Starting phenix.real_space_refine on Tue Sep 24 08:54:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yty_34095/09_2024/7yty_34095.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yty_34095/09_2024/7yty_34095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yty_34095/09_2024/7yty_34095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yty_34095/09_2024/7yty_34095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yty_34095/09_2024/7yty_34095.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yty_34095/09_2024/7yty_34095.cif" } resolution = 3.5 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= -0.000 sd= 0.032 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 62 5.16 5 C 4990 2.51 5 N 1224 2.21 5 O 1332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7608 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3804 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 33, 'TRANS': 467} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 7.15, per 1000 atoms: 0.94 Number of scatterers: 7608 At special positions: 0 Unit cell: (89.38, 107.42, 78.72, 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 62 16.00 O 1332 8.00 N 1224 7.00 C 4990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 136 " 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: 1.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 71.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.507A pdb=" N GLY A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 4.122A pdb=" N PHE A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 108 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.629A pdb=" N ALA A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 152 through 180 removed outlier: 3.775A pdb=" N TRP A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.543A pdb=" N VAL A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 262 through 281 removed outlier: 3.761A pdb=" N LEU A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.831A pdb=" N ALA A 295 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N THR A 297 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP A 298 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG A 300 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 301 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.535A pdb=" N ILE A 306 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.542A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 381 Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.725A pdb=" N ALA A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.553A pdb=" N LEU A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 485 removed outlier: 3.540A pdb=" N LEU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Proline residue: A 479 - end of helix Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.706A pdb=" N GLY A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.853A pdb=" N GLN A 533 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.508A pdb=" N GLY B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 77 removed outlier: 4.123A pdb=" N PHE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 108 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.629A pdb=" N ALA B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 152 through 180 removed outlier: 3.774A pdb=" N TRP B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) Proline residue: B 158 - end of helix Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.543A pdb=" N VAL B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Proline residue: B 197 - end of helix Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 262 through 281 removed outlier: 3.760A pdb=" N LEU B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 301 removed outlier: 3.831A pdb=" N ALA B 295 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N THR B 297 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP B 298 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG B 300 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY B 301 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.535A pdb=" N ILE B 306 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 354 removed outlier: 3.542A pdb=" N GLY B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 381 Processing helix chain 'B' and resid 389 through 399 Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.725A pdb=" N ALA B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.553A pdb=" N LEU B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 485 removed outlier: 3.540A pdb=" N LEU B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Proline residue: B 479 - end of helix Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'B' and resid 506 through 522 removed outlier: 3.706A pdb=" N GLY B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 removed outlier: 3.853A pdb=" N GLN B 533 " --> pdb=" O GLY B 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 117 Processing sheet with id=AA2, first strand: chain 'B' and resid 115 through 117 486 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1999 1.33 - 1.45: 1465 1.45 - 1.57: 4244 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 7804 Sorted by residual: bond pdb=" C LEU A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.91e+00 bond pdb=" C LEU B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.91e+00 bond pdb=" CB PRO B 479 " pdb=" CG PRO B 479 " ideal model delta sigma weight residual 1.492 1.382 0.110 5.00e-02 4.00e+02 4.86e+00 bond pdb=" CB PRO A 479 " pdb=" CG PRO A 479 " ideal model delta sigma weight residual 1.492 1.383 0.109 5.00e-02 4.00e+02 4.78e+00 bond pdb=" CA ARG B 300 " pdb=" CB ARG B 300 " ideal model delta sigma weight residual 1.531 1.466 0.064 3.28e-02 9.30e+02 3.84e+00 ... (remaining 7799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 10253 2.67 - 5.34: 322 5.34 - 8.00: 63 8.00 - 10.67: 12 10.67 - 13.34: 4 Bond angle restraints: 10654 Sorted by residual: angle pdb=" N GLY A 330 " pdb=" CA GLY A 330 " pdb=" C GLY A 330 " ideal model delta sigma weight residual 112.73 106.95 5.78 1.20e+00 6.94e-01 2.32e+01 angle pdb=" N GLY B 330 " pdb=" CA GLY B 330 " pdb=" C GLY B 330 " ideal model delta sigma weight residual 112.73 107.02 5.71 1.20e+00 6.94e-01 2.27e+01 angle pdb=" CB MET A 445 " pdb=" CG MET A 445 " pdb=" SD MET A 445 " ideal model delta sigma weight residual 112.70 126.04 -13.34 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CB MET B 445 " pdb=" CG MET B 445 " pdb=" SD MET B 445 " ideal model delta sigma weight residual 112.70 126.03 -13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" CG ARG A 236 " pdb=" CD ARG A 236 " pdb=" NE ARG A 236 " ideal model delta sigma weight residual 112.00 121.07 -9.07 2.20e+00 2.07e-01 1.70e+01 ... (remaining 10649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 4037 15.76 - 31.51: 404 31.51 - 47.27: 90 47.27 - 63.02: 10 63.02 - 78.78: 4 Dihedral angle restraints: 4545 sinusoidal: 1717 harmonic: 2828 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -40.24 -45.76 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CA LEU B 476 " pdb=" C LEU B 476 " pdb=" N THR B 477 " pdb=" CA THR B 477 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU A 476 " pdb=" C LEU A 476 " pdb=" N THR A 477 " pdb=" CA THR A 477 " ideal model delta harmonic sigma weight residual -180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 4542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 866 0.058 - 0.116: 297 0.116 - 0.175: 84 0.175 - 0.233: 11 0.233 - 0.291: 4 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA PRO A 183 " pdb=" N PRO A 183 " pdb=" C PRO A 183 " pdb=" CB PRO A 183 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1259 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 553 " 0.054 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO A 554 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 554 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 554 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 553 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO B 554 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 554 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 554 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 182 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.38e+00 pdb=" N PRO B 183 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.043 5.00e-02 4.00e+02 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 80 2.60 - 3.18: 6946 3.18 - 3.75: 12987 3.75 - 4.33: 17216 4.33 - 4.90: 27614 Nonbonded interactions: 64843 Sorted by model distance: nonbonded pdb=" SG CYS B 78 " pdb=" SG CYS B 136 " model vdw 2.027 3.760 nonbonded pdb=" O ILE B 167 " pdb=" OG SER B 171 " model vdw 2.228 3.040 nonbonded pdb=" O ILE A 167 " pdb=" OG SER A 171 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU A 341 " pdb=" OG1 THR A 387 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU B 341 " pdb=" OG1 THR B 387 " model vdw 2.240 3.040 ... (remaining 64838 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.410 Find NCS groups from input model: 0.180 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.009 0.110 7804 Z= 0.626 Angle : 1.176 13.340 10654 Z= 0.618 Chirality : 0.064 0.291 1262 Planarity : 0.009 0.080 1328 Dihedral : 13.286 78.778 2738 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -1.66 (0.26), residues: 990 helix: -1.11 (0.18), residues: 662 sheet: None (None), residues: 0 loop : -0.68 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 48 HIS 0.007 0.002 HIS A 58 PHE 0.051 0.004 PHE A 94 TYR 0.017 0.002 TYR B 291 ARG 0.019 0.001 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.6878 (tpp) cc_final: 0.5758 (mtt) REVERT: A 497 ASP cc_start: 0.7620 (t0) cc_final: 0.7391 (t0) REVERT: B 445 MET cc_start: 0.6890 (tpp) cc_final: 0.5755 (mtt) REVERT: B 497 ASP cc_start: 0.7629 (t0) cc_final: 0.7392 (t0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2099 time to fit residues: 32.4822 Evaluate side-chains 88 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.0770 chunk 75 optimal weight: 0.4980 chunk 42 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7804 Z= 0.231 Angle : 0.656 6.870 10654 Z= 0.337 Chirality : 0.044 0.164 1262 Planarity : 0.006 0.058 1328 Dihedral : 5.321 21.040 1062 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.96 % Allowed : 10.36 % Favored : 88.67 % 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: -0.26 (0.27), residues: 990 helix: 0.02 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -0.29 (0.41), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 48 HIS 0.003 0.001 HIS B 58 PHE 0.020 0.002 PHE B 427 TYR 0.010 0.001 TYR B 291 ARG 0.003 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.775 Fit side-chains REVERT: A 445 MET cc_start: 0.7324 (tpp) cc_final: 0.5835 (mtt) REVERT: A 497 ASP cc_start: 0.7686 (t0) cc_final: 0.7437 (t0) REVERT: B 66 THR cc_start: 0.8259 (t) cc_final: 0.8054 (m) REVERT: B 445 MET cc_start: 0.7334 (tpp) cc_final: 0.5831 (mtt) REVERT: B 497 ASP cc_start: 0.7698 (t0) cc_final: 0.7443 (t0) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.1887 time to fit residues: 26.1203 Evaluate side-chains 94 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 493 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7804 Z= 0.263 Angle : 0.632 6.768 10654 Z= 0.324 Chirality : 0.044 0.172 1262 Planarity : 0.005 0.052 1328 Dihedral : 4.870 19.329 1062 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.33 % Allowed : 14.10 % Favored : 84.58 % 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: 0.34 (0.28), residues: 990 helix: 0.46 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.01 (0.43), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 48 HIS 0.002 0.001 HIS A 58 PHE 0.016 0.002 PHE A 427 TYR 0.014 0.002 TYR A 49 ARG 0.005 0.001 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.775 Fit side-chains REVERT: A 445 MET cc_start: 0.7371 (tpp) cc_final: 0.5917 (mtt) REVERT: A 497 ASP cc_start: 0.7868 (t0) cc_final: 0.7586 (t0) REVERT: B 66 THR cc_start: 0.8425 (t) cc_final: 0.8145 (m) REVERT: B 445 MET cc_start: 0.7396 (tpp) cc_final: 0.5938 (mtt) REVERT: B 497 ASP cc_start: 0.7882 (t0) cc_final: 0.7592 (t0) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.1565 time to fit residues: 22.2750 Evaluate side-chains 98 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.0980 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7804 Z= 0.234 Angle : 0.599 6.616 10654 Z= 0.307 Chirality : 0.044 0.166 1262 Planarity : 0.005 0.049 1328 Dihedral : 4.655 17.849 1062 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.41 % Allowed : 13.86 % Favored : 83.73 % 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: 0.56 (0.28), residues: 990 helix: 0.64 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.02 (0.43), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 48 HIS 0.002 0.001 HIS B 58 PHE 0.013 0.001 PHE A 427 TYR 0.028 0.002 TYR B 346 ARG 0.002 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.750 Fit side-chains REVERT: A 445 MET cc_start: 0.7300 (tpp) cc_final: 0.6018 (mtt) REVERT: A 497 ASP cc_start: 0.7835 (t0) cc_final: 0.7592 (t0) REVERT: B 445 MET cc_start: 0.7308 (tpp) cc_final: 0.6019 (mtt) REVERT: B 497 ASP cc_start: 0.7852 (t0) cc_final: 0.7599 (t0) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 0.1602 time to fit residues: 25.4221 Evaluate side-chains 99 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 39 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 480 ASN B 294 GLN B 480 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7804 Z= 0.236 Angle : 0.587 6.595 10654 Z= 0.300 Chirality : 0.043 0.166 1262 Planarity : 0.005 0.048 1328 Dihedral : 4.501 17.866 1062 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.89 % Allowed : 15.78 % Favored : 81.33 % 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: 0.63 (0.28), residues: 990 helix: 0.75 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.09 (0.42), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 48 HIS 0.002 0.001 HIS B 58 PHE 0.011 0.001 PHE A 466 TYR 0.017 0.002 TYR B 346 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.704 Fit side-chains REVERT: A 193 LEU cc_start: 0.7653 (mt) cc_final: 0.7409 (mt) REVERT: A 205 SER cc_start: 0.7739 (t) cc_final: 0.7086 (p) REVERT: A 445 MET cc_start: 0.7248 (tpp) cc_final: 0.6076 (mtt) REVERT: A 497 ASP cc_start: 0.7832 (t0) cc_final: 0.7600 (t0) REVERT: B 193 LEU cc_start: 0.7638 (mt) cc_final: 0.7395 (mt) REVERT: B 205 SER cc_start: 0.7776 (t) cc_final: 0.7129 (p) REVERT: B 445 MET cc_start: 0.7243 (tpp) cc_final: 0.6063 (mtt) REVERT: B 497 ASP cc_start: 0.7852 (t0) cc_final: 0.7605 (t0) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.1428 time to fit residues: 23.6988 Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7804 Z= 0.248 Angle : 0.593 6.629 10654 Z= 0.302 Chirality : 0.044 0.164 1262 Planarity : 0.005 0.047 1328 Dihedral : 4.421 17.878 1062 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.13 % Allowed : 16.39 % Favored : 80.48 % 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: 0.67 (0.28), residues: 990 helix: 0.75 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.00 (0.42), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 48 HIS 0.002 0.001 HIS A 58 PHE 0.013 0.002 PHE A 456 TYR 0.037 0.002 TYR B 346 ARG 0.005 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.820 Fit side-chains REVERT: A 85 MET cc_start: 0.8036 (tmm) cc_final: 0.7741 (tmm) REVERT: A 193 LEU cc_start: 0.7704 (mt) cc_final: 0.7438 (mt) REVERT: A 205 SER cc_start: 0.7760 (t) cc_final: 0.7162 (p) REVERT: A 445 MET cc_start: 0.7242 (tpp) cc_final: 0.6087 (mtt) REVERT: A 497 ASP cc_start: 0.7841 (t0) cc_final: 0.7621 (t0) REVERT: B 85 MET cc_start: 0.8047 (tmm) cc_final: 0.7779 (tmm) REVERT: B 193 LEU cc_start: 0.7689 (mt) cc_final: 0.7428 (mt) REVERT: B 205 SER cc_start: 0.7802 (t) cc_final: 0.7221 (p) REVERT: B 445 MET cc_start: 0.7242 (tpp) cc_final: 0.6093 (mtt) REVERT: B 497 ASP cc_start: 0.7856 (t0) cc_final: 0.7625 (t0) outliers start: 26 outliers final: 21 residues processed: 116 average time/residue: 0.1669 time to fit residues: 27.6676 Evaluate side-chains 110 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 0.0070 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7804 Z= 0.240 Angle : 0.582 6.551 10654 Z= 0.296 Chirality : 0.043 0.168 1262 Planarity : 0.005 0.045 1328 Dihedral : 4.352 17.999 1062 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.89 % Allowed : 16.51 % Favored : 80.60 % 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: 0.75 (0.28), residues: 990 helix: 0.80 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.05 (0.42), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 48 HIS 0.002 0.001 HIS A 58 PHE 0.011 0.001 PHE B 466 TYR 0.029 0.002 TYR B 346 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.736 Fit side-chains REVERT: A 193 LEU cc_start: 0.7668 (mt) cc_final: 0.7412 (mt) REVERT: A 205 SER cc_start: 0.7786 (t) cc_final: 0.7241 (p) REVERT: A 445 MET cc_start: 0.7234 (tpp) cc_final: 0.6089 (mtt) REVERT: A 497 ASP cc_start: 0.7836 (t0) cc_final: 0.7624 (t0) REVERT: B 79 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7868 (t) REVERT: B 193 LEU cc_start: 0.7657 (mt) cc_final: 0.7407 (mt) REVERT: B 205 SER cc_start: 0.7799 (t) cc_final: 0.7268 (p) REVERT: B 445 MET cc_start: 0.7241 (tpp) cc_final: 0.6093 (mtt) REVERT: B 497 ASP cc_start: 0.7849 (t0) cc_final: 0.7633 (t0) outliers start: 24 outliers final: 20 residues processed: 111 average time/residue: 0.1680 time to fit residues: 26.5594 Evaluate side-chains 114 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7804 Z= 0.255 Angle : 0.592 6.559 10654 Z= 0.300 Chirality : 0.044 0.172 1262 Planarity : 0.005 0.045 1328 Dihedral : 4.379 18.110 1062 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.61 % Allowed : 17.11 % Favored : 79.28 % 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: 0.72 (0.28), residues: 990 helix: 0.75 (0.20), residues: 684 sheet: None (None), residues: 0 loop : 0.10 (0.42), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 48 HIS 0.002 0.001 HIS A 58 PHE 0.011 0.002 PHE B 456 TYR 0.027 0.002 TYR A 346 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 0.894 Fit side-chains REVERT: A 85 MET cc_start: 0.8116 (tmm) cc_final: 0.7873 (tmm) REVERT: A 193 LEU cc_start: 0.7676 (mt) cc_final: 0.7408 (mt) REVERT: A 205 SER cc_start: 0.7778 (t) cc_final: 0.7248 (p) REVERT: A 261 MET cc_start: 0.7969 (mmm) cc_final: 0.7706 (mmm) REVERT: A 445 MET cc_start: 0.7238 (tpp) cc_final: 0.6103 (mtt) REVERT: A 503 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7295 (mt) REVERT: B 85 MET cc_start: 0.8044 (tmm) cc_final: 0.7839 (tmm) REVERT: B 193 LEU cc_start: 0.7664 (mt) cc_final: 0.7400 (mt) REVERT: B 205 SER cc_start: 0.7837 (t) cc_final: 0.7316 (p) REVERT: B 261 MET cc_start: 0.8010 (mmm) cc_final: 0.7727 (mmm) REVERT: B 445 MET cc_start: 0.7241 (tpp) cc_final: 0.6107 (mtt) REVERT: B 497 ASP cc_start: 0.7830 (t0) cc_final: 0.7623 (t0) REVERT: B 503 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7306 (mt) outliers start: 30 outliers final: 26 residues processed: 117 average time/residue: 0.1689 time to fit residues: 28.2394 Evaluate side-chains 121 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 57 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7804 Z= 0.258 Angle : 0.593 6.580 10654 Z= 0.301 Chirality : 0.044 0.177 1262 Planarity : 0.005 0.045 1328 Dihedral : 4.391 18.043 1062 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.37 % Allowed : 17.23 % Favored : 79.40 % 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: 0.65 (0.28), residues: 990 helix: 0.71 (0.20), residues: 688 sheet: None (None), residues: 0 loop : 0.06 (0.42), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 318 HIS 0.003 0.001 HIS A 58 PHE 0.012 0.002 PHE A 456 TYR 0.026 0.002 TYR A 346 ARG 0.005 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.806 Fit side-chains REVERT: A 85 MET cc_start: 0.8061 (tmm) cc_final: 0.7784 (tmm) REVERT: A 205 SER cc_start: 0.7842 (t) cc_final: 0.7306 (p) REVERT: A 233 GLN cc_start: 0.8137 (mp10) cc_final: 0.7906 (mm110) REVERT: A 261 MET cc_start: 0.7936 (mmm) cc_final: 0.7646 (mmm) REVERT: A 445 MET cc_start: 0.7281 (tpp) cc_final: 0.6138 (mtt) REVERT: A 503 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7342 (mt) REVERT: B 85 MET cc_start: 0.8034 (tmm) cc_final: 0.7800 (tmm) REVERT: B 205 SER cc_start: 0.7866 (t) cc_final: 0.7345 (p) REVERT: B 233 GLN cc_start: 0.8131 (mp10) cc_final: 0.7903 (mm110) REVERT: B 261 MET cc_start: 0.7947 (mmm) cc_final: 0.7630 (mmm) REVERT: B 445 MET cc_start: 0.7287 (tpp) cc_final: 0.6158 (mtt) REVERT: B 503 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7307 (mt) outliers start: 28 outliers final: 24 residues processed: 118 average time/residue: 0.1440 time to fit residues: 25.1989 Evaluate side-chains 120 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 79 optimal weight: 0.0040 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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: 0.7413 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7804 Z= 0.223 Angle : 0.594 6.460 10654 Z= 0.302 Chirality : 0.044 0.187 1262 Planarity : 0.005 0.045 1328 Dihedral : 4.328 17.931 1062 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.25 % Allowed : 17.83 % Favored : 78.92 % 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: 0.72 (0.29), residues: 990 helix: 0.75 (0.20), residues: 694 sheet: None (None), residues: 0 loop : 0.08 (0.43), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 318 HIS 0.002 0.001 HIS A 58 PHE 0.011 0.001 PHE A 456 TYR 0.026 0.002 TYR A 346 ARG 0.005 0.000 ARG B 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.805 Fit side-chains REVERT: A 85 MET cc_start: 0.8013 (tmm) cc_final: 0.7721 (tmm) REVERT: A 205 SER cc_start: 0.7742 (t) cc_final: 0.7227 (p) REVERT: A 261 MET cc_start: 0.7909 (mmm) cc_final: 0.7601 (mmm) REVERT: A 346 TYR cc_start: 0.7900 (m-80) cc_final: 0.7674 (m-80) REVERT: A 445 MET cc_start: 0.7247 (tpp) cc_final: 0.6117 (mtt) REVERT: A 503 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7286 (mt) REVERT: B 205 SER cc_start: 0.7782 (t) cc_final: 0.7283 (p) REVERT: B 261 MET cc_start: 0.7932 (mmm) cc_final: 0.7607 (mmm) REVERT: B 346 TYR cc_start: 0.7912 (m-80) cc_final: 0.7687 (m-80) REVERT: B 445 MET cc_start: 0.7251 (tpp) cc_final: 0.6131 (mtt) REVERT: B 503 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7340 (mt) outliers start: 27 outliers final: 24 residues processed: 117 average time/residue: 0.1450 time to fit residues: 25.6521 Evaluate side-chains 120 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.0470 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.220706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.197619 restraints weight = 7843.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.200944 restraints weight = 5298.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.203269 restraints weight = 4026.875| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7804 Z= 0.251 Angle : 0.603 6.508 10654 Z= 0.306 Chirality : 0.044 0.181 1262 Planarity : 0.005 0.045 1328 Dihedral : 4.338 17.918 1062 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.86 % Allowed : 18.19 % Favored : 77.95 % 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: 0.70 (0.28), residues: 990 helix: 0.74 (0.20), residues: 688 sheet: None (None), residues: 0 loop : 0.09 (0.42), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 48 HIS 0.003 0.001 HIS B 58 PHE 0.011 0.001 PHE A 466 TYR 0.025 0.002 TYR A 346 ARG 0.005 0.000 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.13 seconds wall clock time: 32 minutes 29.91 seconds (1949.91 seconds total)