Starting phenix.real_space_refine on Wed Sep 17 09:28:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sep_25074/09_2025/7sep_25074.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sep_25074/09_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_25074/09_2025/7sep_25074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sep_25074/09_2025/7sep_25074.map" model { file = "/net/cci-nas-00/data/ceres_data/7sep_25074/09_2025/7sep_25074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sep_25074/09_2025/7sep_25074.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.11, per 1000 atoms: 0.28 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: 0.67 Conformation dependent library (CDL) restraints added in 397.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.27 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: 0.98 Time building geometry restraints manager: 0.90 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: 1.160 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 8.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.980 ------------------------------------------------------------------------------- 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= 0.309 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.000 ARG A 83 TYR 0.019 0.002 TYR A 441 PHE 0.011 0.002 PHE A 124 TRP 0.024 0.002 TRP A 239 HIS 0.006 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 7845) covalent geometry : angle 0.65903 (10652) hydrogen bonds : bond 0.19593 ( 284) hydrogen bonds : angle 7.60313 ( 768) *********************** 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 : 0.305 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: 0.7777 (p) REVERT: A 56 TYR cc_start: 0.7694 (m-80) cc_final: 0.7059 (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: 0.5978 (pt0) REVERT: A 83 ARG cc_start: 0.7854 (mtt-85) cc_final: 0.5571 (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: 0.8275 (mtpp) REVERT: A 106 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7923 (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: 0.6561 (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: 0.8238 (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: 0.7942 (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: 0.8570 (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: 0.7160 (m-80) REVERT: A 182 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 203 GLU cc_start: 0.7549 (tt0) cc_final: 0.7320 (tt0) REVERT: A 204 GLU cc_start: 0.7485 (tp30) cc_final: 0.7125 (tm-30) REVERT: A 206 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7404 (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: 0.7821 (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: 0.8441 (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: 0.7832 (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: 0.7321 (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: 0.7564 (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: 0.7319 (mt0) REVERT: A 417 VAL cc_start: 0.8358 (t) cc_final: 0.8156 (m) REVERT: A 419 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7209 (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: 0.6901 (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: 0.4303 (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: 0.8132 (mm) REVERT: A 483 TYR cc_start: 0.7797 (t80) cc_final: 0.7433 (t80) REVERT: A 492 GLU cc_start: 0.6951 (mp0) cc_final: 0.6729 (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: 0.7823 (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: 0.7695 (mt-10) REVERT: A 524 GLN cc_start: 0.7842 (tp40) cc_final: 0.7526 (mm-40) REVERT: A 529 GLU cc_start: 0.6989 (tp30) cc_final: 0.6758 (tp30) REVERT: A 540 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8003 (mmtt) REVERT: A 545 ASN cc_start: 0.4369 (OUTLIER) cc_final: 0.3364 (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: 0.7858 (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: 0.8165 (tt) REVERT: B 41 MET cc_start: 0.7683 (mtt) cc_final: 0.7458 (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: 0.7320 (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: 0.8107 (mm) REVERT: B 144 TYR cc_start: 0.8691 (m-80) cc_final: 0.8456 (m-80) REVERT: B 175 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.6740 (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: 0.7640 (mmtm) 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: 0.7980 (mt) REVERT: B 322 SER cc_start: 0.8746 (m) cc_final: 0.8240 (t) REVERT: B 328 GLU cc_start: 0.7067 (tt0) cc_final: 0.6849 (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: 0.7919 (tppp) REVERT: B 356 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6510 (mmm160) REVERT: B 357 MET cc_start: 0.6218 (ptp) cc_final: 0.5985 (ptp) REVERT: B 391 LEU cc_start: 0.8518 (mt) cc_final: 0.8038 (mt) REVERT: B 396 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6904 (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: 0.0987 time to fit residues: 55.0685 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 : 0.296 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0170 chunk 74 optimal weight: 0.5980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.133700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116853 restraints weight = 14211.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120836 restraints weight = 7167.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123373 restraints weight = 4280.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125086 restraints weight = 2871.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126187 restraints weight = 2096.330| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7845 Z= 0.129 Angle : 0.601 9.975 10652 Z= 0.308 Chirality : 0.044 0.145 1157 Planarity : 0.005 0.075 1335 Dihedral : 9.727 83.486 1090 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 7.51 % Allowed : 17.76 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.29), residues: 912 helix: 1.36 (0.30), residues: 310 sheet: -0.72 (0.41), residues: 146 loop : -0.57 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.024 0.002 TYR A 319 PHE 0.023 0.001 PHE A 227 TRP 0.016 0.001 TRP A 239 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7845) covalent geometry : angle 0.60050 (10652) hydrogen bonds : bond 0.04194 ( 284) hydrogen bonds : angle 5.31614 ( 768) *********************** 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 416 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 353 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 16 MET cc_start: 0.5935 (mmt) cc_final: 0.5605 (mmt) REVERT: A 29 GLU cc_start: 0.7633 (tm-30) cc_final: 0.6803 (tm-30) REVERT: A 43 LYS cc_start: 0.8312 (tptp) cc_final: 0.8091 (tppt) REVERT: A 47 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6561 (tt) REVERT: A 50 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6600 (mm) REVERT: A 56 TYR cc_start: 0.7581 (m-80) cc_final: 0.7122 (m-80) REVERT: A 83 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.6798 (mtt90) REVERT: A 86 ASP cc_start: 0.6999 (t70) cc_final: 0.6708 (t0) REVERT: A 101 LYS cc_start: 0.8372 (mttm) cc_final: 0.7820 (mttm) REVERT: A 104 LYS cc_start: 0.8561 (tmtt) cc_final: 0.8292 (mtpp) REVERT: A 126 LYS cc_start: 0.8588 (mttm) cc_final: 0.7723 (tptt) REVERT: A 142 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7287 (pt) REVERT: A 162 SER cc_start: 0.8611 (m) cc_final: 0.8401 (p) REVERT: A 166 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8318 (tmtt) REVERT: A 169 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 173 LYS cc_start: 0.8702 (tttt) cc_final: 0.8487 (tttt) REVERT: A 180 ILE cc_start: 0.8492 (tp) cc_final: 0.8174 (mt) REVERT: A 181 TYR cc_start: 0.7434 (m-80) cc_final: 0.7151 (m-80) REVERT: A 182 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6762 (tm-30) REVERT: A 203 GLU cc_start: 0.7247 (tt0) cc_final: 0.7020 (tt0) REVERT: A 204 GLU cc_start: 0.7334 (tp30) cc_final: 0.6979 (tm-30) REVERT: A 206 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7506 (ttm-80) REVERT: A 227 PHE cc_start: 0.7737 (m-80) cc_final: 0.7520 (m-80) REVERT: A 232 TYR cc_start: 0.8028 (m-80) cc_final: 0.7628 (m-80) REVERT: A 295 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7149 (pp) REVERT: A 307 ARG cc_start: 0.6931 (mtp-110) cc_final: 0.6625 (ptm-80) REVERT: A 328 GLU cc_start: 0.7434 (tt0) cc_final: 0.7039 (tt0) REVERT: A 329 ILE cc_start: 0.8410 (mt) cc_final: 0.8154 (mt) REVERT: A 330 GLN cc_start: 0.7671 (mp10) cc_final: 0.7170 (mp10) REVERT: A 347 LYS cc_start: 0.8445 (mttt) cc_final: 0.8036 (mttp) REVERT: A 349 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8580 (mt) REVERT: A 350 LYS cc_start: 0.8424 (tttt) cc_final: 0.8152 (ttpp) REVERT: A 357 MET cc_start: 0.5402 (tpt) cc_final: 0.5140 (tpt) REVERT: A 366 LYS cc_start: 0.8282 (tptm) cc_final: 0.7778 (mtpp) REVERT: A 369 THR cc_start: 0.8111 (m) cc_final: 0.7878 (p) REVERT: A 370 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 374 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8076 (ttpp) REVERT: A 405 TYR cc_start: 0.8078 (t80) cc_final: 0.7831 (t80) REVERT: A 406 TRP cc_start: 0.7801 (p90) cc_final: 0.7225 (p90) REVERT: A 407 GLN cc_start: 0.7663 (mt0) cc_final: 0.7254 (mt0) REVERT: A 422 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7783 (mp) REVERT: A 478 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7089 (mm-30) REVERT: A 479 LEU cc_start: 0.8370 (tp) cc_final: 0.8063 (mm) REVERT: A 483 TYR cc_start: 0.7642 (t80) cc_final: 0.7298 (t80) REVERT: A 494 ASN cc_start: 0.7354 (m110) cc_final: 0.7124 (m110) REVERT: A 500 GLN cc_start: 0.7451 (pt0) cc_final: 0.7218 (pt0) REVERT: A 503 LEU cc_start: 0.8065 (tp) cc_final: 0.7283 (tp) REVERT: A 507 GLN cc_start: 0.8742 (pt0) cc_final: 0.8255 (pt0) REVERT: A 518 VAL cc_start: 0.8996 (t) cc_final: 0.8786 (p) REVERT: A 520 GLN cc_start: 0.7395 (tp40) cc_final: 0.6920 (tp-100) REVERT: A 523 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 548 VAL cc_start: 0.2245 (t) cc_final: 0.1387 (m) REVERT: B 21 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8205 (m) REVERT: B 22 LYS cc_start: 0.8084 (tttp) cc_final: 0.7635 (tttp) REVERT: B 36 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6962 (mt-10) REVERT: B 43 LYS cc_start: 0.8014 (tttp) cc_final: 0.7577 (tttp) REVERT: B 57 ASN cc_start: 0.8040 (t0) cc_final: 0.7796 (t0) REVERT: B 77 PHE cc_start: 0.7860 (m-80) cc_final: 0.7571 (m-10) REVERT: B 82 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8111 (ttmm) REVERT: B 86 ASP cc_start: 0.6902 (p0) cc_final: 0.6664 (p0) REVERT: B 105 SER cc_start: 0.8016 (t) cc_final: 0.7806 (p) REVERT: B 128 THR cc_start: 0.7869 (p) cc_final: 0.7360 (t) REVERT: B 131 THR cc_start: 0.7730 (m) cc_final: 0.7235 (p) REVERT: B 167 ILE cc_start: 0.5119 (OUTLIER) cc_final: 0.4746 (tt) REVERT: B 178 ILE cc_start: 0.8428 (mt) cc_final: 0.7999 (tp) REVERT: B 203 GLU cc_start: 0.7886 (tt0) cc_final: 0.7509 (tm-30) REVERT: B 256 ASP cc_start: 0.6970 (t70) cc_final: 0.6572 (t70) REVERT: B 263 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7632 (ttmp) REVERT: B 264 LEU cc_start: 0.8697 (tp) cc_final: 0.8439 (mm) REVERT: B 266 TRP cc_start: 0.7584 (t60) cc_final: 0.7011 (t60) REVERT: B 275 LYS cc_start: 0.8478 (mttm) cc_final: 0.8183 (mmtt) REVERT: B 298 GLU cc_start: 0.8403 (pt0) cc_final: 0.6886 (tt0) REVERT: B 308 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7570 (tm-30) REVERT: B 322 SER cc_start: 0.8685 (m) cc_final: 0.8278 (p) REVERT: B 328 GLU cc_start: 0.7113 (tt0) cc_final: 0.6879 (tt0) REVERT: B 339 TYR cc_start: 0.8295 (p90) cc_final: 0.7958 (p90) REVERT: B 347 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7875 (mttm) REVERT: B 374 LYS cc_start: 0.8132 (tttt) cc_final: 0.7805 (tptm) REVERT: B 391 LEU cc_start: 0.8430 (mt) cc_final: 0.8073 (mt) REVERT: B 396 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6618 (mt-10) REVERT: B 398 TRP cc_start: 0.8869 (t-100) cc_final: 0.8379 (t-100) REVERT: B 409 THR cc_start: 0.8232 (p) cc_final: 0.7995 (m) outliers start: 63 outliers final: 31 residues processed: 385 average time/residue: 0.1019 time to fit residues: 51.0869 Evaluate side-chains 386 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 344 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 539 HIS 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 74 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 164 MET 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 353 LYS 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 78 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 84 optimal weight: 0.0270 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 0.0370 chunk 28 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 332 GLN A 367 GLN A 480 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 197 GLN B 258 GLN B 373 GLN B 394 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.132856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115943 restraints weight = 14050.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119939 restraints weight = 6931.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122571 restraints weight = 4106.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124194 restraints weight = 2734.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125412 restraints weight = 2020.805| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7845 Z= 0.111 Angle : 0.573 9.631 10652 Z= 0.293 Chirality : 0.044 0.173 1157 Planarity : 0.005 0.055 1335 Dihedral : 8.001 81.729 1038 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 7.15 % Allowed : 20.38 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.28), residues: 912 helix: 1.43 (0.30), residues: 310 sheet: -0.67 (0.41), residues: 146 loop : -0.47 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 143 TYR 0.021 0.001 TYR A 319 PHE 0.022 0.001 PHE A 124 TRP 0.010 0.001 TRP A 239 HIS 0.008 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7845) covalent geometry : angle 0.57291 (10652) hydrogen bonds : bond 0.03357 ( 284) hydrogen bonds : angle 4.74030 ( 768) *********************** 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 407 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 347 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.5818 (mmt) cc_final: 0.5536 (mmt) REVERT: A 30 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8025 (mmtm) REVERT: A 50 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6711 (mt) REVERT: A 56 TYR cc_start: 0.7620 (m-80) cc_final: 0.7122 (m-80) REVERT: A 83 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.6570 (mtt180) REVERT: A 101 LYS cc_start: 0.8344 (mttm) cc_final: 0.7993 (tttm) REVERT: A 104 LYS cc_start: 0.8513 (tmtt) cc_final: 0.8221 (mmtt) REVERT: A 126 LYS cc_start: 0.8439 (mttm) cc_final: 0.7670 (tptt) REVERT: A 142 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7163 (pt) REVERT: A 162 SER cc_start: 0.8516 (m) cc_final: 0.8105 (p) REVERT: A 163 SER cc_start: 0.8907 (t) cc_final: 0.8670 (m) REVERT: A 166 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8322 (tmtt) REVERT: A 169 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 172 LYS cc_start: 0.8805 (tttp) cc_final: 0.8574 (tttp) REVERT: A 173 LYS cc_start: 0.8693 (tttt) cc_final: 0.8481 (tttt) REVERT: A 180 ILE cc_start: 0.8376 (tp) cc_final: 0.8147 (mt) REVERT: A 181 TYR cc_start: 0.7521 (m-80) cc_final: 0.7226 (m-80) REVERT: A 182 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6664 (tm-30) REVERT: A 203 GLU cc_start: 0.7233 (tt0) cc_final: 0.6861 (tt0) REVERT: A 204 GLU cc_start: 0.7311 (tp30) cc_final: 0.6983 (tm-30) REVERT: A 206 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7692 (mtp-110) REVERT: A 232 TYR cc_start: 0.7963 (m-80) cc_final: 0.7743 (m-80) REVERT: A 233 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6374 (mp0) REVERT: A 328 GLU cc_start: 0.7378 (tt0) cc_final: 0.6912 (tt0) REVERT: A 329 ILE cc_start: 0.8388 (mt) cc_final: 0.8098 (mt) REVERT: A 330 GLN cc_start: 0.7628 (mp10) cc_final: 0.6864 (mp10) REVERT: A 342 TYR cc_start: 0.8208 (p90) cc_final: 0.7979 (p90) REVERT: A 344 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 347 LYS cc_start: 0.8369 (mttt) cc_final: 0.7915 (mtpp) REVERT: A 349 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8617 (mt) REVERT: A 350 LYS cc_start: 0.8393 (tttt) cc_final: 0.8090 (ttpp) REVERT: A 357 MET cc_start: 0.5446 (tpt) cc_final: 0.5161 (tpt) REVERT: A 366 LYS cc_start: 0.8238 (tptm) cc_final: 0.7623 (mtpp) REVERT: A 369 THR cc_start: 0.8112 (m) cc_final: 0.7826 (p) REVERT: A 370 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 374 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7992 (ttpp) REVERT: A 378 GLU cc_start: 0.7839 (tp30) cc_final: 0.7536 (tp30) REVERT: A 401 TRP cc_start: 0.8327 (t60) cc_final: 0.7960 (t-100) REVERT: A 406 TRP cc_start: 0.7796 (p90) cc_final: 0.7076 (p90) REVERT: A 407 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: A 422 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7812 (mp) REVERT: A 478 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 494 ASN cc_start: 0.7290 (m110) cc_final: 0.7008 (m110) REVERT: A 500 GLN cc_start: 0.7562 (pt0) cc_final: 0.7271 (pt0) REVERT: A 503 LEU cc_start: 0.8013 (tp) cc_final: 0.7244 (tp) REVERT: A 505 ILE cc_start: 0.8415 (mt) cc_final: 0.8158 (mm) REVERT: A 507 GLN cc_start: 0.8691 (pt0) cc_final: 0.8071 (pt0) REVERT: A 520 GLN cc_start: 0.7352 (tp40) cc_final: 0.6939 (tp40) REVERT: A 523 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 535 TRP cc_start: 0.8584 (t60) cc_final: 0.8319 (t60) REVERT: A 548 VAL cc_start: 0.2214 (OUTLIER) cc_final: 0.1390 (m) REVERT: B 21 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8197 (m) REVERT: B 28 GLU cc_start: 0.7535 (tp30) cc_final: 0.7283 (tp30) REVERT: B 34 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8149 (tt) REVERT: B 36 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6974 (mt-10) REVERT: B 43 LYS cc_start: 0.8015 (tttp) cc_final: 0.7509 (tttp) REVERT: B 44 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7113 (mm-30) REVERT: B 76 ASP cc_start: 0.8262 (t0) cc_final: 0.8024 (t0) REVERT: B 77 PHE cc_start: 0.7832 (m-80) cc_final: 0.7468 (m-10) REVERT: B 79 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7290 (mm-30) REVERT: B 82 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8216 (ttmm) REVERT: B 86 ASP cc_start: 0.6868 (p0) cc_final: 0.6093 (p0) REVERT: B 128 THR cc_start: 0.7871 (p) cc_final: 0.7428 (t) REVERT: B 131 THR cc_start: 0.7624 (m) cc_final: 0.7422 (p) REVERT: B 167 ILE cc_start: 0.4910 (OUTLIER) cc_final: 0.4595 (tt) REVERT: B 178 ILE cc_start: 0.8394 (mt) cc_final: 0.7974 (tp) REVERT: B 182 GLN cc_start: 0.7631 (pt0) cc_final: 0.7373 (pt0) REVERT: B 256 ASP cc_start: 0.7172 (t70) cc_final: 0.6810 (t70) REVERT: B 258 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7582 (tp-100) REVERT: B 260 LEU cc_start: 0.7677 (mt) cc_final: 0.7336 (mt) REVERT: B 263 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7654 (ttmp) REVERT: B 264 LEU cc_start: 0.8659 (tp) cc_final: 0.8413 (mm) REVERT: B 297 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7522 (tp30) REVERT: B 298 GLU cc_start: 0.8323 (pt0) cc_final: 0.6807 (tt0) REVERT: B 300 GLU cc_start: 0.7879 (tt0) cc_final: 0.7516 (tt0) REVERT: B 309 ILE cc_start: 0.8349 (mt) cc_final: 0.8111 (tt) REVERT: B 322 SER cc_start: 0.8709 (m) cc_final: 0.8365 (p) REVERT: B 328 GLU cc_start: 0.7198 (tt0) cc_final: 0.6955 (tt0) REVERT: B 339 TYR cc_start: 0.8076 (p90) cc_final: 0.7641 (p90) REVERT: B 347 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7864 (mttm) REVERT: B 396 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6634 (mt-10) outliers start: 60 outliers final: 32 residues processed: 371 average time/residue: 0.0985 time to fit residues: 47.7521 Evaluate side-chains 383 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 ILE 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 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 430 GLU 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 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 90 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 413 GLU 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 0 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 315 HIS A 332 GLN A 343 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 96 HIS ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 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 = 0.3689 r_free = 0.3689 target = 0.130388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113314 restraints weight = 14469.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117411 restraints weight = 7125.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120082 restraints weight = 4218.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121829 restraints weight = 2809.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122964 restraints weight = 2048.641| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7845 Z= 0.231 Angle : 0.630 8.907 10652 Z= 0.332 Chirality : 0.046 0.160 1157 Planarity : 0.005 0.048 1335 Dihedral : 8.044 82.609 1029 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 7.51 % Allowed : 21.57 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.29), residues: 912 helix: 1.25 (0.30), residues: 305 sheet: -0.98 (0.41), residues: 146 loop : -0.59 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.024 0.002 TYR A 405 PHE 0.024 0.002 PHE A 171 TRP 0.015 0.002 TRP A 406 HIS 0.006 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 7845) covalent geometry : angle 0.62994 (10652) hydrogen bonds : bond 0.04025 ( 284) hydrogen bonds : angle 5.04023 ( 768) *********************** 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: 63 poor density : 349 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6529 (tt) REVERT: A 56 TYR cc_start: 0.7750 (m-80) cc_final: 0.7205 (m-80) REVERT: A 101 LYS cc_start: 0.8367 (mttm) cc_final: 0.7793 (mttm) REVERT: A 123 ASP cc_start: 0.8486 (p0) cc_final: 0.8029 (p0) REVERT: A 126 LYS cc_start: 0.8474 (mttm) cc_final: 0.7685 (tptt) REVERT: A 142 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7329 (pt) REVERT: A 162 SER cc_start: 0.8460 (m) cc_final: 0.8223 (p) REVERT: A 163 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8677 (m) REVERT: A 166 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8359 (tmtt) REVERT: A 169 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7534 (mm-30) REVERT: A 172 LYS cc_start: 0.8850 (tttp) cc_final: 0.8637 (tttp) REVERT: A 180 ILE cc_start: 0.8549 (tp) cc_final: 0.8308 (mt) REVERT: A 181 TYR cc_start: 0.7572 (m-80) cc_final: 0.7241 (m-80) REVERT: A 182 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6819 (tm-30) REVERT: A 203 GLU cc_start: 0.7349 (tt0) cc_final: 0.7111 (tt0) REVERT: A 204 GLU cc_start: 0.7495 (tp30) cc_final: 0.7263 (tp30) REVERT: A 206 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7529 (ttm-80) REVERT: A 227 PHE cc_start: 0.7866 (m-80) cc_final: 0.7593 (m-80) REVERT: A 232 TYR cc_start: 0.8056 (m-80) cc_final: 0.7643 (m-80) REVERT: A 329 ILE cc_start: 0.8428 (mt) cc_final: 0.8073 (mt) REVERT: A 347 LYS cc_start: 0.8409 (mttt) cc_final: 0.8044 (mttp) REVERT: A 350 LYS cc_start: 0.8327 (tttt) cc_final: 0.8066 (ttpp) REVERT: A 357 MET cc_start: 0.5443 (tpt) cc_final: 0.5148 (tpt) REVERT: A 366 LYS cc_start: 0.8282 (tptm) cc_final: 0.7750 (mtpp) REVERT: A 369 THR cc_start: 0.8167 (m) cc_final: 0.7911 (p) REVERT: A 370 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7307 (mt-10) REVERT: A 374 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7962 (ttpp) REVERT: A 406 TRP cc_start: 0.7893 (p90) cc_final: 0.7654 (p90) REVERT: A 407 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: A 414 TRP cc_start: 0.8706 (p-90) cc_final: 0.7969 (p-90) REVERT: A 422 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7824 (mp) REVERT: A 478 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 494 ASN cc_start: 0.7448 (m110) cc_final: 0.7128 (m110) REVERT: A 500 GLN cc_start: 0.7570 (pt0) cc_final: 0.7256 (pt0) REVERT: A 503 LEU cc_start: 0.8069 (tp) cc_final: 0.7310 (tp) REVERT: A 507 GLN cc_start: 0.8709 (pt0) cc_final: 0.8094 (pt0) REVERT: A 520 GLN cc_start: 0.7327 (tp40) cc_final: 0.6912 (tp40) REVERT: A 523 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 535 TRP cc_start: 0.8595 (t60) cc_final: 0.8311 (t60) REVERT: A 545 ASN cc_start: 0.4981 (OUTLIER) cc_final: 0.4074 (p0) REVERT: A 548 VAL cc_start: 0.2261 (OUTLIER) cc_final: 0.1358 (m) REVERT: B 21 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8200 (m) REVERT: B 22 LYS cc_start: 0.7986 (tttp) cc_final: 0.7637 (tttp) REVERT: B 34 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8184 (tt) REVERT: B 36 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7054 (mt-10) REVERT: B 43 LYS cc_start: 0.7999 (tttp) cc_final: 0.7556 (tttp) REVERT: B 77 PHE cc_start: 0.7954 (m-80) cc_final: 0.7578 (m-10) REVERT: B 79 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 82 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8293 (ttmm) REVERT: B 86 ASP cc_start: 0.7007 (p0) cc_final: 0.6667 (p0) REVERT: B 128 THR cc_start: 0.7787 (p) cc_final: 0.7305 (t) REVERT: B 167 ILE cc_start: 0.5149 (OUTLIER) cc_final: 0.4799 (tt) REVERT: B 178 ILE cc_start: 0.8363 (mt) cc_final: 0.7927 (tp) REVERT: B 185 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.5964 (t70) REVERT: B 256 ASP cc_start: 0.7219 (t70) cc_final: 0.6875 (t70) REVERT: B 258 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7512 (tp-100) REVERT: B 260 LEU cc_start: 0.7657 (mt) cc_final: 0.7259 (mt) REVERT: B 263 LYS cc_start: 0.8011 (ttmp) cc_final: 0.7690 (ttmp) REVERT: B 266 TRP cc_start: 0.7781 (t60) cc_final: 0.7244 (t60) REVERT: B 297 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7570 (tp30) REVERT: B 298 GLU cc_start: 0.8447 (pt0) cc_final: 0.7000 (tt0) REVERT: B 300 GLU cc_start: 0.7879 (tt0) cc_final: 0.7450 (tt0) REVERT: B 309 ILE cc_start: 0.8355 (mt) cc_final: 0.8017 (mm) REVERT: B 322 SER cc_start: 0.8775 (m) cc_final: 0.8348 (p) REVERT: B 328 GLU cc_start: 0.7258 (tt0) cc_final: 0.7013 (tt0) REVERT: B 347 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7764 (mtpp) REVERT: B 365 VAL cc_start: 0.8408 (m) cc_final: 0.8132 (p) REVERT: B 370 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7326 (mt-10) REVERT: B 378 GLU cc_start: 0.7202 (tp30) cc_final: 0.6990 (tp30) REVERT: B 396 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6796 (mt-10) REVERT: B 398 TRP cc_start: 0.8806 (t-100) cc_final: 0.8298 (t-100) outliers start: 63 outliers final: 39 residues processed: 378 average time/residue: 0.0997 time to fit residues: 49.3129 Evaluate side-chains 395 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 343 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 79 GLU Chi-restraints excluded: chain A residue 81 ASN 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 237 ASP 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 385 LYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 429 LEU 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 524 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 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 117 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 167 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 397 THR 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 0 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 315 HIS A 332 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN B 96 HIS ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116156 restraints weight = 14267.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120051 restraints weight = 7116.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122613 restraints weight = 4232.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124224 restraints weight = 2830.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125369 restraints weight = 2087.293| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3509 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= 0.147 Angle : 0.595 9.477 10652 Z= 0.306 Chirality : 0.045 0.175 1157 Planarity : 0.005 0.049 1335 Dihedral : 7.418 81.758 1021 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 7.63 % Allowed : 23.24 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.28), residues: 912 helix: 1.16 (0.30), residues: 310 sheet: -0.74 (0.42), residues: 140 loop : -0.68 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.026 0.002 TYR A 319 PHE 0.024 0.002 PHE A 171 TRP 0.016 0.001 TRP A 337 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7845) covalent geometry : angle 0.59487 (10652) hydrogen bonds : bond 0.03420 ( 284) hydrogen bonds : angle 4.79516 ( 768) *********************** 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 404 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 340 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6007 (mmt) cc_final: 0.5693 (mmt) REVERT: A 47 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6421 (tt) REVERT: A 56 TYR cc_start: 0.7618 (m-80) cc_final: 0.7091 (m-80) REVERT: A 101 LYS cc_start: 0.8326 (mttm) cc_final: 0.7776 (mttm) REVERT: A 123 ASP cc_start: 0.8515 (p0) cc_final: 0.8013 (p0) REVERT: A 126 LYS cc_start: 0.8373 (mttm) cc_final: 0.7643 (tptt) REVERT: A 142 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7378 (pt) REVERT: A 162 SER cc_start: 0.8400 (m) cc_final: 0.8171 (p) REVERT: A 163 SER cc_start: 0.8890 (t) cc_final: 0.8633 (m) REVERT: A 166 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8349 (tmtt) REVERT: A 169 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 172 LYS cc_start: 0.8757 (tttp) cc_final: 0.8540 (tttp) REVERT: A 180 ILE cc_start: 0.8476 (tp) cc_final: 0.8217 (mt) REVERT: A 181 TYR cc_start: 0.7553 (m-80) cc_final: 0.7245 (m-80) REVERT: A 182 GLN cc_start: 0.7070 (tm-30) cc_final: 0.6786 (tm-30) REVERT: A 203 GLU cc_start: 0.7254 (tt0) cc_final: 0.7004 (tt0) REVERT: A 204 GLU cc_start: 0.7377 (tp30) cc_final: 0.7013 (tm-30) REVERT: A 206 ARG cc_start: 0.8108 (mtp-110) cc_final: 0.7566 (ttm-80) REVERT: A 232 TYR cc_start: 0.8005 (m-80) cc_final: 0.7627 (m-80) REVERT: A 233 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6716 (mt-10) REVERT: A 271 TYR cc_start: 0.7909 (m-80) cc_final: 0.7460 (m-80) REVERT: A 329 ILE cc_start: 0.8369 (mt) cc_final: 0.8156 (mt) REVERT: A 347 LYS cc_start: 0.8413 (mttt) cc_final: 0.8100 (mtpp) REVERT: A 350 LYS cc_start: 0.8379 (tttt) cc_final: 0.8126 (ttpp) REVERT: A 357 MET cc_start: 0.5392 (tpt) cc_final: 0.5100 (tpt) REVERT: A 366 LYS cc_start: 0.8249 (tptm) cc_final: 0.7794 (mtpp) REVERT: A 369 THR cc_start: 0.8184 (m) cc_final: 0.7938 (p) REVERT: A 370 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 406 TRP cc_start: 0.7792 (p90) cc_final: 0.7198 (p90) REVERT: A 407 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: A 414 TRP cc_start: 0.8720 (p-90) cc_final: 0.7994 (p-90) REVERT: A 422 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 429 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8496 (mp) REVERT: A 478 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 494 ASN cc_start: 0.7436 (m110) cc_final: 0.7117 (m110) REVERT: A 500 GLN cc_start: 0.7500 (pt0) cc_final: 0.7202 (pt0) REVERT: A 503 LEU cc_start: 0.8062 (tp) cc_final: 0.7243 (tp) REVERT: A 507 GLN cc_start: 0.8723 (pt0) cc_final: 0.8081 (pt0) REVERT: A 520 GLN cc_start: 0.7239 (tp40) cc_final: 0.6844 (tp40) REVERT: A 535 TRP cc_start: 0.8608 (t60) cc_final: 0.8366 (t60) REVERT: A 545 ASN cc_start: 0.5091 (OUTLIER) cc_final: 0.4625 (p0) REVERT: A 548 VAL cc_start: 0.2189 (OUTLIER) cc_final: 0.1279 (m) REVERT: B 13 LYS cc_start: 0.7601 (mmtp) cc_final: 0.7269 (mmtp) REVERT: B 21 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8221 (m) REVERT: B 28 GLU cc_start: 0.7481 (tp30) cc_final: 0.7272 (tp30) REVERT: B 34 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8163 (tt) REVERT: B 36 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6979 (mt-10) REVERT: B 43 LYS cc_start: 0.7990 (tttp) cc_final: 0.7789 (tttp) REVERT: B 77 PHE cc_start: 0.7925 (m-80) cc_final: 0.7567 (m-10) REVERT: B 79 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7234 (mm-30) REVERT: B 82 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8272 (ttmm) REVERT: B 86 ASP cc_start: 0.6895 (p0) cc_final: 0.6526 (p0) REVERT: B 102 LYS cc_start: 0.8679 (mppt) cc_final: 0.8238 (mptt) REVERT: B 128 THR cc_start: 0.7813 (p) cc_final: 0.7340 (t) REVERT: B 167 ILE cc_start: 0.5002 (OUTLIER) cc_final: 0.4672 (tt) REVERT: B 178 ILE cc_start: 0.8370 (mt) cc_final: 0.7938 (tp) REVERT: B 192 ASP cc_start: 0.8008 (t0) cc_final: 0.7675 (m-30) REVERT: B 256 ASP cc_start: 0.7208 (t70) cc_final: 0.6817 (t70) REVERT: B 260 LEU cc_start: 0.7576 (mt) cc_final: 0.7266 (mt) REVERT: B 263 LYS cc_start: 0.7947 (ttmp) cc_final: 0.7642 (ttmp) REVERT: B 266 TRP cc_start: 0.7689 (t60) cc_final: 0.7173 (t60) REVERT: B 298 GLU cc_start: 0.8313 (pt0) cc_final: 0.7537 (pt0) REVERT: B 308 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7220 (tm-30) REVERT: B 309 ILE cc_start: 0.8334 (mt) cc_final: 0.7930 (mm) REVERT: B 322 SER cc_start: 0.8720 (m) cc_final: 0.8334 (p) REVERT: B 328 GLU cc_start: 0.7226 (tt0) cc_final: 0.7010 (tt0) REVERT: B 347 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7782 (mtpp) REVERT: B 365 VAL cc_start: 0.8437 (m) cc_final: 0.8165 (p) REVERT: B 370 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7283 (mt-10) REVERT: B 378 GLU cc_start: 0.7136 (tp30) cc_final: 0.6933 (tp30) REVERT: B 388 LYS cc_start: 0.8024 (tttt) cc_final: 0.7725 (tttt) REVERT: B 396 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6657 (mt-10) REVERT: B 398 TRP cc_start: 0.8838 (t-100) cc_final: 0.8286 (t-100) outliers start: 64 outliers final: 35 residues processed: 373 average time/residue: 0.0979 time to fit residues: 48.0527 Evaluate side-chains 377 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 332 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 142 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 ILE 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 311 LYS Chi-restraints excluded: chain A residue 373 GLN 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 429 LEU 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 448 ARG 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 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 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 137 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 414 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: 0.7980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 332 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117111 restraints weight = 14327.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121070 restraints weight = 7091.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123588 restraints weight = 4194.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125292 restraints weight = 2803.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126499 restraints weight = 2035.654| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7845 Z= 0.128 Angle : 0.588 10.309 10652 Z= 0.301 Chirality : 0.044 0.165 1157 Planarity : 0.005 0.056 1335 Dihedral : 7.065 81.034 1017 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 7.03 % Allowed : 24.91 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.29), residues: 912 helix: 1.23 (0.31), residues: 310 sheet: -0.75 (0.39), residues: 152 loop : -0.72 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 83 TYR 0.026 0.002 TYR A 319 PHE 0.025 0.002 PHE A 171 TRP 0.017 0.001 TRP A 337 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7845) covalent geometry : angle 0.58782 (10652) hydrogen bonds : bond 0.03253 ( 284) hydrogen bonds : angle 4.66749 ( 768) *********************** 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 395 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 336 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.5906 (mmt) cc_final: 0.5605 (mmt) REVERT: A 47 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6329 (tt) REVERT: A 56 TYR cc_start: 0.7573 (m-80) cc_final: 0.6993 (m-80) REVERT: A 101 LYS cc_start: 0.8307 (mttm) cc_final: 0.7770 (mttm) REVERT: A 123 ASP cc_start: 0.8466 (p0) cc_final: 0.7965 (p0) REVERT: A 126 LYS cc_start: 0.8343 (mttm) cc_final: 0.7631 (tptt) REVERT: A 142 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7306 (pt) REVERT: A 162 SER cc_start: 0.8440 (m) cc_final: 0.8183 (p) REVERT: A 163 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8637 (m) REVERT: A 166 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8329 (tmtt) REVERT: A 169 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 172 LYS cc_start: 0.8754 (tttp) cc_final: 0.8546 (tttp) REVERT: A 180 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8210 (mt) REVERT: A 181 TYR cc_start: 0.7532 (m-80) cc_final: 0.7261 (m-80) REVERT: A 182 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 203 GLU cc_start: 0.7208 (tt0) cc_final: 0.6838 (tt0) REVERT: A 204 GLU cc_start: 0.7397 (tp30) cc_final: 0.7011 (tm-30) REVERT: A 206 ARG cc_start: 0.8093 (mtp-110) cc_final: 0.7562 (ttm-80) REVERT: A 271 TYR cc_start: 0.7937 (m-80) cc_final: 0.7525 (m-80) REVERT: A 329 ILE cc_start: 0.8386 (mt) cc_final: 0.8123 (mt) REVERT: A 347 LYS cc_start: 0.8399 (mttt) cc_final: 0.8114 (mtpp) REVERT: A 350 LYS cc_start: 0.8367 (tttt) cc_final: 0.8103 (ttpp) REVERT: A 366 LYS cc_start: 0.8263 (tptm) cc_final: 0.7772 (mtpp) REVERT: A 369 THR cc_start: 0.8180 (m) cc_final: 0.7850 (p) REVERT: A 370 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 406 TRP cc_start: 0.7810 (p90) cc_final: 0.7424 (p90) REVERT: A 407 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: A 414 TRP cc_start: 0.8739 (p-90) cc_final: 0.7959 (p-90) REVERT: A 422 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 429 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8356 (mp) REVERT: A 478 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 494 ASN cc_start: 0.7408 (m110) cc_final: 0.7127 (m110) REVERT: A 500 GLN cc_start: 0.7511 (pt0) cc_final: 0.7197 (pt0) REVERT: A 503 LEU cc_start: 0.8089 (tp) cc_final: 0.7203 (tp) REVERT: A 507 GLN cc_start: 0.8683 (pt0) cc_final: 0.8037 (pt0) REVERT: A 520 GLN cc_start: 0.7360 (tp40) cc_final: 0.6917 (tp40) REVERT: A 523 GLU cc_start: 0.7638 (tp30) cc_final: 0.7314 (tm-30) REVERT: A 545 ASN cc_start: 0.5080 (OUTLIER) cc_final: 0.4627 (p0) REVERT: A 548 VAL cc_start: 0.2037 (OUTLIER) cc_final: 0.1093 (m) REVERT: B 13 LYS cc_start: 0.7605 (mmtp) cc_final: 0.7293 (mmtp) REVERT: B 21 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8223 (m) REVERT: B 28 GLU cc_start: 0.7504 (tp30) cc_final: 0.7273 (tp30) REVERT: B 34 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8130 (tt) REVERT: B 36 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6976 (mt-10) REVERT: B 43 LYS cc_start: 0.8015 (tttp) cc_final: 0.7596 (tttp) REVERT: B 77 PHE cc_start: 0.7920 (m-80) cc_final: 0.7567 (m-10) REVERT: B 79 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7258 (mm-30) REVERT: B 82 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8189 (mttm) REVERT: B 86 ASP cc_start: 0.6854 (p0) cc_final: 0.6559 (p0) REVERT: B 102 LYS cc_start: 0.8661 (mppt) cc_final: 0.8188 (mptt) REVERT: B 128 THR cc_start: 0.7823 (p) cc_final: 0.7368 (t) REVERT: B 167 ILE cc_start: 0.4936 (OUTLIER) cc_final: 0.4633 (tt) REVERT: B 178 ILE cc_start: 0.8408 (mt) cc_final: 0.7987 (tp) REVERT: B 256 ASP cc_start: 0.7104 (t70) cc_final: 0.6685 (t70) REVERT: B 260 LEU cc_start: 0.7540 (mt) cc_final: 0.7242 (mt) REVERT: B 263 LYS cc_start: 0.7964 (ttmp) cc_final: 0.7648 (ttmp) REVERT: B 266 TRP cc_start: 0.7691 (t60) cc_final: 0.7146 (t60) REVERT: B 298 GLU cc_start: 0.8270 (pt0) cc_final: 0.7424 (pp20) REVERT: B 308 GLU cc_start: 0.7567 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 309 ILE cc_start: 0.8366 (mt) cc_final: 0.7899 (mm) REVERT: B 312 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: B 322 SER cc_start: 0.8736 (m) cc_final: 0.8354 (p) REVERT: B 328 GLU cc_start: 0.7252 (tt0) cc_final: 0.7035 (tt0) REVERT: B 347 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7868 (mttm) REVERT: B 353 LYS cc_start: 0.8280 (ptpp) cc_final: 0.7735 (ptpp) REVERT: B 365 VAL cc_start: 0.8447 (m) cc_final: 0.8181 (p) REVERT: B 370 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7257 (mt-10) REVERT: B 378 GLU cc_start: 0.7165 (tp30) cc_final: 0.6939 (tp30) REVERT: B 388 LYS cc_start: 0.8036 (tttt) cc_final: 0.7719 (tttt) REVERT: B 396 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6654 (mt-10) outliers start: 59 outliers final: 38 residues processed: 362 average time/residue: 0.1024 time to fit residues: 48.3403 Evaluate side-chains 374 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 323 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 81 ASN 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 180 ILE 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 295 LEU Chi-restraints excluded: chain A residue 373 GLN 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 429 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 435 VAL 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 34 LEU 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 72 ARG 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 138 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 374 LYS 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 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 88 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117352 restraints weight = 14303.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121279 restraints weight = 7195.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123836 restraints weight = 4293.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125447 restraints weight = 2880.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126665 restraints weight = 2130.906| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.4110 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= 0.117 Angle : 0.584 10.664 10652 Z= 0.298 Chirality : 0.044 0.175 1157 Planarity : 0.005 0.044 1335 Dihedral : 6.828 80.303 1016 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 7.03 % Allowed : 26.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.29), residues: 912 helix: 1.30 (0.31), residues: 310 sheet: -0.66 (0.40), residues: 152 loop : -0.65 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.028 0.001 TYR A 319 PHE 0.026 0.002 PHE A 171 TRP 0.028 0.001 TRP A 535 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7845) covalent geometry : angle 0.58383 (10652) hydrogen bonds : bond 0.03092 ( 284) hydrogen bonds : angle 4.54325 ( 768) *********************** 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 383 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 324 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.7532 (m-80) cc_final: 0.6903 (m-80) REVERT: A 101 LYS cc_start: 0.8300 (mttm) cc_final: 0.7787 (mttm) REVERT: A 104 LYS cc_start: 0.8622 (tmtt) cc_final: 0.8229 (mmmm) REVERT: A 126 LYS cc_start: 0.8338 (mttm) cc_final: 0.7973 (mtmm) REVERT: A 162 SER cc_start: 0.8422 (m) cc_final: 0.8155 (p) REVERT: A 163 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8605 (m) REVERT: A 166 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8329 (tmtt) REVERT: A 169 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 172 LYS cc_start: 0.8741 (tttp) cc_final: 0.8537 (tttp) REVERT: A 173 LYS cc_start: 0.8532 (tttt) cc_final: 0.8047 (tppt) REVERT: A 180 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8222 (mt) REVERT: A 181 TYR cc_start: 0.7557 (m-80) cc_final: 0.7287 (m-80) REVERT: A 182 GLN cc_start: 0.7001 (tm-30) cc_final: 0.6708 (tm-30) REVERT: A 203 GLU cc_start: 0.7167 (tt0) cc_final: 0.6750 (tt0) REVERT: A 204 GLU cc_start: 0.7352 (tp30) cc_final: 0.7125 (tp30) REVERT: A 206 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7627 (mtp85) REVERT: A 232 TYR cc_start: 0.8046 (m-10) cc_final: 0.7735 (m-80) REVERT: A 233 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6383 (mp0) REVERT: A 263 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8611 (tttm) REVERT: A 271 TYR cc_start: 0.7961 (m-80) cc_final: 0.7604 (m-80) REVERT: A 328 GLU cc_start: 0.7298 (tt0) cc_final: 0.6894 (tt0) REVERT: A 329 ILE cc_start: 0.8401 (mt) cc_final: 0.8173 (mt) REVERT: A 342 TYR cc_start: 0.8180 (p90) cc_final: 0.7946 (p90) REVERT: A 347 LYS cc_start: 0.8411 (mttt) cc_final: 0.8034 (mttm) REVERT: A 350 LYS cc_start: 0.8407 (tttt) cc_final: 0.8134 (ttpp) REVERT: A 366 LYS cc_start: 0.8221 (tptm) cc_final: 0.7716 (mtpp) REVERT: A 369 THR cc_start: 0.8155 (m) cc_final: 0.7831 (p) REVERT: A 370 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7147 (mt-10) REVERT: A 414 TRP cc_start: 0.8721 (p-90) cc_final: 0.7936 (p-90) REVERT: A 422 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7781 (mp) REVERT: A 430 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7556 (mp0) REVERT: A 476 LYS cc_start: 0.8082 (mttm) cc_final: 0.7795 (mtpp) REVERT: A 478 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 494 ASN cc_start: 0.7361 (m110) cc_final: 0.7125 (m110) REVERT: A 500 GLN cc_start: 0.7413 (pt0) cc_final: 0.7156 (pt0) REVERT: A 503 LEU cc_start: 0.8091 (tp) cc_final: 0.7289 (tp) REVERT: A 507 GLN cc_start: 0.8678 (pt0) cc_final: 0.8057 (pt0) REVERT: A 520 GLN cc_start: 0.7283 (tp40) cc_final: 0.6330 (tp40) REVERT: A 524 GLN cc_start: 0.7388 (mt0) cc_final: 0.6828 (mp10) REVERT: A 545 ASN cc_start: 0.4908 (OUTLIER) cc_final: 0.4443 (p0) REVERT: A 548 VAL cc_start: 0.1977 (OUTLIER) cc_final: 0.1066 (m) REVERT: B 21 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8148 (m) REVERT: B 28 GLU cc_start: 0.7509 (tp30) cc_final: 0.7291 (tp30) REVERT: B 36 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6979 (mt-10) REVERT: B 43 LYS cc_start: 0.8075 (tttp) cc_final: 0.7593 (tttp) REVERT: B 44 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7197 (mm-30) REVERT: B 77 PHE cc_start: 0.7926 (m-80) cc_final: 0.7648 (m-10) REVERT: B 79 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7227 (mm-30) REVERT: B 82 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8186 (mttp) REVERT: B 86 ASP cc_start: 0.6825 (p0) cc_final: 0.6598 (p0) REVERT: B 102 LYS cc_start: 0.8671 (mppt) cc_final: 0.8211 (mptt) REVERT: B 128 THR cc_start: 0.7828 (p) cc_final: 0.7393 (t) REVERT: B 167 ILE cc_start: 0.4878 (OUTLIER) cc_final: 0.4619 (tt) REVERT: B 178 ILE cc_start: 0.8398 (mt) cc_final: 0.7993 (tp) REVERT: B 256 ASP cc_start: 0.7098 (t70) cc_final: 0.6421 (t70) REVERT: B 260 LEU cc_start: 0.7565 (mt) cc_final: 0.7214 (mt) REVERT: B 263 LYS cc_start: 0.7938 (ttmp) cc_final: 0.7696 (ttmp) REVERT: B 266 TRP cc_start: 0.7664 (t60) cc_final: 0.7146 (t60) REVERT: B 298 GLU cc_start: 0.8266 (pt0) cc_final: 0.7403 (pp20) REVERT: B 308 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 309 ILE cc_start: 0.8399 (mt) cc_final: 0.7894 (mm) REVERT: B 312 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: B 322 SER cc_start: 0.8715 (m) cc_final: 0.8331 (p) REVERT: B 328 GLU cc_start: 0.7249 (tt0) cc_final: 0.6933 (tt0) REVERT: B 347 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7865 (mttm) REVERT: B 353 LYS cc_start: 0.8226 (ptpp) cc_final: 0.7704 (ptpp) REVERT: B 365 VAL cc_start: 0.8491 (m) cc_final: 0.8210 (p) REVERT: B 370 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7216 (mt-10) REVERT: B 378 GLU cc_start: 0.7119 (tp30) cc_final: 0.6871 (tp30) REVERT: B 388 LYS cc_start: 0.8025 (tttt) cc_final: 0.7701 (tttt) REVERT: B 398 TRP cc_start: 0.8807 (t-100) cc_final: 0.8313 (t-100) outliers start: 59 outliers final: 39 residues processed: 352 average time/residue: 0.0977 time to fit residues: 45.2010 Evaluate side-chains 365 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU 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 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 180 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 416 PHE 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 56 TYR 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 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 167 ILE Chi-restraints excluded: chain B residue 192 ASP 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 312 GLU Chi-restraints excluded: chain B residue 330 GLN 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 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 367 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 81 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 332 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116374 restraints weight = 14496.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120266 restraints weight = 7251.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122817 restraints weight = 4348.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124514 restraints weight = 2930.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125671 restraints weight = 2146.697| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7845 Z= 0.142 Angle : 0.615 10.865 10652 Z= 0.313 Chirality : 0.046 0.294 1157 Planarity : 0.005 0.046 1335 Dihedral : 6.480 80.235 1011 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.56 % Allowed : 26.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.29), residues: 912 helix: 1.33 (0.31), residues: 304 sheet: -0.68 (0.40), residues: 152 loop : -0.60 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.030 0.002 TYR A 319 PHE 0.027 0.002 PHE A 171 TRP 0.029 0.001 TRP A 535 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7845) covalent geometry : angle 0.61507 (10652) hydrogen bonds : bond 0.03275 ( 284) hydrogen bonds : angle 4.57492 ( 768) *********************** 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 375 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LYS cc_start: 0.8319 (mttm) cc_final: 0.7779 (mttm) REVERT: A 104 LYS cc_start: 0.8608 (tmtt) cc_final: 0.8229 (mmmm) REVERT: A 126 LYS cc_start: 0.8331 (mttm) cc_final: 0.7926 (mtmm) REVERT: A 162 SER cc_start: 0.8463 (m) cc_final: 0.8205 (p) REVERT: A 163 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8631 (m) REVERT: A 166 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8338 (tmtt) REVERT: A 169 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 172 LYS cc_start: 0.8759 (tttp) cc_final: 0.8548 (tttp) REVERT: A 173 LYS cc_start: 0.8542 (tttt) cc_final: 0.8080 (tppt) REVERT: A 180 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8232 (mt) REVERT: A 181 TYR cc_start: 0.7575 (m-80) cc_final: 0.7320 (m-80) REVERT: A 182 GLN cc_start: 0.7041 (tm-30) cc_final: 0.6743 (tm-30) REVERT: A 203 GLU cc_start: 0.7196 (tt0) cc_final: 0.6772 (tt0) REVERT: A 204 GLU cc_start: 0.7394 (tp30) cc_final: 0.7150 (tp30) REVERT: A 206 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7652 (mtp85) REVERT: A 227 PHE cc_start: 0.7836 (m-80) cc_final: 0.7551 (m-80) REVERT: A 232 TYR cc_start: 0.8074 (m-80) cc_final: 0.7759 (m-80) REVERT: A 233 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 271 TYR cc_start: 0.7973 (m-80) cc_final: 0.7587 (m-80) REVERT: A 329 ILE cc_start: 0.8421 (mt) cc_final: 0.8153 (mt) REVERT: A 347 LYS cc_start: 0.8425 (mttt) cc_final: 0.8124 (mtpp) REVERT: A 350 LYS cc_start: 0.8369 (tttt) cc_final: 0.8120 (ttpp) REVERT: A 366 LYS cc_start: 0.8257 (tptm) cc_final: 0.7686 (mtpp) REVERT: A 369 THR cc_start: 0.8165 (m) cc_final: 0.7851 (p) REVERT: A 370 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7152 (mt-10) REVERT: A 415 GLU cc_start: 0.6933 (tp30) cc_final: 0.6664 (tp30) REVERT: A 422 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7790 (mp) REVERT: A 430 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7553 (mp0) REVERT: A 476 LYS cc_start: 0.8077 (mttm) cc_final: 0.7790 (mtpp) REVERT: A 478 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 494 ASN cc_start: 0.7392 (m110) cc_final: 0.7114 (m110) REVERT: A 500 GLN cc_start: 0.7406 (pt0) cc_final: 0.7170 (pt0) REVERT: A 503 LEU cc_start: 0.8131 (tp) cc_final: 0.7256 (tp) REVERT: A 507 GLN cc_start: 0.8673 (pt0) cc_final: 0.8040 (pt0) REVERT: A 520 GLN cc_start: 0.7324 (tp40) cc_final: 0.6349 (tp40) REVERT: A 523 GLU cc_start: 0.7604 (tp30) cc_final: 0.7384 (tm-30) REVERT: A 524 GLN cc_start: 0.7383 (mt0) cc_final: 0.6700 (mp10) REVERT: A 540 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7969 (mmtm) REVERT: A 545 ASN cc_start: 0.5160 (OUTLIER) cc_final: 0.4678 (p0) REVERT: A 548 VAL cc_start: 0.2029 (OUTLIER) cc_final: 0.1098 (m) REVERT: B 21 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8153 (m) REVERT: B 28 GLU cc_start: 0.7534 (tp30) cc_final: 0.7273 (tp30) REVERT: B 36 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7015 (mt-10) REVERT: B 43 LYS cc_start: 0.8103 (tttp) cc_final: 0.7622 (tttp) REVERT: B 44 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 77 PHE cc_start: 0.7957 (m-80) cc_final: 0.7614 (m-10) REVERT: B 79 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7266 (mm-30) REVERT: B 82 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8216 (mttp) REVERT: B 86 ASP cc_start: 0.6838 (p0) cc_final: 0.6572 (p0) REVERT: B 102 LYS cc_start: 0.8686 (mppt) cc_final: 0.8213 (mptt) REVERT: B 128 THR cc_start: 0.7803 (p) cc_final: 0.7372 (t) REVERT: B 167 ILE cc_start: 0.4881 (OUTLIER) cc_final: 0.4582 (tt) REVERT: B 178 ILE cc_start: 0.8371 (mt) cc_final: 0.7969 (tp) REVERT: B 256 ASP cc_start: 0.7158 (t70) cc_final: 0.6650 (t70) REVERT: B 260 LEU cc_start: 0.7578 (mt) cc_final: 0.7308 (mt) REVERT: B 266 TRP cc_start: 0.7646 (t60) cc_final: 0.7172 (t60) REVERT: B 298 GLU cc_start: 0.8251 (pt0) cc_final: 0.7410 (pp20) REVERT: B 308 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7148 (tm-30) REVERT: B 309 ILE cc_start: 0.8408 (mt) cc_final: 0.7891 (mm) REVERT: B 312 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: B 322 SER cc_start: 0.8720 (m) cc_final: 0.8331 (p) REVERT: B 328 GLU cc_start: 0.7205 (tt0) cc_final: 0.6939 (tt0) REVERT: B 347 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7869 (mttm) REVERT: B 353 LYS cc_start: 0.8235 (ptpp) cc_final: 0.7738 (ptpp) REVERT: B 365 VAL cc_start: 0.8471 (m) cc_final: 0.8212 (p) REVERT: B 370 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7193 (mt-10) REVERT: B 378 GLU cc_start: 0.7140 (tp30) cc_final: 0.6908 (tp30) REVERT: B 388 LYS cc_start: 0.7996 (tttt) cc_final: 0.7701 (tttt) REVERT: B 398 TRP cc_start: 0.8806 (t-100) cc_final: 0.8295 (t-100) outliers start: 55 outliers final: 36 residues processed: 345 average time/residue: 0.0961 time to fit residues: 43.6967 Evaluate side-chains 364 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 320 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU 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 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 180 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN 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 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 72 ARG 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 167 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 312 GLU 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 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 84 optimal weight: 0.0000 chunk 18 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 0.0070 chunk 74 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 151 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 96 HIS B 235 HIS B 332 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118122 restraints weight = 14342.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122051 restraints weight = 7193.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124625 restraints weight = 4304.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126349 restraints weight = 2893.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127525 restraints weight = 2111.040| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4450 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= 0.121 Angle : 0.609 11.118 10652 Z= 0.309 Chirality : 0.045 0.266 1157 Planarity : 0.005 0.051 1335 Dihedral : 6.316 79.541 1011 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.72 % Allowed : 27.77 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.29), residues: 912 helix: 1.43 (0.32), residues: 302 sheet: -0.79 (0.41), residues: 145 loop : -0.62 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.030 0.001 TYR A 319 PHE 0.026 0.002 PHE A 171 TRP 0.026 0.001 TRP A 535 HIS 0.006 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7845) covalent geometry : angle 0.60880 (10652) hydrogen bonds : bond 0.02965 ( 284) hydrogen bonds : angle 4.44437 ( 768) *********************** 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 365 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7869 (mtt) cc_final: 0.7566 (mtp) REVERT: A 101 LYS cc_start: 0.8321 (mttm) cc_final: 0.7730 (mtpp) REVERT: A 104 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8207 (mmmm) REVERT: A 123 ASP cc_start: 0.8456 (p0) cc_final: 0.7827 (p0) REVERT: A 126 LYS cc_start: 0.8323 (mttm) cc_final: 0.7910 (mtmm) REVERT: A 162 SER cc_start: 0.8407 (m) cc_final: 0.8148 (p) REVERT: A 163 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8624 (m) REVERT: A 166 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8325 (tmtt) REVERT: A 169 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 172 LYS cc_start: 0.8732 (tttp) cc_final: 0.8523 (tttp) REVERT: A 173 LYS cc_start: 0.8520 (tttt) cc_final: 0.8045 (tppt) REVERT: A 180 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 181 TYR cc_start: 0.7594 (m-80) cc_final: 0.7365 (m-80) REVERT: A 182 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 203 GLU cc_start: 0.7137 (tt0) cc_final: 0.6729 (tt0) REVERT: A 204 GLU cc_start: 0.7347 (tp30) cc_final: 0.7110 (tp30) REVERT: A 206 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7619 (mtp85) REVERT: A 227 PHE cc_start: 0.7838 (m-80) cc_final: 0.6947 (m-80) REVERT: A 233 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6554 (tp30) REVERT: A 263 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8540 (tttm) REVERT: A 271 TYR cc_start: 0.8034 (m-80) cc_final: 0.7696 (m-80) REVERT: A 328 GLU cc_start: 0.7368 (tt0) cc_final: 0.7100 (tt0) REVERT: A 329 ILE cc_start: 0.8454 (mt) cc_final: 0.8193 (mt) REVERT: A 350 LYS cc_start: 0.8402 (tttt) cc_final: 0.8140 (ttpp) REVERT: A 366 LYS cc_start: 0.8246 (tptm) cc_final: 0.7899 (mtpp) REVERT: A 370 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7120 (mt-10) REVERT: A 407 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: A 415 GLU cc_start: 0.6950 (tp30) cc_final: 0.6636 (tp30) REVERT: A 430 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7584 (mp0) REVERT: A 472 THR cc_start: 0.7684 (m) cc_final: 0.7168 (p) REVERT: A 476 LYS cc_start: 0.8083 (mttm) cc_final: 0.7765 (mmmm) REVERT: A 478 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 494 ASN cc_start: 0.7340 (m110) cc_final: 0.7091 (m110) REVERT: A 500 GLN cc_start: 0.7410 (pt0) cc_final: 0.7188 (pt0) REVERT: A 503 LEU cc_start: 0.8064 (tp) cc_final: 0.7185 (tp) REVERT: A 507 GLN cc_start: 0.8642 (pt0) cc_final: 0.8067 (pt0) REVERT: A 520 GLN cc_start: 0.7286 (tp40) cc_final: 0.6395 (tp40) REVERT: A 524 GLN cc_start: 0.7377 (mt0) cc_final: 0.6927 (mp10) REVERT: A 540 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7930 (mmtp) REVERT: A 548 VAL cc_start: 0.1965 (OUTLIER) cc_final: 0.1071 (m) REVERT: B 21 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8126 (m) REVERT: B 28 GLU cc_start: 0.7559 (tp30) cc_final: 0.7248 (tp30) REVERT: B 36 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6971 (mt-10) REVERT: B 43 LYS cc_start: 0.8115 (tttp) cc_final: 0.7616 (tttp) REVERT: B 77 PHE cc_start: 0.7920 (m-80) cc_final: 0.7597 (m-10) REVERT: B 79 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7227 (mm-30) REVERT: B 82 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8200 (mttp) REVERT: B 86 ASP cc_start: 0.6780 (p0) cc_final: 0.6560 (p0) REVERT: B 102 LYS cc_start: 0.8661 (mppt) cc_final: 0.8186 (mptt) REVERT: B 128 THR cc_start: 0.7824 (p) cc_final: 0.7320 (t) REVERT: B 178 ILE cc_start: 0.8370 (mt) cc_final: 0.7960 (tp) REVERT: B 256 ASP cc_start: 0.7100 (t70) cc_final: 0.6377 (t70) REVERT: B 260 LEU cc_start: 0.7575 (mt) cc_final: 0.7334 (mt) REVERT: B 263 LYS cc_start: 0.7991 (ttmp) cc_final: 0.7251 (tppt) REVERT: B 266 TRP cc_start: 0.7597 (t60) cc_final: 0.7112 (t60) REVERT: B 298 GLU cc_start: 0.8118 (pt0) cc_final: 0.7235 (pt0) REVERT: B 309 ILE cc_start: 0.8406 (mt) cc_final: 0.7848 (mm) REVERT: B 312 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: B 322 SER cc_start: 0.8697 (m) cc_final: 0.8341 (p) REVERT: B 328 GLU cc_start: 0.7185 (tt0) cc_final: 0.6954 (tt0) REVERT: B 347 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7864 (mttm) REVERT: B 353 LYS cc_start: 0.8181 (ptpp) cc_final: 0.7659 (ptpp) REVERT: B 364 ASP cc_start: 0.8199 (t70) cc_final: 0.7951 (t0) REVERT: B 365 VAL cc_start: 0.8488 (m) cc_final: 0.8253 (p) REVERT: B 370 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7151 (mt-10) REVERT: B 388 LYS cc_start: 0.8007 (tttt) cc_final: 0.7717 (tttt) outliers start: 48 outliers final: 34 residues processed: 336 average time/residue: 0.0935 time to fit residues: 41.2653 Evaluate side-chains 353 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 313 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU 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 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 180 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN 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 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 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 413 GLU 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 70 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 82 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 182 GLN B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116519 restraints weight = 14320.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120510 restraints weight = 7115.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123169 restraints weight = 4234.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124907 restraints weight = 2821.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126116 restraints weight = 2059.751| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7845 Z= 0.129 Angle : 0.622 11.273 10652 Z= 0.314 Chirality : 0.046 0.311 1157 Planarity : 0.005 0.050 1335 Dihedral : 6.140 79.368 1007 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.13 % Allowed : 28.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.29), residues: 912 helix: 1.50 (0.32), residues: 296 sheet: -0.67 (0.40), residues: 152 loop : -0.49 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.030 0.001 TYR A 319 PHE 0.028 0.002 PHE A 171 TRP 0.024 0.001 TRP A 535 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7845) covalent geometry : angle 0.62249 (10652) hydrogen bonds : bond 0.03052 ( 284) hydrogen bonds : angle 4.48664 ( 768) ********************** 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 362 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 319 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7866 (mtt) cc_final: 0.7538 (mtp) REVERT: A 101 LYS cc_start: 0.8321 (mttm) cc_final: 0.7745 (mttm) REVERT: A 104 LYS cc_start: 0.8596 (tmtt) cc_final: 0.8173 (mmmm) REVERT: A 121 ASP cc_start: 0.6595 (m-30) cc_final: 0.6388 (m-30) REVERT: A 123 ASP cc_start: 0.8464 (p0) cc_final: 0.7797 (p0) REVERT: A 126 LYS cc_start: 0.8367 (mttm) cc_final: 0.7933 (mtmm) REVERT: A 162 SER cc_start: 0.8466 (m) cc_final: 0.8189 (p) REVERT: A 163 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8655 (m) REVERT: A 166 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8320 (tmtt) REVERT: A 169 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7505 (mm-30) REVERT: A 172 LYS cc_start: 0.8797 (tttp) cc_final: 0.8569 (tttp) REVERT: A 173 LYS cc_start: 0.8593 (tttt) cc_final: 0.8087 (tppt) REVERT: A 180 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8197 (mt) REVERT: A 181 TYR cc_start: 0.7583 (m-80) cc_final: 0.7292 (m-80) REVERT: A 182 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6790 (tm-30) REVERT: A 203 GLU cc_start: 0.7205 (tt0) cc_final: 0.6798 (tt0) REVERT: A 204 GLU cc_start: 0.7402 (tp30) cc_final: 0.7159 (tp30) REVERT: A 206 ARG cc_start: 0.8040 (mtp-110) cc_final: 0.7613 (mtp85) REVERT: A 227 PHE cc_start: 0.7802 (m-80) cc_final: 0.6898 (m-10) REVERT: A 232 TYR cc_start: 0.8096 (m-80) cc_final: 0.7746 (m-10) REVERT: A 233 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6450 (tp30) REVERT: A 263 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8527 (tttm) REVERT: A 271 TYR cc_start: 0.8025 (m-80) cc_final: 0.7763 (m-80) REVERT: A 328 GLU cc_start: 0.7328 (tt0) cc_final: 0.7000 (tt0) REVERT: A 329 ILE cc_start: 0.8419 (mt) cc_final: 0.8167 (mt) REVERT: A 350 LYS cc_start: 0.8345 (tttt) cc_final: 0.8112 (ttpp) REVERT: A 366 LYS cc_start: 0.8260 (tptm) cc_final: 0.7838 (mtpp) REVERT: A 370 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 407 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: A 415 GLU cc_start: 0.6944 (tp30) cc_final: 0.6637 (tp30) REVERT: A 430 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7524 (mp0) REVERT: A 472 THR cc_start: 0.7684 (m) cc_final: 0.7172 (p) REVERT: A 476 LYS cc_start: 0.8130 (mttm) cc_final: 0.7825 (mmmm) REVERT: A 478 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 494 ASN cc_start: 0.7364 (m110) cc_final: 0.7088 (m110) REVERT: A 503 LEU cc_start: 0.8063 (tp) cc_final: 0.7152 (tp) REVERT: A 507 GLN cc_start: 0.8644 (pt0) cc_final: 0.8007 (pt0) REVERT: A 520 GLN cc_start: 0.7346 (tp40) cc_final: 0.6446 (tp40) REVERT: A 524 GLN cc_start: 0.7472 (mt0) cc_final: 0.7005 (mp10) REVERT: A 530 LYS cc_start: 0.7088 (mmtp) cc_final: 0.6711 (mtpp) REVERT: A 540 LYS cc_start: 0.8308 (mmmm) cc_final: 0.7956 (mmtm) REVERT: A 548 VAL cc_start: 0.2016 (OUTLIER) cc_final: 0.1128 (m) REVERT: B 21 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8092 (m) REVERT: B 28 GLU cc_start: 0.7564 (tp30) cc_final: 0.7246 (tp30) REVERT: B 36 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7013 (mt-10) REVERT: B 43 LYS cc_start: 0.8127 (tttp) cc_final: 0.7618 (tttp) REVERT: B 77 PHE cc_start: 0.7877 (m-80) cc_final: 0.7592 (m-10) REVERT: B 79 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 82 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8204 (mttp) REVERT: B 86 ASP cc_start: 0.6826 (p0) cc_final: 0.6615 (p0) REVERT: B 102 LYS cc_start: 0.8669 (mppt) cc_final: 0.8159 (mptt) REVERT: B 128 THR cc_start: 0.7793 (p) cc_final: 0.7281 (t) REVERT: B 178 ILE cc_start: 0.8361 (mt) cc_final: 0.7943 (tp) REVERT: B 181 TYR cc_start: 0.7891 (t80) cc_final: 0.7673 (t80) REVERT: B 256 ASP cc_start: 0.7192 (t70) cc_final: 0.6457 (t70) REVERT: B 260 LEU cc_start: 0.7582 (mt) cc_final: 0.7338 (mt) REVERT: B 263 LYS cc_start: 0.8134 (ttmp) cc_final: 0.7365 (tppt) REVERT: B 298 GLU cc_start: 0.8179 (pt0) cc_final: 0.7310 (pt0) REVERT: B 309 ILE cc_start: 0.8375 (mt) cc_final: 0.8056 (mm) REVERT: B 312 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: B 322 SER cc_start: 0.8752 (m) cc_final: 0.8375 (p) REVERT: B 328 GLU cc_start: 0.7211 (tt0) cc_final: 0.6884 (tt0) REVERT: B 347 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7775 (mtpp) REVERT: B 353 LYS cc_start: 0.8192 (ptpp) cc_final: 0.7735 (ptpp) REVERT: B 364 ASP cc_start: 0.8234 (t70) cc_final: 0.7988 (t0) REVERT: B 365 VAL cc_start: 0.8445 (m) cc_final: 0.8228 (p) REVERT: B 370 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7132 (mt-10) REVERT: B 388 LYS cc_start: 0.7969 (tttt) cc_final: 0.7668 (tttt) REVERT: B 398 TRP cc_start: 0.8819 (t-100) cc_final: 0.8312 (t-100) outliers start: 43 outliers final: 34 residues processed: 336 average time/residue: 0.1027 time to fit residues: 45.2435 Evaluate side-chains 355 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 315 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU 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 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 180 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 407 GLN 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 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 134 SER Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 413 GLU 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 84 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 182 GLN B 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116568 restraints weight = 14278.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120598 restraints weight = 7035.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123174 restraints weight = 4154.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124873 restraints weight = 2778.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.126114 restraints weight = 2033.286| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7845 Z= 0.130 Angle : 0.623 11.147 10652 Z= 0.313 Chirality : 0.046 0.317 1157 Planarity : 0.005 0.051 1335 Dihedral : 6.137 79.288 1007 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.24 % Allowed : 28.49 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.29), residues: 912 helix: 1.46 (0.31), residues: 296 sheet: -0.71 (0.40), residues: 152 loop : -0.48 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.032 0.002 TYR A 319 PHE 0.028 0.002 PHE A 171 TRP 0.028 0.002 TRP A 337 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7845) covalent geometry : angle 0.62280 (10652) hydrogen bonds : bond 0.02998 ( 284) hydrogen bonds : angle 4.48139 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1578.24 seconds wall clock time: 27 minutes 59.85 seconds (1679.85 seconds total)