Starting phenix.real_space_refine on Wed Jan 17 14:52:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/01_2024/7p9u_13266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/01_2024/7p9u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/01_2024/7p9u_13266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/01_2024/7p9u_13266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/01_2024/7p9u_13266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9u_13266/01_2024/7p9u_13266.pdb" } 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 Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 446": "OD1" <-> "OD2" Residue "B GLU 493": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 2.77, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 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: 1.84 Conformation dependent library (CDL) restraints added in 739.2 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: 0.36 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: 0.98 Time building geometry restraints manager: 1.98 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: 95.00 - 102.81: 23 102.81 - 110.61: 1182 110.61 - 118.41: 1970 118.41 - 126.22: 2261 126.22 - 134.02: 75 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 2.520 nonbonded pdb=" O VAL B 455 " pdb=" OG1 THR B 459 " model vdw 2.237 2.440 nonbonded pdb=" NH2 ARG A 183 " pdb=" O ILE B 490 " model vdw 2.241 2.520 nonbonded pdb=" O TRP A 179 " pdb=" OG1 THR A 182 " model vdw 2.248 2.440 nonbonded pdb=" O ILE B 378 " pdb=" OG SER B 382 " model vdw 2.250 2.440 ... (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 ========== 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: 1.380 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: 6.730 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.443 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: 0.1158 time to fit residues: 18.4058 Evaluate side-chains 97 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1211 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= 0.190 Angle : 0.653 9.026 5511 Z= 0.326 Chirality : 0.042 0.141 659 Planarity : 0.004 0.028 666 Dihedral : 4.889 45.296 540 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.02 % Favored : 93.57 % Rotamer: Outliers : 2.10 % Allowed : 13.08 % 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: 0.93 (0.41), residues: 498 helix: 1.71 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.39 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.027 0.002 PHE B 391 TYR 0.021 0.002 TYR B 149 ARG 0.002 0.000 ARG B 478 *********************** 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 110 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.394 Fit side-chains REVERT: A 172 LYS cc_start: 0.7240 (pttm) cc_final: 0.7018 (tptp) REVERT: B 78 MET cc_start: 0.7662 (tpt) cc_final: 0.7163 (tpp) REVERT: B 86 CYS cc_start: 0.8449 (m) cc_final: 0.7931 (m) REVERT: B 270 ILE cc_start: 0.9402 (tp) cc_final: 0.9100 (tp) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 0.1001 time to fit residues: 13.9022 Evaluate side-chains 101 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ILE 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 332 ASN 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 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4045 Z= 0.161 Angle : 0.613 7.023 5511 Z= 0.307 Chirality : 0.041 0.143 659 Planarity : 0.004 0.030 666 Dihedral : 4.834 46.475 540 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.82 % Favored : 93.78 % Rotamer: Outliers : 2.10 % Allowed : 17.29 % Favored : 80.61 % 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: 0.89 (0.40), residues: 498 helix: 1.72 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 249 HIS 0.002 0.001 HIS B 359 PHE 0.039 0.001 PHE B 239 TYR 0.014 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 113 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.438 Fit side-chains REVERT: A 172 LYS cc_start: 0.7228 (pttm) cc_final: 0.6990 (tptp) REVERT: A 214 LEU cc_start: 0.6506 (mt) cc_final: 0.6042 (mt) REVERT: B 78 MET cc_start: 0.7667 (tpt) cc_final: 0.7168 (tpp) REVERT: B 86 CYS cc_start: 0.8513 (m) cc_final: 0.8021 (m) REVERT: B 490 ILE cc_start: 0.8149 (mm) cc_final: 0.7939 (mm) outliers start: 9 outliers final: 6 residues processed: 105 average time/residue: 0.1150 time to fit residues: 16.3331 Evaluate side-chains 101 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 173 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 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4045 Z= 0.214 Angle : 0.638 8.742 5511 Z= 0.320 Chirality : 0.042 0.127 659 Planarity : 0.004 0.031 666 Dihedral : 4.862 47.818 540 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.63 % Favored : 92.97 % Rotamer: Outliers : 2.57 % Allowed : 20.79 % Favored : 76.64 % 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: 0.85 (0.40), residues: 498 helix: 1.68 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.51 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 249 HIS 0.004 0.001 HIS B 359 PHE 0.040 0.002 PHE B 239 TYR 0.018 0.002 TYR B 240 ARG 0.001 0.000 ARG B 189 *********************** 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 111 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.797 Fit side-chains REVERT: B 78 MET cc_start: 0.7692 (tpt) cc_final: 0.7293 (tpp) REVERT: B 113 TYR cc_start: 0.7425 (m-80) cc_final: 0.6959 (m-80) REVERT: B 211 MET cc_start: 0.6730 (mtp) cc_final: 0.6500 (mtt) REVERT: B 490 ILE cc_start: 0.8157 (mm) cc_final: 0.7924 (mm) outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 0.1387 time to fit residues: 19.3326 Evaluate side-chains 102 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 305 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.0020 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1806 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= 0.178 Angle : 0.621 7.305 5511 Z= 0.310 Chirality : 0.042 0.155 659 Planarity : 0.004 0.030 666 Dihedral : 4.828 47.297 540 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.02 % Favored : 93.57 % Rotamer: Outliers : 3.04 % Allowed : 22.66 % Favored : 74.30 % 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: 0.80 (0.40), residues: 498 helix: 1.66 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.59 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 249 HIS 0.002 0.001 HIS B 359 PHE 0.039 0.001 PHE B 239 TYR 0.014 0.001 TYR B 240 ARG 0.001 0.000 ARG B 189 *********************** 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 114 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.439 Fit side-chains REVERT: A 214 LEU cc_start: 0.6562 (mt) cc_final: 0.6160 (mt) REVERT: B 78 MET cc_start: 0.7668 (tpt) cc_final: 0.7252 (tpp) REVERT: B 86 CYS cc_start: 0.8550 (m) cc_final: 0.8122 (m) REVERT: B 113 TYR cc_start: 0.7431 (m-80) cc_final: 0.6958 (m-80) REVERT: B 490 ILE cc_start: 0.8179 (mm) cc_final: 0.7948 (mm) outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 0.1259 time to fit residues: 17.2688 Evaluate side-chains 106 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4045 Z= 0.179 Angle : 0.652 12.951 5511 Z= 0.318 Chirality : 0.042 0.153 659 Planarity : 0.004 0.030 666 Dihedral : 4.835 47.478 540 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.82 % Favored : 93.78 % Rotamer: Outliers : 3.04 % Allowed : 24.07 % Favored : 72.90 % 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: 0.80 (0.40), residues: 498 helix: 1.69 (0.29), residues: 357 sheet: None (None), residues: 0 loop : -2.65 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.036 0.001 PHE B 239 TYR 0.034 0.002 TYR B 240 ARG 0.001 0.000 ARG B 411 *********************** 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 117 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.425 Fit side-chains REVERT: A 214 LEU cc_start: 0.6607 (mt) cc_final: 0.6232 (mt) REVERT: B 78 MET cc_start: 0.7645 (tpt) cc_final: 0.7239 (tpp) REVERT: B 86 CYS cc_start: 0.8542 (m) cc_final: 0.8122 (m) REVERT: B 490 ILE cc_start: 0.8174 (mm) cc_final: 0.7946 (mm) outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 0.1229 time to fit residues: 17.6633 Evaluate side-chains 108 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.0030 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2056 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= 0.160 Angle : 0.670 14.019 5511 Z= 0.319 Chirality : 0.042 0.155 659 Planarity : 0.004 0.029 666 Dihedral : 4.796 47.347 540 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.62 % Favored : 93.98 % Rotamer: Outliers : 3.50 % Allowed : 25.23 % Favored : 71.26 % 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: 0.81 (0.40), residues: 498 helix: 1.70 (0.29), residues: 358 sheet: None (None), residues: 0 loop : -2.71 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 249 HIS 0.003 0.000 HIS B 359 PHE 0.037 0.001 PHE B 239 TYR 0.050 0.002 TYR B 240 ARG 0.001 0.000 ARG B 126 *********************** 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 124 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.400 Fit side-chains REVERT: B 78 MET cc_start: 0.7655 (tpt) cc_final: 0.7249 (tpp) REVERT: B 86 CYS cc_start: 0.8502 (m) cc_final: 0.8123 (m) REVERT: B 113 TYR cc_start: 0.7415 (m-80) cc_final: 0.6864 (m-80) REVERT: B 240 TYR cc_start: 0.7939 (m-80) cc_final: 0.7669 (m-80) REVERT: B 490 ILE cc_start: 0.8165 (mm) cc_final: 0.7934 (mm) outliers start: 15 outliers final: 11 residues processed: 113 average time/residue: 0.1173 time to fit residues: 17.6622 Evaluate side-chains 112 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 321 ILE Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 45 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2145 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= 0.175 Angle : 0.673 13.435 5511 Z= 0.325 Chirality : 0.042 0.158 659 Planarity : 0.004 0.031 666 Dihedral : 4.784 48.146 540 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.62 % Favored : 93.98 % Rotamer: Outliers : 3.27 % Allowed : 26.40 % Favored : 70.33 % 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: 0.89 (0.40), residues: 498 helix: 1.65 (0.29), residues: 364 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 249 HIS 0.002 0.000 HIS B 359 PHE 0.036 0.001 PHE B 239 TYR 0.041 0.002 TYR B 240 ARG 0.001 0.000 ARG B 396 *********************** 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 117 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.426 Fit side-chains REVERT: B 78 MET cc_start: 0.7639 (tpt) cc_final: 0.7248 (tpp) REVERT: B 86 CYS cc_start: 0.8503 (m) cc_final: 0.8127 (m) REVERT: B 113 TYR cc_start: 0.7390 (m-80) cc_final: 0.6849 (m-80) REVERT: B 223 ASP cc_start: 0.6527 (m-30) cc_final: 0.6214 (m-30) REVERT: B 240 TYR cc_start: 0.7988 (m-80) cc_final: 0.7755 (m-80) REVERT: B 295 GLU cc_start: 0.8261 (mp0) cc_final: 0.7725 (tm-30) REVERT: B 490 ILE cc_start: 0.8188 (mm) cc_final: 0.7952 (mm) outliers start: 14 outliers final: 11 residues processed: 108 average time/residue: 0.1136 time to fit residues: 16.2654 Evaluate side-chains 112 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 366 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.0270 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2235 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 : 0.693 14.389 5511 Z= 0.335 Chirality : 0.042 0.152 659 Planarity : 0.004 0.030 666 Dihedral : 4.870 48.636 540 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.02 % Favored : 93.57 % Rotamer: Outliers : 2.80 % Allowed : 28.04 % 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: 0.74 (0.40), residues: 498 helix: 1.44 (0.29), residues: 369 sheet: None (None), residues: 0 loop : -2.40 (0.52), residues: 129 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 0.039 0.002 TYR B 240 ARG 0.001 0.000 ARG B 396 *********************** 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 118 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 78 MET cc_start: 0.7622 (tpt) cc_final: 0.7225 (tpp) REVERT: B 86 CYS cc_start: 0.8474 (m) cc_final: 0.8117 (m) REVERT: B 223 ASP cc_start: 0.6554 (m-30) cc_final: 0.6233 (m-30) REVERT: B 240 TYR cc_start: 0.7975 (m-80) cc_final: 0.7738 (m-80) REVERT: B 295 GLU cc_start: 0.8287 (mp0) cc_final: 0.7712 (tm-30) REVERT: B 490 ILE cc_start: 0.8188 (mm) cc_final: 0.7956 (mm) outliers start: 12 outliers final: 10 residues processed: 110 average time/residue: 0.1183 time to fit residues: 17.1947 Evaluate side-chains 112 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4045 Z= 0.203 Angle : 0.705 14.140 5511 Z= 0.342 Chirality : 0.043 0.161 659 Planarity : 0.004 0.033 666 Dihedral : 4.978 49.789 540 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 2.80 % Allowed : 27.57 % Favored : 69.63 % 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: 0.58 (0.40), residues: 498 helix: 1.34 (0.29), residues: 369 sheet: None (None), residues: 0 loop : -2.52 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 249 HIS 0.003 0.001 HIS B 359 PHE 0.036 0.001 PHE B 239 TYR 0.039 0.002 TYR B 240 ARG 0.001 0.000 ARG B 396 ********************** 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 113 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: B 78 MET cc_start: 0.7649 (tpt) cc_final: 0.7327 (tpp) REVERT: B 86 CYS cc_start: 0.8502 (m) cc_final: 0.8140 (m) REVERT: B 223 ASP cc_start: 0.6695 (m-30) cc_final: 0.6416 (m-30) REVERT: B 240 TYR cc_start: 0.8060 (m-80) cc_final: 0.7849 (m-80) REVERT: B 295 GLU cc_start: 0.8325 (mp0) cc_final: 0.8025 (mt-10) REVERT: B 490 ILE cc_start: 0.8202 (mm) cc_final: 0.7980 (mm) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 0.1251 time to fit residues: 16.9594 Evaluate side-chains 110 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.141183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129739 restraints weight = 8314.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132764 restraints weight = 4614.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134819 restraints weight = 2877.658| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2371 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 : 0.705 14.027 5511 Z= 0.340 Chirality : 0.043 0.163 659 Planarity : 0.004 0.031 666 Dihedral : 4.969 50.441 540 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.43 % Favored : 93.37 % Rotamer: Outliers : 2.57 % Allowed : 27.34 % Favored : 70.09 % 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: 0.60 (0.40), residues: 498 helix: 1.33 (0.29), residues: 371 sheet: None (None), residues: 0 loop : -2.46 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 249 HIS 0.002 0.000 HIS B 359 PHE 0.036 0.001 PHE B 239 TYR 0.039 0.002 TYR B 240 ARG 0.001 0.000 ARG B 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1181.22 seconds wall clock time: 22 minutes 14.99 seconds (1334.99 seconds total)