Starting phenix.real_space_refine on Mon Feb 10 22:03:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wyj_21966/02_2025/6wyj_21966.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wyj_21966/02_2025/6wyj_21966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wyj_21966/02_2025/6wyj_21966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wyj_21966/02_2025/6wyj_21966.map" model { file = "/net/cci-nas-00/data/ceres_data/6wyj_21966/02_2025/6wyj_21966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wyj_21966/02_2025/6wyj_21966.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 18 5.16 5 C 1942 2.51 5 N 465 2.21 5 O 524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2949 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2949 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain breaks: 2 Time building chain proxies: 2.53, per 1000 atoms: 0.86 Number of scatterers: 2949 At special positions: 0 Unit cell: (69.02, 70.006, 78.88, 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 18 16.00 O 524 8.00 N 465 7.00 C 1942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 399.6 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.735A pdb=" N LYS A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 44 through 73 removed outlier: 4.195A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.565A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 108 removed outlier: 3.549A pdb=" N GLY A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.816A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.573A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 218 removed outlier: 3.560A pdb=" N ARG A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 225 through 255 removed outlier: 3.585A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.590A pdb=" N LYS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.729A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.507A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 4.087A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.639A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.814A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.714A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 690 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: 0.79 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 907 1.34 - 1.46: 524 1.46 - 1.57: 1532 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 2997 Sorted by residual: bond pdb=" N GLU A 174 " pdb=" CA GLU A 174 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.35e-02 5.49e+03 8.99e+00 bond pdb=" CA MET A 311 " pdb=" CB MET A 311 " ideal model delta sigma weight residual 1.531 1.467 0.064 3.28e-02 9.30e+02 3.77e+00 bond pdb=" CB THR A 154 " pdb=" CG2 THR A 154 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB THR A 275 " pdb=" CG2 THR A 275 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.54e+00 bond pdb=" CG LEU A 190 " pdb=" CD1 LEU A 190 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.37e+00 ... (remaining 2992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 3723 0.99 - 1.99: 281 1.99 - 2.98: 45 2.98 - 3.97: 19 3.97 - 4.97: 10 Bond angle restraints: 4078 Sorted by residual: angle pdb=" C ASN A 173 " pdb=" N GLU A 174 " pdb=" CA GLU A 174 " ideal model delta sigma weight residual 120.99 125.55 -4.56 1.86e+00 2.89e-01 6.00e+00 angle pdb=" N PRO A 356 " pdb=" CA PRO A 356 " pdb=" C PRO A 356 " ideal model delta sigma weight residual 112.47 117.44 -4.97 2.06e+00 2.36e-01 5.81e+00 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 118.19 -4.29 1.80e+00 3.09e-01 5.68e+00 angle pdb=" C ALA A 205 " pdb=" CA ALA A 205 " pdb=" CB ALA A 205 " ideal model delta sigma weight residual 113.49 109.32 4.17 1.82e+00 3.02e-01 5.26e+00 angle pdb=" CA ALA A 205 " pdb=" C ALA A 205 " pdb=" N PRO A 206 " ideal model delta sigma weight residual 120.52 118.83 1.69 8.30e-01 1.45e+00 4.13e+00 ... (remaining 4073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 1653 17.19 - 34.37: 107 34.37 - 51.56: 15 51.56 - 68.74: 3 68.74 - 85.93: 3 Dihedral angle restraints: 1781 sinusoidal: 649 harmonic: 1132 Sorted by residual: dihedral pdb=" CA VAL A 355 " pdb=" C VAL A 355 " pdb=" N PRO A 356 " pdb=" CA PRO A 356 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR A 352 " pdb=" C THR A 352 " pdb=" N ALA A 353 " pdb=" CA ALA A 353 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 37 " pdb=" CB ASP A 37 " pdb=" CG ASP A 37 " pdb=" OD1 ASP A 37 " ideal model delta sinusoidal sigma weight residual -30.00 -89.49 59.49 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 1778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 271 0.035 - 0.069: 173 0.069 - 0.104: 64 0.104 - 0.139: 8 0.139 - 0.173: 4 Chirality restraints: 520 Sorted by residual: chirality pdb=" CA PRO A 356 " pdb=" N PRO A 356 " pdb=" C PRO A 356 " pdb=" CB PRO A 356 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA PRO A 60 " pdb=" N PRO A 60 " pdb=" C PRO A 60 " pdb=" CB PRO A 60 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CB ILE A 411 " pdb=" CA ILE A 411 " pdb=" CG1 ILE A 411 " pdb=" CG2 ILE A 411 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 517 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 206 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " 0.010 2.00e-02 2.50e+03 6.87e-03 9.43e-01 pdb=" CG TYR A 299 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 59 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.33e-01 pdb=" N PRO A 60 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.013 5.00e-02 4.00e+02 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 840 2.79 - 3.32: 3220 3.32 - 3.85: 4503 3.85 - 4.37: 5358 4.37 - 4.90: 8867 Nonbonded interactions: 22788 Sorted by model distance: nonbonded pdb=" O SER A 179 " pdb=" OG1 THR A 182 " model vdw 2.268 3.040 nonbonded pdb=" O GLU A 172 " pdb=" NH2 ARG A 177 " model vdw 2.322 3.120 nonbonded pdb=" O LEU A 282 " pdb=" OG1 THR A 285 " model vdw 2.328 3.040 nonbonded pdb=" O THR A 271 " pdb=" OG1 THR A 275 " model vdw 2.377 3.040 nonbonded pdb=" O ILE A 187 " pdb=" N LEU A 190 " model vdw 2.422 3.120 ... (remaining 22783 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: 0.690 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.110 Find NCS groups from input model: 0.020 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.010 0.064 2997 Z= 0.632 Angle : 0.644 4.965 4078 Z= 0.351 Chirality : 0.049 0.173 520 Planarity : 0.003 0.030 496 Dihedral : 12.333 85.929 1061 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: -4.80 (0.30), residues: 393 helix: -2.79 (0.21), residues: 301 sheet: None (None), residues: 0 loop : -3.77 (0.47), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.010 0.001 PHE A 50 TYR 0.016 0.002 TYR A 299 ARG 0.003 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.316 Fit side-chains REVERT: A 215 TYR cc_start: 0.7777 (t80) cc_final: 0.7532 (t80) REVERT: A 310 ASN cc_start: 0.9176 (t0) cc_final: 0.8693 (t0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1456 time to fit residues: 5.7879 Evaluate side-chains 29 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.159922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.143355 restraints weight = 3306.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.140074 restraints weight = 4647.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.138915 restraints weight = 4780.565| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2997 Z= 0.253 Angle : 0.590 5.471 4078 Z= 0.318 Chirality : 0.043 0.175 520 Planarity : 0.005 0.037 496 Dihedral : 4.492 27.091 421 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.64 % Allowed : 7.03 % Favored : 92.33 % 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: -0.31 (0.39), residues: 393 helix: 0.32 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -2.29 (0.65), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 32 PHE 0.012 0.001 PHE A 273 TYR 0.022 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.303 Fit side-chains REVERT: A 169 MET cc_start: 0.7288 (mtm) cc_final: 0.6953 (mtm) outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.1285 time to fit residues: 6.0029 Evaluate side-chains 34 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.155818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3397 r_free = 0.3397 target = 0.137320 restraints weight = 3324.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.137272 restraints weight = 5744.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.137272 restraints weight = 5277.881| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2997 Z= 0.248 Angle : 0.555 5.392 4078 Z= 0.296 Chirality : 0.042 0.182 520 Planarity : 0.004 0.035 496 Dihedral : 4.182 23.699 421 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.28 % Allowed : 10.86 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.41), residues: 393 helix: 1.33 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -2.08 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 32 PHE 0.013 0.001 PHE A 210 TYR 0.018 0.002 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.331 Fit side-chains REVERT: A 90 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 217 MET cc_start: 0.7997 (mmt) cc_final: 0.7753 (mmt) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.1189 time to fit residues: 7.1871 Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.157323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 147)---------------| | r_work = 0.3403 r_free = 0.3403 target = 0.137939 restraints weight = 3363.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.128792 restraints weight = 4747.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.128792 restraints weight = 4040.997| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2997 Z= 0.209 Angle : 0.520 5.351 4078 Z= 0.272 Chirality : 0.041 0.163 520 Planarity : 0.004 0.035 496 Dihedral : 4.078 22.694 421 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.60 % Allowed : 12.14 % Favored : 86.26 % 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: 1.51 (0.41), residues: 393 helix: 1.55 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.63 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 32 PHE 0.011 0.001 PHE A 273 TYR 0.017 0.001 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.317 Fit side-chains REVERT: A 90 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 367 LEU cc_start: 0.7607 (mt) cc_final: 0.7380 (mt) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1332 time to fit residues: 8.4161 Evaluate side-chains 42 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 3 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.160380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 183)---------------| | r_work = 0.3432 r_free = 0.3432 target = 0.140441 restraints weight = 3382.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.139490 restraints weight = 4992.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.130303 restraints weight = 5310.044| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2997 Z= 0.178 Angle : 0.490 5.378 4078 Z= 0.256 Chirality : 0.040 0.180 520 Planarity : 0.004 0.034 496 Dihedral : 3.891 21.967 421 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.60 % Allowed : 13.74 % Favored : 84.66 % 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: 1.91 (0.42), residues: 393 helix: 1.83 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.48 (0.67), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.012 0.001 PHE A 273 TYR 0.016 0.001 TYR A 383 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.323 Fit side-chains REVERT: A 90 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8345 (mp) REVERT: A 367 LEU cc_start: 0.7713 (mt) cc_final: 0.7506 (mt) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.1397 time to fit residues: 8.3184 Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.155375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.142447 restraints weight = 3441.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.137457 restraints weight = 5502.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.136184 restraints weight = 7413.600| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2997 Z= 0.232 Angle : 0.542 6.296 4078 Z= 0.278 Chirality : 0.041 0.173 520 Planarity : 0.004 0.032 496 Dihedral : 3.929 19.240 421 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.92 % Allowed : 15.65 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.41), residues: 393 helix: 1.69 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.30 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.012 0.001 PHE A 210 TYR 0.016 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.319 Fit side-chains REVERT: A 56 MET cc_start: 0.8655 (ttt) cc_final: 0.8436 (ttt) REVERT: A 90 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 367 LEU cc_start: 0.8176 (mt) cc_final: 0.7928 (mt) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.1298 time to fit residues: 7.7285 Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.155151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.137542 restraints weight = 3401.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.132857 restraints weight = 6543.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 83)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.124883 restraints weight = 5872.037| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2997 Z= 0.253 Angle : 0.558 5.386 4078 Z= 0.288 Chirality : 0.042 0.170 520 Planarity : 0.004 0.031 496 Dihedral : 3.987 15.983 421 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.92 % Allowed : 16.61 % Favored : 81.47 % 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: 1.51 (0.41), residues: 393 helix: 1.54 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.36 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.013 0.001 PHE A 273 TYR 0.016 0.002 TYR A 299 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.261 Fit side-chains REVERT: A 90 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 367 LEU cc_start: 0.7758 (mt) cc_final: 0.7507 (mt) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.1358 time to fit residues: 7.5106 Evaluate side-chains 42 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.0370 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.0020 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.3266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.165612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.3500 r_free = 0.3500 target = 0.145987 restraints weight = 3376.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.145987 restraints weight = 5251.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.145987 restraints weight = 5251.152| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2997 Z= 0.170 Angle : 0.502 5.347 4078 Z= 0.255 Chirality : 0.040 0.196 520 Planarity : 0.004 0.031 496 Dihedral : 3.817 18.941 421 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.88 % Allowed : 15.65 % Favored : 81.47 % 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: 1.85 (0.42), residues: 393 helix: 1.76 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -1.41 (0.69), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.013 0.001 PHE A 273 TYR 0.013 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.277 Fit side-chains REVERT: A 90 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 367 LEU cc_start: 0.8216 (mt) cc_final: 0.7955 (mt) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.1095 time to fit residues: 6.9296 Evaluate side-chains 45 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.159323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.143889 restraints weight = 3337.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.139452 restraints weight = 5032.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 78)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.138446 restraints weight = 5552.809| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2997 Z= 0.235 Angle : 0.553 7.015 4078 Z= 0.283 Chirality : 0.041 0.188 520 Planarity : 0.004 0.030 496 Dihedral : 3.881 16.891 421 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.24 % Allowed : 16.29 % Favored : 81.47 % 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: 1.72 (0.41), residues: 393 helix: 1.72 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.41 (0.64), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.013 0.001 PHE A 273 TYR 0.016 0.002 TYR A 383 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.316 Fit side-chains REVERT: A 90 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8396 (mp) REVERT: A 367 LEU cc_start: 0.8225 (mt) cc_final: 0.7958 (mt) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.1141 time to fit residues: 7.0518 Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.159641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.145331 restraints weight = 3370.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.141794 restraints weight = 5780.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.140930 restraints weight = 6326.910| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2997 Z= 0.204 Angle : 0.530 5.362 4078 Z= 0.273 Chirality : 0.040 0.200 520 Planarity : 0.004 0.036 496 Dihedral : 3.836 15.728 421 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.92 % Allowed : 16.61 % Favored : 81.47 % 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: 1.80 (0.41), residues: 393 helix: 1.77 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.44 (0.62), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.041 0.002 PHE A 273 TYR 0.017 0.001 TYR A 383 ARG 0.001 0.000 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.324 Fit side-chains REVERT: A 90 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8381 (mp) REVERT: A 367 LEU cc_start: 0.8284 (mt) cc_final: 0.8006 (mt) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.1208 time to fit residues: 7.0511 Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 chunk 12 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 overall best weight: 0.2334 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.174350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.158666 restraints weight = 3279.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.155482 restraints weight = 5243.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.154825 restraints weight = 4845.438| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2997 Z= 0.161 Angle : 0.501 5.345 4078 Z= 0.255 Chirality : 0.039 0.215 520 Planarity : 0.004 0.043 496 Dihedral : 3.660 15.756 421 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.60 % Allowed : 16.93 % Favored : 81.47 % 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: 2.18 (0.42), residues: 393 helix: 2.00 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -1.38 (0.66), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.041 0.002 PHE A 273 TYR 0.017 0.001 TYR A 215 ARG 0.001 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1263.84 seconds wall clock time: 23 minutes 20.85 seconds (1400.85 seconds total)