Starting phenix.real_space_refine on Wed Mar 5 15:07:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7py2_13708/03_2025/7py2_13708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py2_13708/03_2025/7py2_13708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7py2_13708/03_2025/7py2_13708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py2_13708/03_2025/7py2_13708.map" model { file = "/net/cci-nas-00/data/ceres_data/7py2_13708/03_2025/7py2_13708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py2_13708/03_2025/7py2_13708.cif" } resolution = 2.59 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= 0.004 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 32 5.16 5 C 1264 2.51 5 N 420 2.21 5 O 436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2152 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 538 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Restraints were copied for chains: C, B, D Time building chain proxies: 1.86, per 1000 atoms: 0.86 Number of scatterers: 2152 At special positions: 0 Unit cell: (79.05, 67.89, 40.92, 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 32 16.00 O 436 8.00 N 420 7.00 C 1264 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: 0.54 Conformation dependent library (CDL) restraints added in 314.7 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 472 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 283 through 285 removed outlier: 6.524A pdb=" N GLY A 284 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY C 284 " --> pdb=" O ASN D 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 298 through 299 removed outlier: 5.853A pdb=" N GLY A 298 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLY C 298 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 302 through 303 removed outlier: 6.660A pdb=" N ASN A 302 " --> pdb=" O GLN D 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 313 removed outlier: 6.669A pdb=" N ASN A 312 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 312 " --> pdb=" O PHE D 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 329 removed outlier: 8.352A pdb=" N GLN A 327 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 329 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLN C 327 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 333 through 343 removed outlier: 6.920A pdb=" N GLN B 343 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER A 333 " --> pdb=" O TRP D 334 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N MET D 336 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 335 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY D 338 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N MET A 337 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU D 340 " --> pdb=" O MET A 337 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET A 339 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER D 342 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ALA A 341 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN D 343 " --> pdb=" O SER C 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.744A pdb=" N GLN A 346 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 356 removed outlier: 6.897A pdb=" N GLN A 354 " --> pdb=" O ASN D 355 " (cutoff:3.500A) 32 hydrogen bonds defined for protein. 96 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: 0.53 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 662 1.34 - 1.46: 325 1.46 - 1.59: 1129 1.59 - 1.71: 0 1.71 - 1.83: 64 Bond restraints: 2180 Sorted by residual: bond pdb=" C ALA C 321 " pdb=" O ALA C 321 " ideal model delta sigma weight residual 1.232 1.292 -0.060 1.34e-02 5.57e+03 2.00e+01 bond pdb=" C ALA D 321 " pdb=" O ALA D 321 " ideal model delta sigma weight residual 1.232 1.291 -0.060 1.34e-02 5.57e+03 2.00e+01 bond pdb=" C ALA A 321 " pdb=" O ALA A 321 " ideal model delta sigma weight residual 1.232 1.291 -0.060 1.34e-02 5.57e+03 1.98e+01 bond pdb=" C ALA B 321 " pdb=" O ALA B 321 " ideal model delta sigma weight residual 1.232 1.291 -0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" N GLY A 348 " pdb=" CA GLY A 348 " ideal model delta sigma weight residual 1.434 1.477 -0.044 1.22e-02 6.72e+03 1.28e+01 ... (remaining 2175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 1641 1.39 - 2.79: 893 2.79 - 4.18: 278 4.18 - 5.58: 68 5.58 - 6.97: 20 Bond angle restraints: 2900 Sorted by residual: angle pdb=" C ARG D 293 " pdb=" N GLY D 294 " pdb=" CA GLY D 294 " ideal model delta sigma weight residual 119.92 124.57 -4.65 9.60e-01 1.09e+00 2.35e+01 angle pdb=" C ARG A 293 " pdb=" N GLY A 294 " pdb=" CA GLY A 294 " ideal model delta sigma weight residual 119.92 124.55 -4.63 9.60e-01 1.09e+00 2.33e+01 angle pdb=" C ARG C 293 " pdb=" N GLY C 294 " pdb=" CA GLY C 294 " ideal model delta sigma weight residual 119.92 124.55 -4.63 9.60e-01 1.09e+00 2.33e+01 angle pdb=" C ARG B 293 " pdb=" N GLY B 294 " pdb=" CA GLY B 294 " ideal model delta sigma weight residual 119.92 124.53 -4.61 9.60e-01 1.09e+00 2.30e+01 angle pdb=" C LEU B 330 " pdb=" N GLN B 331 " pdb=" CA GLN B 331 " ideal model delta sigma weight residual 122.34 128.90 -6.56 1.39e+00 5.18e-01 2.23e+01 ... (remaining 2895 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.20: 1080 17.20 - 34.38: 116 34.38 - 51.57: 36 51.57 - 68.76: 4 68.76 - 85.95: 8 Dihedral angle restraints: 1244 sinusoidal: 460 harmonic: 784 Sorted by residual: dihedral pdb=" CA GLY B 284 " pdb=" C GLY B 284 " pdb=" N ASN B 285 " pdb=" CA ASN B 285 " ideal model delta harmonic sigma weight residual 180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY D 284 " pdb=" C GLY D 284 " pdb=" N ASN D 285 " pdb=" CA ASN D 285 " ideal model delta harmonic sigma weight residual 180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLY A 284 " pdb=" C GLY A 284 " pdb=" N ASN A 285 " pdb=" CA ASN A 285 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 1241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 102 0.044 - 0.088: 82 0.088 - 0.132: 48 0.132 - 0.176: 16 0.176 - 0.220: 4 Chirality restraints: 252 Sorted by residual: chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE D 318 " pdb=" N ILE D 318 " pdb=" C ILE D 318 " pdb=" CB ILE D 318 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 249 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 336 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C MET C 336 " 0.033 2.00e-02 2.50e+03 pdb=" O MET C 336 " -0.013 2.00e-02 2.50e+03 pdb=" N MET C 337 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 336 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C MET D 336 " 0.033 2.00e-02 2.50e+03 pdb=" O MET D 336 " -0.013 2.00e-02 2.50e+03 pdb=" N MET D 337 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 336 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C MET A 336 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 336 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A 337 " -0.011 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 761 2.92 - 3.41: 2046 3.41 - 3.91: 3535 3.91 - 4.40: 4076 4.40 - 4.90: 7455 Nonbonded interactions: 17873 Sorted by model distance: nonbonded pdb=" O ASN C 355 " pdb=" ND2 ASN D 358 " model vdw 2.423 3.120 nonbonded pdb=" ND2 ASN A 358 " pdb=" O ASN D 355 " model vdw 2.423 3.120 nonbonded pdb=" O ASN A 355 " pdb=" ND2 ASN B 358 " model vdw 2.424 3.120 nonbonded pdb=" OG SER A 333 " pdb=" O GLY B 300 " model vdw 2.559 3.040 nonbonded pdb=" O GLY A 300 " pdb=" OG SER D 333 " model vdw 2.559 3.040 ... (remaining 17868 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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 individual isotropic 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.015 0.060 2180 Z= 1.017 Angle : 1.835 6.975 2900 Z= 1.282 Chirality : 0.079 0.220 252 Planarity : 0.007 0.019 432 Dihedral : 17.258 85.948 772 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.00 % Allowed : 8.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.22), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP B 334 PHE 0.017 0.006 PHE D 289 ARG 0.002 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.274 Fit side-chains REVERT: A 293 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8336 (mmt90) REVERT: A 339 MET cc_start: 0.8144 (ttt) cc_final: 0.7915 (ttp) REVERT: B 359 MET cc_start: 0.8258 (ttt) cc_final: 0.8030 (mtp) REVERT: C 293 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8543 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 68 average time/residue: 1.4863 time to fit residues: 102.7034 Evaluate side-chains 51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN C 286 GLN C 346 GLN D 286 GLN D 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095986 restraints weight = 2434.503| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.59 r_work: 0.3359 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2180 Z= 0.227 Angle : 0.640 4.831 2900 Z= 0.348 Chirality : 0.043 0.129 252 Planarity : 0.003 0.020 432 Dihedral : 5.353 14.996 316 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.50 % Allowed : 19.50 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 334 PHE 0.012 0.002 PHE A 313 ARG 0.002 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.238 Fit side-chains REVERT: A 293 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7991 (mmt90) REVERT: A 339 MET cc_start: 0.8382 (ttt) cc_final: 0.8158 (ttp) REVERT: A 356 GLN cc_start: 0.8163 (mt0) cc_final: 0.7789 (mt0) outliers start: 9 outliers final: 3 residues processed: 61 average time/residue: 1.5807 time to fit residues: 97.9063 Evaluate side-chains 56 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain C residue 342 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 354 GLN C 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.101626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090633 restraints weight = 2441.129| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.59 r_work: 0.3291 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2180 Z= 0.301 Angle : 0.687 5.043 2900 Z= 0.377 Chirality : 0.047 0.126 252 Planarity : 0.003 0.023 432 Dihedral : 5.227 15.776 316 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.50 % Allowed : 18.00 % Favored : 75.50 % 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: -4.29 (0.22), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 334 PHE 0.010 0.002 PHE B 283 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.270 Fit side-chains REVERT: A 339 MET cc_start: 0.8607 (ttt) cc_final: 0.8320 (ttp) REVERT: B 293 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7833 (mmt90) REVERT: B 337 MET cc_start: 0.8996 (ttm) cc_final: 0.8744 (ttm) outliers start: 13 outliers final: 1 residues processed: 61 average time/residue: 1.7941 time to fit residues: 111.0716 Evaluate side-chains 59 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.102195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.091430 restraints weight = 2416.356| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.56 r_work: 0.3303 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2180 Z= 0.215 Angle : 0.614 4.395 2900 Z= 0.335 Chirality : 0.043 0.123 252 Planarity : 0.003 0.018 432 Dihedral : 5.053 15.713 316 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.00 % Allowed : 16.50 % Favored : 77.50 % 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: -4.09 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 334 PHE 0.007 0.001 PHE B 283 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.231 Fit side-chains REVERT: B 293 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7813 (mmt90) REVERT: B 337 MET cc_start: 0.8978 (ttm) cc_final: 0.8736 (ttm) outliers start: 12 outliers final: 5 residues processed: 61 average time/residue: 1.6464 time to fit residues: 101.8940 Evaluate side-chains 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 354 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN D 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.101791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090958 restraints weight = 2444.000| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.58 r_work: 0.3300 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2180 Z= 0.248 Angle : 0.631 4.274 2900 Z= 0.345 Chirality : 0.044 0.126 252 Planarity : 0.003 0.017 432 Dihedral : 4.979 15.424 316 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.50 % Allowed : 14.50 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 334 PHE 0.007 0.001 PHE B 283 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.250 Fit side-chains REVERT: B 293 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7834 (mmt90) REVERT: B 337 MET cc_start: 0.8961 (ttm) cc_final: 0.8733 (ttm) REVERT: C 356 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8229 (mt0) outliers start: 17 outliers final: 4 residues processed: 61 average time/residue: 1.6083 time to fit residues: 99.7217 Evaluate side-chains 63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN D 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.102787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.091935 restraints weight = 2459.604| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.58 r_work: 0.3316 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2180 Z= 0.185 Angle : 0.587 3.839 2900 Z= 0.318 Chirality : 0.042 0.122 252 Planarity : 0.002 0.016 432 Dihedral : 4.835 15.069 316 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.00 % Allowed : 17.50 % Favored : 76.50 % 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: -3.97 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.18), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 PHE 0.006 0.001 PHE B 289 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.212 Fit side-chains REVERT: B 293 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7834 (mmt90) REVERT: B 337 MET cc_start: 0.8943 (ttm) cc_final: 0.8724 (ttm) outliers start: 12 outliers final: 4 residues processed: 62 average time/residue: 1.5414 time to fit residues: 96.9885 Evaluate side-chains 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.0270 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090872 restraints weight = 2495.261| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.60 r_work: 0.3302 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2180 Z= 0.230 Angle : 0.612 4.031 2900 Z= 0.333 Chirality : 0.043 0.123 252 Planarity : 0.002 0.015 432 Dihedral : 4.846 15.291 316 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 9.00 % Allowed : 15.00 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 PHE 0.007 0.001 PHE B 289 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.239 Fit side-chains REVERT: B 293 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7856 (mmt90) REVERT: B 337 MET cc_start: 0.8947 (ttm) cc_final: 0.8730 (ttm) REVERT: C 356 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8215 (mt0) outliers start: 18 outliers final: 7 residues processed: 61 average time/residue: 1.6095 time to fit residues: 99.5957 Evaluate side-chains 67 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 0.0170 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090592 restraints weight = 2506.589| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.60 r_work: 0.3296 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2180 Z= 0.243 Angle : 0.630 4.096 2900 Z= 0.341 Chirality : 0.044 0.122 252 Planarity : 0.003 0.015 432 Dihedral : 4.863 15.127 316 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.50 % Allowed : 18.00 % Favored : 75.50 % 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: -3.97 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 PHE 0.007 0.001 PHE B 289 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.213 Fit side-chains REVERT: A 307 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.9057 (mtp) REVERT: B 293 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7886 (mmt90) REVERT: B 337 MET cc_start: 0.8948 (ttm) cc_final: 0.8714 (ttm) REVERT: C 356 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8210 (mt0) outliers start: 13 outliers final: 4 residues processed: 61 average time/residue: 1.5707 time to fit residues: 97.2208 Evaluate side-chains 65 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.101914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090939 restraints weight = 2463.947| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.59 r_work: 0.3308 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2180 Z= 0.229 Angle : 0.622 4.002 2900 Z= 0.336 Chirality : 0.044 0.122 252 Planarity : 0.002 0.015 432 Dihedral : 4.835 15.011 316 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.00 % Allowed : 18.50 % Favored : 75.50 % 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: -3.93 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 PHE 0.007 0.001 PHE B 289 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.232 Fit side-chains REVERT: A 307 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.9043 (mtp) REVERT: B 293 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7888 (mmt90) REVERT: B 337 MET cc_start: 0.8948 (ttm) cc_final: 0.8716 (ttm) REVERT: C 356 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8194 (mt0) outliers start: 12 outliers final: 4 residues processed: 61 average time/residue: 1.5423 time to fit residues: 95.4768 Evaluate side-chains 66 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 354 GLN B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088016 restraints weight = 2490.959| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.59 r_work: 0.3263 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2180 Z= 0.427 Angle : 0.752 5.019 2900 Z= 0.408 Chirality : 0.049 0.135 252 Planarity : 0.003 0.018 432 Dihedral : 5.142 15.174 316 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.00 % Allowed : 20.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.23), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 334 PHE 0.010 0.002 PHE B 283 ARG 0.001 0.001 ARG D 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.215 Fit side-chains REVERT: A 336 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8519 (ttt) REVERT: B 293 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7947 (mmt90) REVERT: B 337 MET cc_start: 0.8966 (ttm) cc_final: 0.8739 (ttm) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 1.6999 time to fit residues: 93.0755 Evaluate side-chains 60 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 293 ARG Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.3980 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092998 restraints weight = 2443.616| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.57 r_work: 0.3347 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2180 Z= 0.135 Angle : 0.560 3.622 2900 Z= 0.300 Chirality : 0.041 0.119 252 Planarity : 0.002 0.016 432 Dihedral : 4.876 15.046 316 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.50 % Allowed : 20.50 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.22), residues: 308 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.17), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 PHE 0.005 0.001 PHE B 289 ARG 0.001 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.33 seconds wall clock time: 43 minutes 48.80 seconds (2628.80 seconds total)