Starting phenix.real_space_refine on Mon Feb 10 19:59:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q92_18268/02_2025/8q92_18268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q92_18268/02_2025/8q92_18268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q92_18268/02_2025/8q92_18268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q92_18268/02_2025/8q92_18268.map" model { file = "/net/cci-nas-00/data/ceres_data/8q92_18268/02_2025/8q92_18268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q92_18268/02_2025/8q92_18268.cif" } resolution = 3.05 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= 0.001 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 6 5.16 5 C 1296 2.51 5 N 387 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2091 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 697 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Restraints were copied for chains: C, B Time building chain proxies: 3.27, per 1000 atoms: 1.56 Number of scatterers: 2091 At special positions: 0 Unit cell: (56.856, 129.368, 40.376, 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 6 16.00 O 402 8.00 N 387 7.00 C 1296 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: 0.45 Conformation dependent library (CDL) restraints added in 277.1 milliseconds 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 274 through 279 removed outlier: 6.416A pdb=" N VAL A 275 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE C 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 277 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 282 through 287 removed outlier: 7.005A pdb=" N LEU A 282 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER B 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 284 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL B 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN A 286 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 294 through 296 removed outlier: 6.575A pdb=" N ASP A 295 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 300 through 302 removed outlier: 6.432A pdb=" N VAL A 300 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.397A pdb=" N VAL A 306 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL B 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 308 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 323 removed outlier: 6.417A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.203A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.329A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LYS B 343 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU A 342 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ASP B 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 344 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.743A pdb=" N ASP A 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR B 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) 39 hydrogen bonds defined for protein. 117 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: 0.46 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 479 1.33 - 1.45: 421 1.45 - 1.57: 1209 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 2115 Sorted by residual: bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.324 0.030 1.10e-02 8.26e+03 7.56e+00 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.324 0.030 1.10e-02 8.26e+03 7.32e+00 bond pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 1.354 1.324 0.030 1.10e-02 8.26e+03 7.22e+00 bond pdb=" CB HIS B 299 " pdb=" CG HIS B 299 " ideal model delta sigma weight residual 1.497 1.464 0.033 1.40e-02 5.10e+03 5.71e+00 bond pdb=" CB HIS C 299 " pdb=" CG HIS C 299 " ideal model delta sigma weight residual 1.497 1.464 0.033 1.40e-02 5.10e+03 5.70e+00 ... (remaining 2110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 2104 1.39 - 2.77: 559 2.77 - 4.16: 142 4.16 - 5.54: 18 5.54 - 6.92: 3 Bond angle restraints: 2826 Sorted by residual: angle pdb=" N PRO B 332 " pdb=" CA PRO B 332 " pdb=" CB PRO B 332 " ideal model delta sigma weight residual 102.92 104.99 -2.07 5.60e-01 3.19e+00 1.37e+01 angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" CB PRO A 332 " ideal model delta sigma weight residual 102.92 104.99 -2.07 5.60e-01 3.19e+00 1.37e+01 angle pdb=" N PRO C 332 " pdb=" CA PRO C 332 " pdb=" CB PRO C 332 " ideal model delta sigma weight residual 102.92 104.98 -2.06 5.60e-01 3.19e+00 1.35e+01 angle pdb=" CA ASP C 348 " pdb=" CB ASP C 348 " pdb=" CG ASP C 348 " ideal model delta sigma weight residual 112.60 116.18 -3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " ideal model delta sigma weight residual 112.60 116.18 -3.58 1.00e+00 1.00e+00 1.28e+01 ... (remaining 2821 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.75: 1143 15.75 - 31.49: 123 31.49 - 47.23: 27 47.23 - 62.97: 3 62.97 - 78.71: 3 Dihedral angle restraints: 1299 sinusoidal: 531 harmonic: 768 Sorted by residual: dihedral pdb=" CA LYS A 298 " pdb=" C LYS A 298 " pdb=" N HIS A 299 " pdb=" CA HIS A 299 " ideal model delta harmonic sigma weight residual -180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LYS B 298 " pdb=" C LYS B 298 " pdb=" N HIS B 299 " pdb=" CA HIS B 299 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LYS C 298 " pdb=" C LYS C 298 " pdb=" N HIS C 299 " pdb=" CA HIS C 299 " ideal model delta harmonic sigma weight residual -180.00 -153.65 -26.35 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 1296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 114 0.046 - 0.092: 108 0.092 - 0.137: 63 0.137 - 0.183: 24 0.183 - 0.229: 12 Chirality restraints: 321 Sorted by residual: chirality pdb=" CA ILE B 297 " pdb=" N ILE B 297 " pdb=" C ILE B 297 " pdb=" CB ILE B 297 " both_signs ideal model delta sigma weight residual False 2.43 2.20 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE A 297 " pdb=" N ILE A 297 " pdb=" C ILE A 297 " pdb=" CB ILE A 297 " both_signs ideal model delta sigma weight residual False 2.43 2.20 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE C 297 " pdb=" N ILE C 297 " pdb=" C ILE C 297 " pdb=" CB ILE C 297 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 318 not shown) Planarity restraints: 363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 331 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 332 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 332 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 332 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 331 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 332 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 331 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO C 332 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 332 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 332 " 0.024 5.00e-02 4.00e+02 ... (remaining 360 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 1060 3.01 - 3.48: 2002 3.48 - 3.95: 3077 3.95 - 4.43: 3312 4.43 - 4.90: 6936 Nonbonded interactions: 16387 Sorted by model distance: nonbonded pdb=" OD2 ASP C 295 " pdb=" NZ LYS C 298 " model vdw 2.531 3.120 nonbonded pdb=" OD2 ASP B 295 " pdb=" NZ LYS B 298 " model vdw 2.532 3.120 nonbonded pdb=" OD2 ASP A 295 " pdb=" NZ LYS A 298 " model vdw 2.532 3.120 nonbonded pdb=" O VAL A 313 " pdb=" OG SER A 316 " model vdw 2.608 3.040 nonbonded pdb=" O VAL C 313 " pdb=" OG SER C 316 " model vdw 2.608 3.040 ... (remaining 16382 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' } 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: 3.650 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.950 Find NCS groups from input model: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.008 0.045 2115 Z= 0.566 Angle : 1.366 6.925 2826 Z= 0.875 Chirality : 0.089 0.229 321 Planarity : 0.008 0.043 363 Dihedral : 13.953 78.712 813 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.23 % Allowed : 2.47 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 329 PHE 0.005 0.003 PHE B 346 TYR 0.008 0.003 TYR B 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.200 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1606 time to fit residues: 4.2977 Evaluate side-chains 15 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.122927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104735 restraints weight = 2647.704| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.46 r_work: 0.3600 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2115 Z= 0.312 Angle : 0.668 6.182 2826 Z= 0.338 Chirality : 0.054 0.141 321 Planarity : 0.005 0.041 363 Dihedral : 6.602 29.907 294 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.65 % Allowed : 5.76 % Favored : 92.59 % 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: -2.91 (0.42), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.005 0.001 PHE C 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.245 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 0.0797 time to fit residues: 2.5144 Evaluate side-chains 17 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.131402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.111401 restraints weight = 2287.873| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.51 r_work: 0.3657 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2115 Z= 0.193 Angle : 0.569 5.861 2826 Z= 0.286 Chirality : 0.051 0.134 321 Planarity : 0.003 0.030 363 Dihedral : 4.836 16.720 285 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.47 % Allowed : 9.47 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.004 0.001 PHE C 346 TYR 0.001 0.000 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.249 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 21 average time/residue: 0.0788 time to fit residues: 2.4346 Evaluate side-chains 19 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.135942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.116012 restraints weight = 2202.591| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.47 r_work: 0.3678 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2115 Z= 0.177 Angle : 0.562 5.716 2826 Z= 0.279 Chirality : 0.051 0.135 321 Planarity : 0.003 0.027 363 Dihedral : 4.650 16.339 285 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.23 % Allowed : 11.52 % Favored : 87.24 % 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: -2.59 (0.43), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 330 PHE 0.004 0.001 PHE C 346 TYR 0.002 0.000 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.251 Fit side-chains REVERT: B 288 GLN cc_start: 0.8620 (mt0) cc_final: 0.8351 (mt0) REVERT: C 342 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7004 (tt0) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.0829 time to fit residues: 2.2269 Evaluate side-chains 18 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.126870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.106890 restraints weight = 2331.975| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.41 r_work: 0.3603 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2115 Z= 0.452 Angle : 0.722 7.503 2826 Z= 0.366 Chirality : 0.057 0.145 321 Planarity : 0.004 0.040 363 Dihedral : 5.594 19.759 285 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.65 % Allowed : 12.35 % Favored : 86.01 % 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: -2.75 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.006 0.001 PHE A 346 TYR 0.005 0.001 TYR B 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.231 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.0812 time to fit residues: 2.6110 Evaluate side-chains 20 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.130021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.109692 restraints weight = 2341.180| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.52 r_work: 0.3643 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2115 Z= 0.234 Angle : 0.599 6.802 2826 Z= 0.300 Chirality : 0.052 0.136 321 Planarity : 0.003 0.030 363 Dihedral : 4.987 17.152 285 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.82 % Allowed : 14.40 % Favored : 84.77 % 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: -2.67 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.005 0.001 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.222 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.0922 time to fit residues: 2.7856 Evaluate side-chains 18 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.129537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.109178 restraints weight = 2322.423| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.49 r_work: 0.3639 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2115 Z= 0.274 Angle : 0.610 6.833 2826 Z= 0.307 Chirality : 0.053 0.136 321 Planarity : 0.003 0.030 363 Dihedral : 5.023 17.436 285 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.23 % Allowed : 14.81 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.005 0.001 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.231 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.0758 time to fit residues: 2.3285 Evaluate side-chains 19 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.130661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.110219 restraints weight = 2349.895| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.55 r_work: 0.3648 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2115 Z= 0.215 Angle : 0.573 6.685 2826 Z= 0.288 Chirality : 0.052 0.135 321 Planarity : 0.003 0.035 363 Dihedral : 4.820 16.584 285 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.47 % Allowed : 13.99 % Favored : 83.54 % 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: -2.69 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.004 0.001 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.234 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.0937 time to fit residues: 3.0705 Evaluate side-chains 20 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.133524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.113082 restraints weight = 2362.008| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.53 r_work: 0.3647 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2115 Z= 0.229 Angle : 0.596 6.672 2826 Z= 0.295 Chirality : 0.052 0.135 321 Planarity : 0.004 0.036 363 Dihedral : 4.839 16.602 285 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.65 % Allowed : 14.81 % Favored : 83.54 % 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: -2.70 (0.41), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.004 0.001 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.275 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 20 average time/residue: 0.0982 time to fit residues: 2.6870 Evaluate side-chains 21 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.128450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.108076 restraints weight = 2321.359| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.47 r_work: 0.3609 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2115 Z= 0.382 Angle : 0.682 7.500 2826 Z= 0.342 Chirality : 0.055 0.141 321 Planarity : 0.004 0.041 363 Dihedral : 5.356 18.355 285 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.06 % Allowed : 15.23 % Favored : 82.72 % 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: -2.78 (0.40), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.006 0.001 PHE C 346 TYR 0.004 0.001 TYR A 310 ARG 0.002 0.001 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.277 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 20 average time/residue: 0.0827 time to fit residues: 2.4125 Evaluate side-chains 19 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.129722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.109315 restraints weight = 2328.753| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.51 r_work: 0.3633 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2115 Z= 0.261 Angle : 0.621 7.385 2826 Z= 0.308 Chirality : 0.053 0.137 321 Planarity : 0.004 0.036 363 Dihedral : 5.067 17.075 285 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.65 % Allowed : 16.46 % Favored : 81.89 % 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: -2.76 (0.40), residues: 276 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.005 0.001 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.22 seconds wall clock time: 35 minutes 9.80 seconds (2109.80 seconds total)