERT: B 260 LEU cc_start: 0.7542 (mt) cc_final: 0.7174 (mt) REVERT: B 263 LYS cc_start: 0.7948 (ttmp) cc_final: 0.7716 (ttmp) REVERT: B 266 TRP cc_start: 0.7762 (t60) cc_final: 0.7167 (t60) REVERT: B 298 GLU cc_start: 0.8382 (pt0) cc_final: 0.7739 (tt0) REVERT: B 300 GLU cc_start: 0.7871 (tt0) cc_final: 0.7600 (tt0) REVERT: B 309 ILE cc_start: 0.8369 (mt) cc_final: 0.7986 (mm) REVERT: B 322 SER cc_start: 0.8720 (m) cc_final: 0.8327 (p) REVERT: B 328 GLU cc_start: 0.7303 (tt0) cc_final: 0.6991 (tt0) REVERT: B 347 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7819 (mttm) REVERT: B 353 LYS cc_start: 0.8312 (ptpp) cc_final: 0.8004 (ptpp) REVERT: B 370 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7291 (mt-10) REVERT: B 388 LYS cc_start: 0.8046 (tttt) cc_final: 0.7707 (tttt) REVERT: B 396 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6668 (mt-10) REVERT: B 398 TRP cc_start: 0.8885 (t-100) cc_final: 0.8503 (t-100) outliers start: 64 outliers final: 37 residues processed: 369 average time/residue: 0.2312 time to fit residues: 109.5489 Evaluate side-chains 382 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 333 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS A 332 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN B 23 GLN B 81 ASN B 96 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116145 restraints weight = 14300.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119982 restraints weight = 7192.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122524 restraints weight = 4317.344| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7845 Z= 0.219 Angle : 0.586 9.961 10652 Z= 0.301 Chirality : 0.045 0.140 1157 Planarity : 0.005 0.041 1335 Dihedral : 7.271 85.324 1020 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 8.22 % Allowed : 23.84 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 912 helix: 1.25 (0.30), residues: 310 sheet: -0.80 (0.41), residues: 140 loop : -0.70 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 337 HIS 0.005 0.001 HIS A 315 PHE 0.026 0.002 PHE A 171 TYR 0.028 0.002 TYR A 319 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 330 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6218 (tt) REVERT: A 50 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6241 (mt) REVERT: A 56 TYR cc_start: 0.7644 (m-80) cc_final: 0.7107 (m-80) REVERT: A 101 LYS cc_start: 0.8252 (mttm) cc_final: 0.7735 (mtpt) REVERT: A 104 LYS cc_start: 0.8616 (tmtt) cc_final: 0.8246 (mmmm) REVERT: A 123 ASP cc_start: 0.8479 (p0) cc_final: 0.7976 (p0) REVERT: A 126 LYS cc_start: 0.8434 (mttm) cc_final: 0.7873 (tptt) REVERT: A 142 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7374 (pt) REVERT: A 163 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8624 (m) REVERT: A 166 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8362 (tmtt) REVERT: A 169 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 172 LYS cc_start: 0.8755 (tttp) cc_final: 0.8535 (tttp) REVERT: A 173 LYS cc_start: 0.8619 (tttt) cc_final: 0.8262 (tppt) REVERT: A 180 ILE cc_start: 0.8505 (tp) cc_final: 0.8260 (mt) REVERT: A 181 TYR cc_start: 0.7664 (m-80) cc_final: 0.7378 (m-80) REVERT: A 182 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6716 (tm-30) REVERT: A 201 LYS cc_start: 0.8121 (tppt) cc_final: 0.7832 (tptp) REVERT: A 203 GLU cc_start: 0.7277 (tt0) cc_final: 0.6856 (tt0) REVERT: A 204 GLU cc_start: 0.7448 (tp30) cc_final: 0.7059 (tm-30) REVERT: A 206 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7677 (mtp85) REVERT: A 233 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6180 (mp0) REVERT: A 240 THR cc_start: 0.7513 (OUTLIER) cc_final: 0.7154 (t) REVERT: A 263 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8680 (tttm) REVERT: A 329 ILE cc_start: 0.8401 (mt) cc_final: 0.8024 (mt) REVERT: A 330 GLN cc_start: 0.7904 (mp10) cc_final: 0.7447 (mp10) REVERT: A 347 LYS cc_start: 0.8398 (mttt) cc_final: 0.8031 (mttp) REVERT: A 350 LYS cc_start: 0.8360 (tttt) cc_final: 0.8155 (ttpp) REVERT: A 357 MET cc_start: 0.5441 (tpt) cc_final: 0.5170 (tpt) REVERT: A 366 LYS cc_start: 0.8270 (tptm) cc_final: 0.7786 (mtpp) REVERT: A 369 THR cc_start: 0.8206 (m) cc_final: 0.7899 (p) REVERT: A 370 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7217 (mt-10) REVERT: A 374 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7975 (ttpp) REVERT: A 406 TRP cc_start: 0.7838 (p90) cc_final: 0.7110 (p90) REVERT: A 407 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7213 (mt0) REVERT: A 422 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 476 LYS cc_start: 0.8127 (mttm) cc_final: 0.7810 (mtpp) REVERT: A 478 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 494 ASN cc_start: 0.7437 (m110) cc_final: 0.7119 (m110) REVERT: A 500 GLN cc_start: 0.7492 (pt0) cc_final: 0.7271 (pt0) REVERT: A 503 LEU cc_start: 0.8114 (tp) cc_final: 0.7196 (tp) REVERT: A 507 GLN cc_start: 0.8660 (pt0) cc_final: 0.8051 (pt0) REVERT: A 520 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: A 540 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7991 (mmmm) REVERT: A 545 ASN cc_start: 0.5146 (OUTLIER) cc_final: 0.4710 (p0) REVERT: A 548 VAL cc_start: 0.2084 (OUTLIER) cc_final: 0.1154 (m) REVERT: B 13 LYS cc_start: 0.7511 (mptt) cc_final: 0.7100 (mmtm) REVERT: B 21 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8231 (m) REVERT: B 36 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7018 (mt-10) REVERT: B 43 LYS cc_start: 0.8014 (tttp) cc_final: 0.7534 (tttp) REVERT: B 44 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7193 (mm-30) REVERT: B 57 ASN cc_start: 0.8114 (t0) cc_final: 0.7877 (t0) REVERT: B 77 PHE cc_start: 0.7962 (m-80) cc_final: 0.7615 (m-10) REVERT: B 79 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7279 (mm-30) REVERT: B 82 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8197 (ttmm) REVERT: B 86 ASP cc_start: 0.6974 (p0) cc_final: 0.6301 (p0) REVERT: B 105 SER cc_start: 0.7976 (t) cc_final: 0.7750 (p) REVERT: B 128 THR cc_start: 0.7797 (p) cc_final: 0.7406 (t) REVERT: B 143 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6366 (ptt180) REVERT: B 167 ILE cc_start: 0.4954 (OUTLIER) cc_final: 0.4626 (tt) REVERT: B 178 ILE cc_start: 0.8404 (mt) cc_final: 0.8001 (tp) REVERT: B 256 ASP cc_start: 0.7036 (t70) cc_final: 0.6300 (t70) REVERT: B 260 LEU cc_start: 0.7569 (mt) cc_final: 0.7260 (mt) REVERT: B 263 LYS cc_start: 0.7933 (ttmp) cc_final: 0.7698 (ttmp) REVERT: B 266 TRP cc_start: 0.7714 (t60) cc_final: 0.7165 (t60) REVERT: B 295 LEU cc_start: 0.7019 (pt) cc_final: 0.6619 (pt) REVERT: B 297 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: B 298 GLU cc_start: 0.8344 (pt0) cc_final: 0.7445 (tt0) REVERT: B 308 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 309 ILE cc_start: 0.8381 (mt) cc_final: 0.8073 (mm) REVERT: B 322 SER cc_start: 0.8710 (m) cc_final: 0.8327 (p) REVERT: B 328 GLU cc_start: 0.7308 (tt0) cc_final: 0.7044 (tt0) REVERT: B 347 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7847 (mttm) REVERT: B 353 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7803 (ptpp) REVERT: B 370 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7266 (mt-10) REVERT: B 388 LYS cc_start: 0.8045 (tttt) cc_final: 0.7741 (tttt) REVERT: B 396 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6691 (mt-10) REVERT: B 398 TRP cc_start: 0.8871 (t-100) cc_final: 0.8468 (t-100) outliers start: 69 outliers final: 45 residues processed: 358 average time/residue: 0.2243 time to fit residues: 103.3332 Evaluate side-chains 386 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 326 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 48 optimal weight: 0.0000 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 81 ASN B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117546 restraints weight = 14255.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121386 restraints weight = 7194.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123933 restraints weight = 4305.797| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7845 Z= 0.173 Angle : 0.588 10.767 10652 Z= 0.299 Chirality : 0.044 0.139 1157 Planarity : 0.005 0.043 1335 Dihedral : 6.950 83.238 1019 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 7.51 % Allowed : 25.74 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 912 helix: 1.39 (0.31), residues: 304 sheet: -0.83 (0.38), residues: 162 loop : -0.62 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 401 HIS 0.005 0.001 HIS A 208 PHE 0.026 0.002 PHE A 171 TYR 0.028 0.001 TYR A 319 ARG 0.006 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 341 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.7534 (m-80) cc_final: 0.7026 (m-80) REVERT: A 101 LYS cc_start: 0.8231 (mttm) cc_final: 0.7630 (mtpp) REVERT: A 122 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5727 (tp30) REVERT: A 123 ASP cc_start: 0.8443 (p0) cc_final: 0.8116 (p0) REVERT: A 125 ARG cc_start: 0.7754 (ptt180) cc_final: 0.7178 (ttt180) REVERT: A 126 LYS cc_start: 0.8454 (mttm) cc_final: 0.7794 (tptt) REVERT: A 144 TYR cc_start: 0.6585 (m-80) cc_final: 0.6359 (m-80) REVERT: A 163 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8589 (m) REVERT: A 166 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8337 (tmtt) REVERT: A 169 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 172 LYS cc_start: 0.8712 (tttp) cc_final: 0.8496 (tttp) REVERT: A 173 LYS cc_start: 0.8584 (tttt) cc_final: 0.8330 (tttt) REVERT: A 180 ILE cc_start: 0.8483 (tp) cc_final: 0.8254 (mt) REVERT: A 181 TYR cc_start: 0.7675 (m-80) cc_final: 0.7419 (m-80) REVERT: A 182 GLN cc_start: 0.6995 (tm-30) cc_final: 0.6647 (tm-30) REVERT: A 203 GLU cc_start: 0.7193 (tt0) cc_final: 0.6792 (tt0) REVERT: A 204 GLU cc_start: 0.7377 (tp30) cc_final: 0.7025 (tm-30) REVERT: A 206 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7636 (mtp85) REVERT: A 329 ILE cc_start: 0.8366 (mt) cc_final: 0.8007 (mt) REVERT: A 330 GLN cc_start: 0.7902 (mp10) cc_final: 0.7323 (mp10) REVERT: A 342 TYR cc_start: 0.8138 (p90) cc_final: 0.7936 (p90) REVERT: A 347 LYS cc_start: 0.8364 (mttt) cc_final: 0.8063 (mtpp) REVERT: A 350 LYS cc_start: 0.8390 (tttt) cc_final: 0.8137 (ttpp) REVERT: A 354 TYR cc_start: 0.6112 (t80) cc_final: 0.5741 (t80) REVERT: A 357 MET cc_start: 0.5399 (tpt) cc_final: 0.5134 (tpt) REVERT: A 366 LYS cc_start: 0.8215 (tptm) cc_final: 0.7657 (mtpp) REVERT: A 369 THR cc_start: 0.8175 (m) cc_final: 0.7859 (p) REVERT: A 370 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 374 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8019 (ttpp) REVERT: A 383 TRP cc_start: 0.8203 (m-90) cc_final: 0.7232 (m-90) REVERT: A 406 TRP cc_start: 0.7754 (p90) cc_final: 0.7268 (p90) REVERT: A 407 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7383 (mt0) REVERT: A 414 TRP cc_start: 0.8728 (p-90) cc_final: 0.7956 (p-90) REVERT: A 422 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7787 (mp) REVERT: A 430 GLU cc_start: 0.7780 (mp0) cc_final: 0.7553 (mp0) REVERT: A 478 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 494 ASN cc_start: 0.7385 (m110) cc_final: 0.7083 (m110) REVERT: A 500 GLN cc_start: 0.7460 (pt0) cc_final: 0.7174 (pt0) REVERT: A 503 LEU cc_start: 0.8120 (tp) cc_final: 0.7191 (tp) REVERT: A 507 GLN cc_start: 0.8631 (pt0) cc_final: 0.8003 (pt0) REVERT: A 520 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: A 545 ASN cc_start: 0.4902 (OUTLIER) cc_final: 0.4471 (p0) REVERT: A 548 VAL cc_start: 0.1990 (OUTLIER) cc_final: 0.1098 (m) REVERT: B 13 LYS cc_start: 0.7402 (mptt) cc_final: 0.6960 (mmtp) REVERT: B 21 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8203 (m) REVERT: B 36 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6979 (mt-10) REVERT: B 43 LYS cc_start: 0.8035 (tttp) cc_final: 0.7531 (tttp) REVERT: B 44 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 57 ASN cc_start: 0.8073 (t0) cc_final: 0.7859 (t0) REVERT: B 77 PHE cc_start: 0.7934 (m-80) cc_final: 0.7681 (m-10) REVERT: B 82 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8089 (mttm) REVERT: B 86 ASP cc_start: 0.6962 (p0) cc_final: 0.6241 (p0) REVERT: B 102 LYS cc_start: 0.8619 (mppt) cc_final: 0.8146 (mptt) REVERT: B 105 SER cc_start: 0.7839 (t) cc_final: 0.7633 (p) REVERT: B 126 LYS cc_start: 0.8446 (ptpp) cc_final: 0.8229 (ptpp) REVERT: B 128 THR cc_start: 0.7826 (p) cc_final: 0.7339 (t) REVERT: B 143 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6336 (ptt180) REVERT: B 167 ILE cc_start: 0.4914 (OUTLIER) cc_final: 0.4669 (tt) REVERT: B 178 ILE cc_start: 0.8392 (mt) cc_final: 0.8001 (tp) REVERT: B 256 ASP cc_start: 0.6936 (t70) cc_final: 0.6147 (t70) REVERT: B 260 LEU cc_start: 0.7563 (mt) cc_final: 0.7224 (mt) REVERT: B 263 LYS cc_start: 0.7879 (ttmp) cc_final: 0.7631 (ttmp) REVERT: B 266 TRP cc_start: 0.7658 (t60) cc_final: 0.7118 (t60) REVERT: B 295 LEU cc_start: 0.7157 (pt) cc_final: 0.6758 (pt) REVERT: B 298 GLU cc_start: 0.8265 (pt0) cc_final: 0.7017 (tt0) REVERT: B 309 ILE cc_start: 0.8401 (mt) cc_final: 0.8030 (mm) REVERT: B 322 SER cc_start: 0.8679 (m) cc_final: 0.8318 (p) REVERT: B 328 GLU cc_start: 0.7302 (tt0) cc_final: 0.7076 (tt0) REVERT: B 347 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7852 (mttm) REVERT: B 353 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7730 (ptpp) REVERT: B 370 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7147 (mt-10) REVERT: B 388 LYS cc_start: 0.8086 (tttt) cc_final: 0.7766 (tttt) REVERT: B 396 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6616 (mt-10) outliers start: 63 outliers final: 43 residues processed: 366 average time/residue: 0.2385 time to fit residues: 112.1307 Evaluate side-chains 390 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 336 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 37 optimal weight: 0.5980 chunk 51 optimal weight: 0.0050 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 overall best weight: 0.2110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117232 restraints weight = 14427.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121222 restraints weight = 7122.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123922 restraints weight = 4219.413| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7845 Z= 0.178 Angle : 0.623 12.540 10652 Z= 0.311 Chirality : 0.045 0.310 1157 Planarity : 0.005 0.045 1335 Dihedral : 6.565 82.862 1015 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.91 % Allowed : 26.46 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 912 helix: 1.37 (0.31), residues: 308 sheet: -0.79 (0.40), residues: 145 loop : -0.60 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 535 HIS 0.005 0.001 HIS A 208 PHE 0.027 0.002 PHE A 171 TYR 0.028 0.001 TYR A 319 ARG 0.006 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 329 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8231 (mttm) cc_final: 0.7627 (mtpp) REVERT: A 104 LYS cc_start: 0.8574 (tmtt) cc_final: 0.8180 (mmmm) REVERT: A 123 ASP cc_start: 0.8460 (p0) cc_final: 0.8101 (p0) REVERT: A 125 ARG cc_start: 0.7755 (ptt180) cc_final: 0.7484 (ttt180) REVERT: A 126 LYS cc_start: 0.8510 (mttm) cc_final: 0.8017 (mtmm) REVERT: A 163 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 166 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8330 (tmtt) REVERT: A 169 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 172 LYS cc_start: 0.8781 (tttp) cc_final: 0.8542 (tttp) REVERT: A 173 LYS cc_start: 0.8640 (tttt) cc_final: 0.8209 (tppt) REVERT: A 181 TYR cc_start: 0.7669 (m-80) cc_final: 0.7375 (m-80) REVERT: A 182 GLN cc_start: 0.7009 (tm-30) cc_final: 0.6657 (tm-30) REVERT: A 184 MET cc_start: 0.5619 (tpp) cc_final: 0.5337 (tpp) REVERT: A 203 GLU cc_start: 0.7217 (tt0) cc_final: 0.6796 (tt0) REVERT: A 204 GLU cc_start: 0.7411 (tp30) cc_final: 0.7050 (tm-30) REVERT: A 206 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7639 (mtp85) REVERT: A 224 GLU cc_start: 0.7024 (pt0) cc_final: 0.6817 (pt0) REVERT: A 227 PHE cc_start: 0.7607 (m-80) cc_final: 0.7356 (m-80) REVERT: A 233 GLU cc_start: 0.7255 (tp30) cc_final: 0.6787 (mt-10) REVERT: A 244 ILE cc_start: 0.8533 (mm) cc_final: 0.8269 (mm) REVERT: A 271 TYR cc_start: 0.8157 (m-80) cc_final: 0.7850 (m-80) REVERT: A 329 ILE cc_start: 0.8361 (mt) cc_final: 0.8093 (mt) REVERT: A 350 LYS cc_start: 0.8364 (tttt) cc_final: 0.8122 (ttpp) REVERT: A 357 MET cc_start: 0.5450 (tpt) cc_final: 0.5165 (tpt) REVERT: A 366 LYS cc_start: 0.8218 (tptm) cc_final: 0.8015 (mtpp) REVERT: A 369 THR cc_start: 0.8174 (m) cc_final: 0.7819 (p) REVERT: A 374 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7957 (ttpp) REVERT: A 383 TRP cc_start: 0.8147 (m-90) cc_final: 0.7205 (m-90) REVERT: A 395 LYS cc_start: 0.8410 (mmtm) cc_final: 0.7740 (tppt) REVERT: A 406 TRP cc_start: 0.7777 (p90) cc_final: 0.7287 (p90) REVERT: A 407 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: A 414 TRP cc_start: 0.8712 (p-90) cc_final: 0.7865 (p-90) REVERT: A 422 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7753 (mp) REVERT: A 430 GLU cc_start: 0.7725 (mp0) cc_final: 0.7492 (mp0) REVERT: A 472 THR cc_start: 0.7710 (m) cc_final: 0.7135 (p) REVERT: A 476 LYS cc_start: 0.8188 (mttm) cc_final: 0.7870 (mtpp) REVERT: A 478 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7225 (mm-30) REVERT: A 494 ASN cc_start: 0.7331 (m110) cc_final: 0.7044 (m110) REVERT: A 503 LEU cc_start: 0.8091 (tp) cc_final: 0.6994 (tp) REVERT: A 507 GLN cc_start: 0.8613 (pt0) cc_final: 0.7949 (pt0) REVERT: A 511 ASP cc_start: 0.6689 (m-30) cc_final: 0.6458 (m-30) REVERT: A 520 GLN cc_start: 0.7028 (tp40) cc_final: 0.6766 (tm-30) REVERT: A 545 ASN cc_start: 0.4740 (OUTLIER) cc_final: 0.4302 (p0) REVERT: A 548 VAL cc_start: 0.1969 (OUTLIER) cc_final: 0.1118 (m) REVERT: B 13 LYS cc_start: 0.7476 (mptt) cc_final: 0.6981 (mmtp) REVERT: B 21 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8152 (m) REVERT: B 36 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7029 (mt-10) REVERT: B 43 LYS cc_start: 0.8040 (tttp) cc_final: 0.7539 (tttp) REVERT: B 44 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 77 PHE cc_start: 0.7789 (m-80) cc_final: 0.7531 (m-10) REVERT: B 79 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 82 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8089 (mttp) REVERT: B 86 ASP cc_start: 0.7017 (p0) cc_final: 0.6256 (p0) REVERT: B 102 LYS cc_start: 0.8598 (mppt) cc_final: 0.8053 (mptt) REVERT: B 128 THR cc_start: 0.7808 (p) cc_final: 0.7330 (t) REVERT: B 143 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6310 (ptt180) REVERT: B 178 ILE cc_start: 0.8369 (mt) cc_final: 0.7957 (tp) REVERT: B 256 ASP cc_start: 0.7087 (t70) cc_final: 0.6250 (t70) REVERT: B 260 LEU cc_start: 0.7539 (mt) cc_final: 0.7247 (mt) REVERT: B 263 LYS cc_start: 0.7909 (ttmp) cc_final: 0.7688 (ttmp) REVERT: B 266 TRP cc_start: 0.7742 (t60) cc_final: 0.7123 (t60) REVERT: B 295 LEU cc_start: 0.7046 (pt) cc_final: 0.6666 (pt) REVERT: B 298 GLU cc_start: 0.8266 (pt0) cc_final: 0.6992 (tt0) REVERT: B 309 ILE cc_start: 0.8407 (mt) cc_final: 0.8100 (mm) REVERT: B 322 SER cc_start: 0.8682 (m) cc_final: 0.8321 (p) REVERT: B 328 GLU cc_start: 0.7349 (tt0) cc_final: 0.7074 (tt0) REVERT: B 347 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7831 (mttm) REVERT: B 353 LYS cc_start: 0.8152 (ptpp) cc_final: 0.7692 (ptpp) REVERT: B 370 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7089 (mt-10) REVERT: B 388 LYS cc_start: 0.8047 (tttt) cc_final: 0.7716 (tttt) REVERT: B 396 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 405 TYR cc_start: 0.8039 (m-80) cc_final: 0.7759 (m-80) outliers start: 58 outliers final: 39 residues processed: 351 average time/residue: 0.2315 time to fit residues: 105.9756 Evaluate side-chains 368 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 0.0270 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 82 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 367 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 57 ASN B 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.117424 restraints weight = 14443.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121452 restraints weight = 7133.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124069 restraints weight = 4194.231| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7845 Z= 0.185 Angle : 0.627 11.298 10652 Z= 0.310 Chirality : 0.045 0.306 1157 Planarity : 0.005 0.048 1335 Dihedral : 6.473 82.497 1013 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 6.08 % Allowed : 27.53 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 912 helix: 1.35 (0.31), residues: 308 sheet: -0.83 (0.38), residues: 156 loop : -0.56 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 535 HIS 0.005 0.001 HIS A 208 PHE 0.023 0.002 PHE A 171 TYR 0.029 0.001 TYR A 319 ARG 0.006 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8226 (mttm) cc_final: 0.7621 (mtpp) REVERT: A 104 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8174 (mmmm) REVERT: A 126 LYS cc_start: 0.8502 (mttm) cc_final: 0.8031 (mtmm) REVERT: A 163 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 166 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8335 (tmtt) REVERT: A 169 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 172 LYS cc_start: 0.8785 (tttp) cc_final: 0.8545 (tttp) REVERT: A 173 LYS cc_start: 0.8622 (tttt) cc_final: 0.8202 (tppt) REVERT: A 181 TYR cc_start: 0.7631 (m-80) cc_final: 0.7427 (m-80) REVERT: A 182 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6698 (tm-30) REVERT: A 184 MET cc_start: 0.5562 (tpp) cc_final: 0.5269 (tpp) REVERT: A 203 GLU cc_start: 0.7224 (tt0) cc_final: 0.6801 (tt0) REVERT: A 204 GLU cc_start: 0.7423 (tp30) cc_final: 0.7057 (tm-30) REVERT: A 206 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7655 (mtp85) REVERT: A 233 GLU cc_start: 0.7245 (tp30) cc_final: 0.6823 (mt-10) REVERT: A 244 ILE cc_start: 0.8498 (mm) cc_final: 0.8259 (mm) REVERT: A 328 GLU cc_start: 0.7273 (tt0) cc_final: 0.6749 (tt0) REVERT: A 329 ILE cc_start: 0.8322 (mt) cc_final: 0.7883 (mt) REVERT: A 330 GLN cc_start: 0.7915 (mp10) cc_final: 0.7059 (mp10) REVERT: A 350 LYS cc_start: 0.8368 (tttt) cc_final: 0.8115 (ttpp) REVERT: A 357 MET cc_start: 0.5457 (tpt) cc_final: 0.5166 (tpt) REVERT: A 369 THR cc_start: 0.8163 (m) cc_final: 0.7842 (p) REVERT: A 374 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7992 (ttpp) REVERT: A 406 TRP cc_start: 0.7765 (p90) cc_final: 0.7250 (p90) REVERT: A 407 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: A 422 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 430 GLU cc_start: 0.7721 (mp0) cc_final: 0.7517 (mp0) REVERT: A 472 THR cc_start: 0.7686 (m) cc_final: 0.7124 (p) REVERT: A 476 LYS cc_start: 0.8194 (mttm) cc_final: 0.7881 (mtpp) REVERT: A 478 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7235 (mm-30) REVERT: A 494 ASN cc_start: 0.7365 (m110) cc_final: 0.7068 (m110) REVERT: A 503 LEU cc_start: 0.8160 (tp) cc_final: 0.7060 (tp) REVERT: A 507 GLN cc_start: 0.8652 (pt0) cc_final: 0.7969 (pt0) REVERT: A 520 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: A 540 LYS cc_start: 0.8266 (mmmm) cc_final: 0.7961 (mmtm) REVERT: A 545 ASN cc_start: 0.4679 (OUTLIER) cc_final: 0.3806 (p0) REVERT: A 548 VAL cc_start: 0.1992 (OUTLIER) cc_final: 0.1136 (m) REVERT: B 13 LYS cc_start: 0.7511 (mptt) cc_final: 0.6985 (mmtp) REVERT: B 36 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 43 LYS cc_start: 0.8046 (tttp) cc_final: 0.7554 (tttp) REVERT: B 77 PHE cc_start: 0.7866 (m-80) cc_final: 0.7569 (m-10) REVERT: B 79 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 82 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8104 (mttp) REVERT: B 86 ASP cc_start: 0.7033 (p0) cc_final: 0.6249 (p0) REVERT: B 102 LYS cc_start: 0.8600 (mppt) cc_final: 0.8047 (mptt) REVERT: B 126 LYS cc_start: 0.8375 (ptpp) cc_final: 0.8146 (ptpp) REVERT: B 128 THR cc_start: 0.7804 (p) cc_final: 0.7327 (t) REVERT: B 143 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6350 (ptt180) REVERT: B 178 ILE cc_start: 0.8369 (mt) cc_final: 0.7950 (tp) REVERT: B 256 ASP cc_start: 0.7089 (t70) cc_final: 0.6245 (t70) REVERT: B 260 LEU cc_start: 0.7576 (mt) cc_final: 0.7283 (mt) REVERT: B 266 TRP cc_start: 0.7729 (t60) cc_final: 0.7053 (t60) REVERT: B 298 GLU cc_start: 0.8204 (pt0) cc_final: 0.6745 (tt0) REVERT: B 309 ILE cc_start: 0.8395 (mt) cc_final: 0.8074 (mm) REVERT: B 322 SER cc_start: 0.8699 (m) cc_final: 0.8340 (p) REVERT: B 328 GLU cc_start: 0.7357 (tt0) cc_final: 0.7088 (tt0) REVERT: B 347 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7835 (mttm) REVERT: B 353 LYS cc_start: 0.8153 (ptpp) cc_final: 0.7725 (ptpp) REVERT: B 370 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 388 LYS cc_start: 0.8044 (tttt) cc_final: 0.7708 (tttt) REVERT: B 396 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6712 (mt-10) REVERT: B 427 TYR cc_start: 0.7542 (m-80) cc_final: 0.6907 (m-80) outliers start: 51 outliers final: 39 residues processed: 342 average time/residue: 0.2274 time to fit residues: 102.5354 Evaluate side-chains 358 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 311 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 57 ASN ** B 258 GLN ** 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 = 0.3690 r_free = 0.3690 target = 0.131260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114628 restraints weight = 14557.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118595 restraints weight = 7161.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121205 restraints weight = 4222.203| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7845 Z= 0.268 Angle : 0.675 11.090 10652 Z= 0.340 Chirality : 0.047 0.301 1157 Planarity : 0.005 0.048 1335 Dihedral : 6.729 82.303 1012 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.96 % Allowed : 28.37 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 912 helix: 1.05 (0.30), residues: 309 sheet: -0.72 (0.40), residues: 152 loop : -0.66 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 535 HIS 0.005 0.001 HIS A 208 PHE 0.025 0.002 PHE A 171 TYR 0.033 0.002 TYR A 319 ARG 0.005 0.000 ARG A 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7698 (mtt90) REVERT: A 101 LYS cc_start: 0.8255 (mttm) cc_final: 0.7628 (mtpp) REVERT: A 104 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8215 (mmmm) REVERT: A 122 GLU cc_start: 0.6655 (mm-30) cc_final: 0.4831 (tp30) REVERT: A 125 ARG cc_start: 0.7671 (ptt180) cc_final: 0.7253 (ptt180) REVERT: A 126 LYS cc_start: 0.8542 (mttm) cc_final: 0.8015 (mtmm) REVERT: A 163 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8652 (m) REVERT: A 166 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8354 (tmtt) REVERT: A 169 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 172 LYS cc_start: 0.8854 (tttp) cc_final: 0.8608 (tttp) REVERT: A 173 LYS cc_start: 0.8677 (tttt) cc_final: 0.8271 (tppt) REVERT: A 182 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6815 (tm-30) REVERT: A 184 MET cc_start: 0.5632 (tpp) cc_final: 0.5320 (tpp) REVERT: A 203 GLU cc_start: 0.7324 (tt0) cc_final: 0.6943 (tt0) REVERT: A 204 GLU cc_start: 0.7505 (tp30) cc_final: 0.7098 (tm-30) REVERT: A 206 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7526 (ttm-80) REVERT: A 233 GLU cc_start: 0.7253 (tp30) cc_final: 0.6836 (mt-10) REVERT: A 329 ILE cc_start: 0.8371 (mt) cc_final: 0.8000 (mt) REVERT: A 330 GLN cc_start: 0.8039 (mp10) cc_final: 0.7635 (mp10) REVERT: A 350 LYS cc_start: 0.8369 (tttt) cc_final: 0.8168 (ttpp) REVERT: A 357 MET cc_start: 0.5284 (tpt) cc_final: 0.5050 (tpt) REVERT: A 366 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8101 (mtpp) REVERT: A 369 THR cc_start: 0.8139 (m) cc_final: 0.7848 (p) REVERT: A 374 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7949 (ttpp) REVERT: A 383 TRP cc_start: 0.8207 (m-90) cc_final: 0.7227 (m-90) REVERT: A 406 TRP cc_start: 0.7785 (p90) cc_final: 0.7394 (p90) REVERT: A 407 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: A 414 TRP cc_start: 0.8698 (p-90) cc_final: 0.7787 (p-90) REVERT: A 416 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.7034 (t80) REVERT: A 422 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 430 GLU cc_start: 0.7811 (mp0) cc_final: 0.7535 (mp0) REVERT: A 448 ARG cc_start: 0.7647 (tpm170) cc_final: 0.7422 (tpm170) REVERT: A 476 LYS cc_start: 0.8171 (mttm) cc_final: 0.7850 (mtpp) REVERT: A 478 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 494 ASN cc_start: 0.7473 (m110) cc_final: 0.7164 (m110) REVERT: A 503 LEU cc_start: 0.8107 (tp) cc_final: 0.6989 (tp) REVERT: A 507 GLN cc_start: 0.8643 (pt0) cc_final: 0.7980 (pt0) REVERT: A 520 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: A 540 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7966 (mmtm) REVERT: A 545 ASN cc_start: 0.5176 (OUTLIER) cc_final: 0.4246 (p0) REVERT: A 548 VAL cc_start: 0.2011 (OUTLIER) cc_final: 0.1097 (m) REVERT: B 13 LYS cc_start: 0.7591 (mptt) cc_final: 0.7323 (mttm) REVERT: B 36 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7068 (mt-10) REVERT: B 43 LYS cc_start: 0.8030 (tttp) cc_final: 0.7571 (tttp) REVERT: B 77 PHE cc_start: 0.7912 (m-80) cc_final: 0.7651 (m-10) REVERT: B 79 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7401 (mm-30) REVERT: B 82 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8064 (mttp) REVERT: B 102 LYS cc_start: 0.8612 (mppt) cc_final: 0.8083 (mptt) REVERT: B 128 THR cc_start: 0.7737 (p) cc_final: 0.7334 (t) REVERT: B 143 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6429 (ptt180) REVERT: B 178 ILE cc_start: 0.8351 (mt) cc_final: 0.7926 (tp) REVERT: B 256 ASP cc_start: 0.7267 (t70) cc_final: 0.6510 (t70) REVERT: B 260 LEU cc_start: 0.7605 (mt) cc_final: 0.7343 (mt) REVERT: B 263 LYS cc_start: 0.8135 (ttmp) cc_final: 0.7358 (tppt) REVERT: B 298 GLU cc_start: 0.8342 (pt0) cc_final: 0.7159 (tt0) REVERT: B 309 ILE cc_start: 0.8444 (mt) cc_final: 0.8158 (mm) REVERT: B 322 SER cc_start: 0.8760 (m) cc_final: 0.8362 (p) REVERT: B 328 GLU cc_start: 0.7365 (tt0) cc_final: 0.7086 (tt0) REVERT: B 332 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7053 (mm110) REVERT: B 347 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7710 (mtpp) REVERT: B 353 LYS cc_start: 0.8247 (ptpp) cc_final: 0.7813 (ptpp) REVERT: B 370 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 388 LYS cc_start: 0.8030 (tttt) cc_final: 0.7699 (tttt) REVERT: B 396 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6804 (mt-10) REVERT: B 398 TRP cc_start: 0.8854 (t-100) cc_final: 0.8460 (t-100) REVERT: B 427 TYR cc_start: 0.7596 (m-80) cc_final: 0.6955 (m-80) outliers start: 50 outliers final: 38 residues processed: 348 average time/residue: 0.2314 time to fit residues: 104.3088 Evaluate side-chains 363 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 316 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 539 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 88 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116588 restraints weight = 14244.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120519 restraints weight = 7041.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123082 restraints weight = 4175.817| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7845 Z= 0.198 Angle : 0.646 11.208 10652 Z= 0.322 Chirality : 0.046 0.305 1157 Planarity : 0.005 0.047 1335 Dihedral : 6.604 81.986 1012 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.84 % Allowed : 28.72 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.29), residues: 912 helix: 1.27 (0.31), residues: 303 sheet: -0.88 (0.37), residues: 172 loop : -0.48 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 535 HIS 0.006 0.001 HIS A 208 PHE 0.025 0.002 PHE A 171 TYR 0.031 0.002 TYR A 319 ARG 0.006 0.000 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2962.64 seconds wall clock time: 53 minutes 47.71 seconds (3227.71 seconds total)