Starting phenix.real_space_refine on Wed Mar 5 22:45:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p9u_13266/03_2025/7p9u_13266.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p9u_13266/03_2025/7p9u_13266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p9u_13266/03_2025/7p9u_13266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p9u_13266/03_2025/7p9u_13266.map" model { file = "/net/cci-nas-00/data/ceres_data/7p9u_13266/03_2025/7p9u_13266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p9u_13266/03_2025/7p9u_13266.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.041 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 22 5.16 5 C 2631 2.51 5 N 625 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3943 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 375 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "B" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3568 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 432} Chain breaks: 1 Time building chain proxies: 3.24, per 1000 atoms: 0.82 Number of scatterers: 3943 At special positions: 0 Unit cell: (68.224, 81.536, 89.856, 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 22 16.00 O 665 8.00 N 625 7.00 C 2631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 158 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 488.6 milliseconds 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 77.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 178 through 208 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 60 through 63 Processing helix chain 'B' and resid 64 through 74 removed outlier: 4.132A pdb=" N GLY B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 105 Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.718A pdb=" N TYR B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.814A pdb=" N ALA B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 152 Processing helix chain 'B' and resid 162 through 183 Processing helix chain 'B' and resid 184 through 190 removed outlier: 3.597A pdb=" N ILE B 190 " --> pdb=" O TRP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 216 removed outlier: 3.523A pdb=" N ILE B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 234 through 246 removed outlier: 3.547A pdb=" N TYR B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 245 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 292 removed outlier: 3.941A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 302 through 312 Processing helix chain 'B' and resid 318 through 349 removed outlier: 3.738A pdb=" N SER B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET B 331 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 344 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 347 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 384 through 413 removed outlier: 3.930A pdb=" N ASN B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 395 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 442 removed outlier: 3.626A pdb=" N ALA B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 460 removed outlier: 3.573A pdb=" N THR B 450 " --> pdb=" O ASP B 446 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 467 Processing helix chain 'B' and resid 478 through 493 Processing sheet with id=AA1, first strand: chain 'B' and resid 358 through 359 263 hydrogen bonds defined for protein. 762 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: 0.99 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1179 1.34 - 1.46: 916 1.46 - 1.58: 1914 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4045 Sorted by residual: bond pdb=" CG MET B 243 " pdb=" SD MET B 243 " ideal model delta sigma weight residual 1.803 1.760 0.043 2.50e-02 1.60e+03 2.92e+00 bond pdb=" CG MET B 357 " pdb=" SD MET B 357 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" SD MET B 357 " pdb=" CE MET B 357 " ideal model delta sigma weight residual 1.791 1.765 0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" CB THR B 169 " pdb=" CG2 THR B 169 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.33e-01 bond pdb=" CA ASP B 446 " pdb=" CB ASP B 446 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.58e-02 4.01e+03 8.08e-01 ... (remaining 4040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 5315 1.46 - 2.93: 140 2.93 - 4.39: 35 4.39 - 5.86: 17 5.86 - 7.32: 4 Bond angle restraints: 5511 Sorted by residual: angle pdb=" CA LYS B 362 " pdb=" CB LYS B 362 " pdb=" CG LYS B 362 " ideal model delta sigma weight residual 114.10 120.16 -6.06 2.00e+00 2.50e-01 9.19e+00 angle pdb=" C PRO B 262 " pdb=" N GLU B 263 " pdb=" CA GLU B 263 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.73e+00 angle pdb=" CG MET B 357 " pdb=" SD MET B 357 " pdb=" CE MET B 357 " ideal model delta sigma weight residual 100.90 95.00 5.90 2.20e+00 2.07e-01 7.19e+00 angle pdb=" CA PHE B 239 " pdb=" CB PHE B 239 " pdb=" CG PHE B 239 " ideal model delta sigma weight residual 113.80 116.39 -2.59 1.00e+00 1.00e+00 6.70e+00 angle pdb=" C PRO B 161 " pdb=" N GLU B 162 " pdb=" CA GLU B 162 " ideal model delta sigma weight residual 121.54 126.45 -4.91 1.91e+00 2.74e-01 6.61e+00 ... (remaining 5506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2090 17.16 - 34.32: 222 34.32 - 51.47: 37 51.47 - 68.63: 5 68.63 - 85.79: 4 Dihedral angle restraints: 2358 sinusoidal: 909 harmonic: 1449 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 158 " pdb=" CB CYS B 158 " ideal model delta sinusoidal sigma weight residual -86.00 -171.79 85.79 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CA ARG A 212 " pdb=" C ARG A 212 " pdb=" N GLU A 213 " pdb=" CA GLU A 213 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LYS B 362 " pdb=" C LYS B 362 " pdb=" N HIS B 363 " pdb=" CA HIS B 363 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 375 0.030 - 0.060: 181 0.060 - 0.090: 67 0.090 - 0.120: 31 0.120 - 0.150: 5 Chirality restraints: 659 Sorted by residual: chirality pdb=" CB THR B 169 " pdb=" CA THR B 169 " pdb=" OG1 THR B 169 " pdb=" CG2 THR B 169 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ASP B 446 " pdb=" N ASP B 446 " pdb=" C ASP B 446 " pdb=" CB ASP B 446 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA VAL B 495 " pdb=" N VAL B 495 " pdb=" C VAL B 495 " pdb=" CB VAL B 495 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 656 not shown) Planarity restraints: 666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 249 " 0.020 2.00e-02 2.50e+03 2.45e-02 1.50e+01 pdb=" CG TRP B 249 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 249 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP B 249 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 249 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 249 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 249 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 249 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 249 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 249 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 239 " -0.020 2.00e-02 2.50e+03 1.30e-02 2.95e+00 pdb=" CG PHE B 239 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 239 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 239 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 239 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 239 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 239 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 366 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO B 367 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.024 5.00e-02 4.00e+02 ... (remaining 663 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 261 2.73 - 3.27: 4305 3.27 - 3.82: 6575 3.82 - 4.36: 7277 4.36 - 4.90: 12570 Nonbonded interactions: 30988 Sorted by model distance: nonbonded pdb=" O PRO B 161 " pdb=" N LEU B 163 " model vdw 2.188 3.120 nonbonded pdb=" O VAL B 455 " pdb=" OG1 THR B 459 " model vdw 2.237 3.040 nonbonded pdb=" NH2 ARG A 183 " pdb=" O ILE B 490 " model vdw 2.241 3.120 nonbonded pdb=" O TRP A 179 " pdb=" OG1 THR A 182 " model vdw 2.248 3.040 nonbonded pdb=" O ILE B 378 " pdb=" OG SER B 382 " model vdw 2.250 3.040 ... (remaining 30983 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4045 Z= 0.206 Angle : 0.678 7.320 5511 Z= 0.350 Chirality : 0.043 0.150 659 Planarity : 0.004 0.042 666 Dihedral : 14.105 80.165 1423 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.83 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.41), residues: 498 helix: 1.76 (0.30), residues: 346 sheet: None (None), residues: 0 loop : -1.99 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP B 249 HIS 0.002 0.001 HIS B 373 PHE 0.023 0.002 PHE B 250 TYR 0.014 0.002 TYR B 251 ARG 0.002 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.435 Fit side-chains REVERT: B 78 MET cc_start: 0.7635 (tpt) cc_final: 0.7138 (tpp) REVERT: B 86 CYS cc_start: 0.8361 (m) cc_final: 0.7918 (m) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1093 time to fit residues: 17.4508 Evaluate side-chains 97 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.0370 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129161 restraints weight = 8477.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.132287 restraints weight = 4648.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134329 restraints weight = 2861.903| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4045 Z= 0.205 Angle : 0.691 9.352 5511 Z= 0.348 Chirality : 0.044 0.160 659 Planarity : 0.004 0.029 666 Dihedral : 4.899 45.664 540 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.42 % Favored : 94.18 % Rotamer: Outliers : 1.64 % Allowed : 13.55 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.41), residues: 498 helix: 1.66 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.37 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 249 HIS 0.004 0.001 HIS B 359 PHE 0.030 0.002 PHE B 239 TYR 0.019 0.002 TYR B 149 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.401 Fit side-chains REVERT: A 172 LYS cc_start: 0.7252 (pttm) cc_final: 0.7048 (tptp) REVERT: B 78 MET cc_start: 0.7724 (tpt) cc_final: 0.7227 (tpp) REVERT: B 86 CYS cc_start: 0.8412 (m) cc_final: 0.7892 (m) REVERT: B 270 ILE cc_start: 0.9438 (tp) cc_final: 0.9150 (tp) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.1055 time to fit residues: 14.6163 Evaluate side-chains 99 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128562 restraints weight = 8472.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131673 restraints weight = 4656.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133673 restraints weight = 2896.100| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4045 Z= 0.197 Angle : 0.646 7.046 5511 Z= 0.329 Chirality : 0.043 0.190 659 Planarity : 0.004 0.029 666 Dihedral : 4.916 46.926 540 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.22 % Favored : 93.37 % Rotamer: Outliers : 1.87 % Allowed : 17.06 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.41), residues: 498 helix: 1.70 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -2.49 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.037 0.002 PHE B 239 TYR 0.016 0.001 TYR B 149 ARG 0.001 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.389 Fit side-chains REVERT: B 78 MET cc_start: 0.7751 (tpt) cc_final: 0.7311 (tpp) REVERT: B 113 TYR cc_start: 0.7396 (m-80) cc_final: 0.6881 (m-80) REVERT: B 407 LEU cc_start: 0.8868 (mt) cc_final: 0.8652 (mt) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.1253 time to fit residues: 16.7460 Evaluate side-chains 96 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 360 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.0010 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128580 restraints weight = 8348.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131664 restraints weight = 4599.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133678 restraints weight = 2858.393| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4045 Z= 0.194 Angle : 0.654 8.851 5511 Z= 0.330 Chirality : 0.043 0.178 659 Planarity : 0.004 0.028 666 Dihedral : 4.881 46.905 540 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.02 % Favored : 93.57 % Rotamer: Outliers : 2.80 % Allowed : 20.79 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.41), residues: 498 helix: 1.74 (0.29), residues: 356 sheet: None (None), residues: 0 loop : -2.66 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.039 0.002 PHE B 239 TYR 0.020 0.001 TYR B 240 ARG 0.001 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.445 Fit side-chains REVERT: B 78 MET cc_start: 0.7688 (tpt) cc_final: 0.7279 (tpp) REVERT: B 86 CYS cc_start: 0.8520 (m) cc_final: 0.8085 (m) REVERT: B 99 GLU cc_start: 0.7712 (tt0) cc_final: 0.7446 (tt0) REVERT: B 113 TYR cc_start: 0.7414 (m-80) cc_final: 0.7174 (m-80) REVERT: B 379 MET cc_start: 0.7845 (mmt) cc_final: 0.7617 (mmt) REVERT: B 407 LEU cc_start: 0.8841 (mt) cc_final: 0.8200 (mt) REVERT: B 490 ILE cc_start: 0.8329 (mm) cc_final: 0.8101 (mm) outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 0.1124 time to fit residues: 16.2730 Evaluate side-chains 104 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 360 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128180 restraints weight = 8661.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131232 restraints weight = 4724.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133263 restraints weight = 2916.664| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4045 Z= 0.196 Angle : 0.650 7.384 5511 Z= 0.328 Chirality : 0.043 0.173 659 Planarity : 0.004 0.030 666 Dihedral : 4.910 46.946 540 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.43 % Favored : 93.17 % Rotamer: Outliers : 3.27 % Allowed : 23.13 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.40), residues: 498 helix: 1.69 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.83 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.042 0.002 PHE B 239 TYR 0.013 0.001 TYR B 240 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.415 Fit side-chains REVERT: B 78 MET cc_start: 0.7711 (tpt) cc_final: 0.7299 (tpp) REVERT: B 86 CYS cc_start: 0.8515 (m) cc_final: 0.8083 (m) REVERT: B 99 GLU cc_start: 0.7694 (tt0) cc_final: 0.7438 (tt0) REVERT: B 407 LEU cc_start: 0.8833 (mt) cc_final: 0.8157 (mt) REVERT: B 490 ILE cc_start: 0.8338 (mm) cc_final: 0.8126 (mm) outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 0.1087 time to fit residues: 16.1118 Evaluate side-chains 103 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 0.3980 chunk 25 optimal weight: 0.0000 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129052 restraints weight = 8425.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132098 restraints weight = 4619.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.134101 restraints weight = 2856.054| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4045 Z= 0.179 Angle : 0.666 13.536 5511 Z= 0.328 Chirality : 0.043 0.170 659 Planarity : 0.004 0.028 666 Dihedral : 4.891 46.227 540 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.43 % Favored : 93.37 % Rotamer: Outliers : 3.50 % Allowed : 23.13 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.40), residues: 498 helix: 1.76 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -2.83 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.041 0.001 PHE B 239 TYR 0.013 0.001 TYR B 149 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.472 Fit side-chains REVERT: A 214 LEU cc_start: 0.6657 (mt) cc_final: 0.6255 (mt) REVERT: B 78 MET cc_start: 0.7649 (tpt) cc_final: 0.7273 (tpp) REVERT: B 86 CYS cc_start: 0.8528 (m) cc_final: 0.8113 (m) REVERT: B 407 LEU cc_start: 0.8786 (mt) cc_final: 0.8473 (mt) REVERT: B 490 ILE cc_start: 0.8350 (mm) cc_final: 0.8139 (mm) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 0.1175 time to fit residues: 17.2151 Evaluate side-chains 104 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 0.0970 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.141423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.130138 restraints weight = 8529.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.133152 restraints weight = 4691.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135200 restraints weight = 2917.672| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4045 Z= 0.168 Angle : 0.666 12.046 5511 Z= 0.325 Chirality : 0.043 0.169 659 Planarity : 0.004 0.033 666 Dihedral : 4.836 45.635 540 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 3.27 % Allowed : 24.30 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.40), residues: 498 helix: 1.66 (0.29), residues: 359 sheet: None (None), residues: 0 loop : -2.82 (0.48), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 249 HIS 0.002 0.001 HIS B 359 PHE 0.038 0.001 PHE B 239 TYR 0.034 0.002 TYR B 240 ARG 0.003 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.441 Fit side-chains REVERT: A 214 LEU cc_start: 0.6541 (mt) cc_final: 0.6113 (mt) REVERT: B 78 MET cc_start: 0.7655 (tpt) cc_final: 0.7220 (tpp) REVERT: B 86 CYS cc_start: 0.8487 (m) cc_final: 0.8089 (m) REVERT: B 113 TYR cc_start: 0.7368 (m-80) cc_final: 0.6876 (m-80) REVERT: B 274 MET cc_start: 0.7988 (mmm) cc_final: 0.7779 (mmm) REVERT: B 407 LEU cc_start: 0.8763 (mt) cc_final: 0.8421 (mt) REVERT: B 490 ILE cc_start: 0.8340 (mm) cc_final: 0.8105 (mm) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.1070 time to fit residues: 15.4853 Evaluate side-chains 108 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 360 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128125 restraints weight = 8440.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.131143 restraints weight = 4636.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.133119 restraints weight = 2878.445| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4045 Z= 0.210 Angle : 0.695 11.215 5511 Z= 0.341 Chirality : 0.044 0.163 659 Planarity : 0.004 0.028 666 Dihedral : 4.884 45.923 540 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.22 % Favored : 93.57 % Rotamer: Outliers : 3.04 % Allowed : 26.40 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.40), residues: 498 helix: 1.59 (0.29), residues: 359 sheet: None (None), residues: 0 loop : -2.92 (0.47), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.036 0.002 PHE B 239 TYR 0.053 0.002 TYR B 240 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.409 Fit side-chains REVERT: B 78 MET cc_start: 0.7632 (tpt) cc_final: 0.7277 (tpp) REVERT: B 86 CYS cc_start: 0.8488 (m) cc_final: 0.8094 (m) REVERT: B 240 TYR cc_start: 0.7935 (m-80) cc_final: 0.7640 (m-80) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.1039 time to fit residues: 14.8070 Evaluate side-chains 109 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 360 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 25 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129573 restraints weight = 8344.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132590 restraints weight = 4579.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134601 restraints weight = 2845.619| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4045 Z= 0.182 Angle : 0.707 15.921 5511 Z= 0.338 Chirality : 0.044 0.165 659 Planarity : 0.004 0.030 666 Dihedral : 4.843 45.086 540 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.83 % Favored : 92.97 % Rotamer: Outliers : 3.27 % Allowed : 26.87 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.40), residues: 498 helix: 1.52 (0.29), residues: 365 sheet: None (None), residues: 0 loop : -2.69 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.035 0.001 PHE B 239 TYR 0.047 0.002 TYR B 240 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.425 Fit side-chains REVERT: A 214 LEU cc_start: 0.6611 (mt) cc_final: 0.6183 (mt) REVERT: B 78 MET cc_start: 0.7641 (tpt) cc_final: 0.7277 (tpp) REVERT: B 86 CYS cc_start: 0.8460 (m) cc_final: 0.8083 (m) REVERT: B 240 TYR cc_start: 0.7952 (m-80) cc_final: 0.7658 (m-80) REVERT: B 379 MET cc_start: 0.7852 (mmt) cc_final: 0.7612 (mmt) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1135 time to fit residues: 15.6238 Evaluate side-chains 109 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128776 restraints weight = 8469.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131808 restraints weight = 4672.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133804 restraints weight = 2904.640| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4045 Z= 0.215 Angle : 0.740 15.290 5511 Z= 0.360 Chirality : 0.045 0.162 659 Planarity : 0.004 0.031 666 Dihedral : 4.897 47.398 540 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 2.80 % Allowed : 28.27 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.40), residues: 498 helix: 1.48 (0.29), residues: 367 sheet: None (None), residues: 0 loop : -2.72 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.035 0.002 PHE B 239 TYR 0.046 0.002 TYR B 240 ARG 0.002 0.000 ARG B 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.437 Fit side-chains REVERT: B 78 MET cc_start: 0.7621 (tpt) cc_final: 0.7288 (tpp) REVERT: B 86 CYS cc_start: 0.8522 (m) cc_final: 0.8155 (m) REVERT: B 240 TYR cc_start: 0.7985 (m-80) cc_final: 0.7766 (m-80) REVERT: B 295 GLU cc_start: 0.8295 (mp0) cc_final: 0.7877 (tm-30) REVERT: B 438 MET cc_start: 0.6398 (ttm) cc_final: 0.6165 (ppp) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.1079 time to fit residues: 15.1494 Evaluate side-chains 108 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129634 restraints weight = 8386.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132661 restraints weight = 4620.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134671 restraints weight = 2872.772| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4045 Z= 0.197 Angle : 0.723 15.458 5511 Z= 0.350 Chirality : 0.044 0.186 659 Planarity : 0.004 0.032 666 Dihedral : 4.947 51.087 540 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 3.04 % Allowed : 27.80 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.40), residues: 498 helix: 1.45 (0.29), residues: 367 sheet: None (None), residues: 0 loop : -2.71 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 249 HIS 0.002 0.001 HIS B 359 PHE 0.035 0.001 PHE B 239 TYR 0.045 0.002 TYR B 240 ARG 0.002 0.000 ARG B 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.23 seconds wall clock time: 26 minutes 25.04 seconds (1585.04 seconds total)