Starting phenix.real_space_refine on Tue Feb 11 03:45:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8org_17123/02_2025/8org_17123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8org_17123/02_2025/8org_17123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8org_17123/02_2025/8org_17123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8org_17123/02_2025/8org_17123.map" model { file = "/net/cci-nas-00/data/ceres_data/8org_17123/02_2025/8org_17123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8org_17123/02_2025/8org_17123.cif" } resolution = 2.3 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1206 2.51 5 N 357 2.21 5 O 372 1.98 5 H 2025 0.53 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: 3966 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1322 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Restraints were copied for chains: C, B Time building chain proxies: 2.28, per 1000 atoms: 0.57 Number of scatterers: 3966 At special positions: 0 Unit cell: (70.8825, 92.6925, 35.9865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 372 8.00 N 357 7.00 C 1206 6.00 H 2025 1.00 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: 0.95 Conformation dependent library (CDL) restraints added in 289.4 milliseconds 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 456 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 283 removed outlier: 6.401A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 299 removed outlier: 6.398A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 310 removed outlier: 6.827A pdb=" N GLY B 304 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY B 303 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL C 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER B 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE C 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 318 removed outlier: 6.459A pdb=" N ASP B 314 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LYS A 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER B 316 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N SER C 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 315 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL C 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.760A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.457A pdb=" N ASN B 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS C 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS B 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 341 removed outlier: 6.392A pdb=" N VAL B 337 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS A 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 339 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.729A pdb=" N ILE B 360 " --> pdb=" O THR A 361 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 126 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: 1.24 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 2019 1.03 - 1.22: 6 1.22 - 1.41: 755 1.41 - 1.61: 1204 1.61 - 1.80: 6 Bond restraints: 3990 Sorted by residual: bond pdb=" CB PRO C 312 " pdb=" CG PRO C 312 " ideal model delta sigma weight residual 1.492 1.411 0.081 5.00e-02 4.00e+02 2.62e+00 bond pdb=" CB PRO B 312 " pdb=" CG PRO B 312 " ideal model delta sigma weight residual 1.492 1.411 0.081 5.00e-02 4.00e+02 2.59e+00 bond pdb=" CB PRO A 312 " pdb=" CG PRO A 312 " ideal model delta sigma weight residual 1.492 1.412 0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" CE LYS C 311 " pdb=" NZ LYS C 311 " ideal model delta sigma weight residual 1.489 1.442 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CE LYS A 311 " pdb=" NZ LYS A 311 " ideal model delta sigma weight residual 1.489 1.443 0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 3985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 6364 1.52 - 3.05: 757 3.05 - 4.57: 126 4.57 - 6.10: 25 6.10 - 7.62: 9 Bond angle restraints: 7281 Sorted by residual: angle pdb=" CA LYS C 281 " pdb=" CB LYS C 281 " pdb=" CG LYS C 281 " ideal model delta sigma weight residual 114.10 120.92 -6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA LYS A 281 " pdb=" CB LYS A 281 " pdb=" CG LYS A 281 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA LYS B 281 " pdb=" CB LYS B 281 " pdb=" CG LYS B 281 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N LYS A 281 " pdb=" CA LYS A 281 " pdb=" C LYS A 281 " ideal model delta sigma weight residual 109.23 114.31 -5.08 1.55e+00 4.16e-01 1.08e+01 angle pdb=" N LYS B 281 " pdb=" CA LYS B 281 " pdb=" C LYS B 281 " ideal model delta sigma weight residual 109.23 114.30 -5.07 1.55e+00 4.16e-01 1.07e+01 ... (remaining 7276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 1566 13.45 - 26.91: 149 26.91 - 40.36: 31 40.36 - 53.81: 36 53.81 - 67.26: 54 Dihedral angle restraints: 1836 sinusoidal: 1059 harmonic: 777 Sorted by residual: dihedral pdb=" CA LEU A 357 " pdb=" C LEU A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU B 357 " pdb=" C LEU B 357 " pdb=" N ASP B 358 " pdb=" CA ASP B 358 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LEU C 357 " pdb=" C LEU C 357 " pdb=" N ASP C 358 " pdb=" CA ASP C 358 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 1833 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.076: 228 0.076 - 0.152: 63 0.152 - 0.227: 3 0.227 - 0.303: 3 0.303 - 0.378: 3 Chirality restraints: 300 Sorted by residual: chirality pdb=" CB ILE B 360 " pdb=" CA ILE B 360 " pdb=" CG1 ILE B 360 " pdb=" CG2 ILE B 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB ILE C 360 " pdb=" CA ILE C 360 " pdb=" CG1 ILE C 360 " pdb=" CG2 ILE C 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB ILE A 360 " pdb=" CA ILE A 360 " pdb=" CG1 ILE A 360 " pdb=" CG2 ILE A 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 297 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 288 " -0.025 2.00e-02 2.50e+03 3.22e-02 1.55e+01 pdb=" CD GLN B 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN B 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN B 288 " 0.053 2.00e-02 2.50e+03 pdb="HE21 GLN B 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN B 288 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 288 " -0.025 2.00e-02 2.50e+03 3.21e-02 1.55e+01 pdb=" CD GLN A 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN A 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 288 " 0.054 2.00e-02 2.50e+03 pdb="HE21 GLN A 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 288 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 288 " -0.025 2.00e-02 2.50e+03 3.20e-02 1.53e+01 pdb=" CD GLN C 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN C 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN C 288 " 0.053 2.00e-02 2.50e+03 pdb="HE21 GLN C 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN C 288 " -0.049 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1175 2.32 - 2.89: 9040 2.89 - 3.46: 8824 3.46 - 4.03: 13749 4.03 - 4.60: 19241 Nonbonded interactions: 52029 Sorted by model distance: nonbonded pdb=" OD2 ASP C 295 " pdb=" HZ3 LYS C 311 " model vdw 1.746 2.450 nonbonded pdb=" OD2 ASP B 295 " pdb=" HZ3 LYS B 311 " model vdw 1.747 2.450 nonbonded pdb=" OD2 ASP A 295 " pdb=" HZ3 LYS A 311 " model vdw 1.748 2.450 nonbonded pdb="HD22 ASN A 296 " pdb=" OD2 ASP A 358 " model vdw 1.764 2.450 nonbonded pdb="HD22 ASN B 296 " pdb=" OD2 ASP B 358 " model vdw 1.765 2.450 ... (remaining 52024 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: 0.01 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: 0.900 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: 0.070 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 1965 Z= 0.651 Angle : 1.263 7.621 2628 Z= 0.667 Chirality : 0.075 0.378 300 Planarity : 0.005 0.032 336 Dihedral : 11.917 66.727 759 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: -2.52 (0.43), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.006 HIS A 299 PHE 0.012 0.005 PHE C 346 TYR 0.016 0.009 TYR A 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 281 LYS cc_start: 0.7478 (ptpt) cc_final: 0.7251 (ptmt) REVERT: B 317 LYS cc_start: 0.8471 (tttt) cc_final: 0.8201 (tttm) REVERT: B 331 LYS cc_start: 0.8517 (mttt) cc_final: 0.8284 (mttt) REVERT: B 341 SER cc_start: 0.8619 (m) cc_final: 0.8368 (t) REVERT: A 281 LYS cc_start: 0.8333 (ptpt) cc_final: 0.8063 (ptmt) REVERT: A 340 LYS cc_start: 0.8368 (mttt) cc_final: 0.8123 (mtpp) REVERT: A 349 ARG cc_start: 0.7520 (mtt180) cc_final: 0.5917 (mmp-170) REVERT: A 351 GLN cc_start: 0.7767 (tt0) cc_final: 0.7484 (tt0) REVERT: A 356 SER cc_start: 0.8520 (t) cc_final: 0.8006 (p) REVERT: A 358 ASP cc_start: 0.7114 (t0) cc_final: 0.6881 (t0) REVERT: C 314 ASP cc_start: 0.7593 (t0) cc_final: 0.7113 (t0) REVERT: C 331 LYS cc_start: 0.8541 (mttt) cc_final: 0.8314 (mttt) REVERT: C 338 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7337 (mp0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 2.5724 time to fit residues: 250.8638 Evaluate side-chains 58 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN A 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.150574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.131706 restraints weight = 6744.259| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 1.95 r_work: 0.4050 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1965 Z= 0.170 Angle : 0.590 4.591 2628 Z= 0.298 Chirality : 0.052 0.141 300 Planarity : 0.003 0.021 336 Dihedral : 6.699 17.869 261 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.51 % Allowed : 14.91 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.40), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 299 PHE 0.004 0.001 PHE C 346 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.316 Fit side-chains REVERT: A 340 LYS cc_start: 0.8685 (mttt) cc_final: 0.8309 (mtpp) REVERT: A 349 ARG cc_start: 0.7885 (mtt180) cc_final: 0.6409 (mtt-85) REVERT: C 317 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8833 (tptm) REVERT: C 338 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7895 (mp0) REVERT: C 340 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8603 (mtpm) outliers start: 8 outliers final: 1 residues processed: 70 average time/residue: 2.0147 time to fit residues: 143.9608 Evaluate side-chains 53 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN B 286 ASN A 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.143217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.124711 restraints weight = 6958.220| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.88 r_work: 0.3983 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1965 Z= 0.199 Angle : 0.544 3.842 2628 Z= 0.275 Chirality : 0.052 0.127 300 Planarity : 0.003 0.023 336 Dihedral : 5.942 16.519 261 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.51 % Allowed : 19.74 % Favored : 76.75 % 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: -3.00 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 PHE 0.002 0.001 PHE C 346 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.411 Fit side-chains REVERT: B 327 ASN cc_start: 0.8299 (m110) cc_final: 0.8098 (m110) REVERT: A 340 LYS cc_start: 0.8759 (mttt) cc_final: 0.8347 (mtpp) REVERT: A 349 ARG cc_start: 0.8147 (mtt180) cc_final: 0.6204 (mmp-170) REVERT: A 351 GLN cc_start: 0.8020 (mt0) cc_final: 0.7800 (mt0) REVERT: C 338 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7927 (mp0) REVERT: C 340 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8572 (mtpm) outliers start: 8 outliers final: 2 residues processed: 57 average time/residue: 1.5789 time to fit residues: 92.6131 Evaluate side-chains 52 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN A 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.146692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.128908 restraints weight = 7008.833| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.89 r_work: 0.4040 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3948 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1965 Z= 0.146 Angle : 0.492 3.538 2628 Z= 0.251 Chirality : 0.052 0.126 300 Planarity : 0.003 0.026 336 Dihedral : 5.346 15.123 261 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.19 % Allowed : 21.49 % Favored : 76.32 % 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: -2.98 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 PHE 0.001 0.000 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.000 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 325 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8649 (mt) REVERT: A 336 GLN cc_start: 0.8542 (mt0) cc_final: 0.8199 (tt0) REVERT: A 340 LYS cc_start: 0.8731 (mttt) cc_final: 0.8322 (mtpp) REVERT: A 349 ARG cc_start: 0.8104 (mtt180) cc_final: 0.6561 (mtt-85) REVERT: A 351 GLN cc_start: 0.8049 (mt0) cc_final: 0.7832 (mt0) REVERT: C 338 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7909 (mp0) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 1.4707 time to fit residues: 80.3468 Evaluate side-chains 52 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.141916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.123257 restraints weight = 7009.470| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.93 r_work: 0.3971 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1965 Z= 0.188 Angle : 0.484 3.553 2628 Z= 0.250 Chirality : 0.051 0.124 300 Planarity : 0.003 0.025 336 Dihedral : 5.354 15.319 261 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.95 % Allowed : 19.74 % Favored : 76.32 % 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: -2.90 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLN cc_start: 0.8491 (mt0) cc_final: 0.8167 (tt0) REVERT: A 340 LYS cc_start: 0.8729 (mttt) cc_final: 0.8394 (mtpp) REVERT: A 349 ARG cc_start: 0.8159 (mtt180) cc_final: 0.6121 (mmp-170) REVERT: C 338 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7920 (mp0) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 1.3497 time to fit residues: 78.2162 Evaluate side-chains 55 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.120921 restraints weight = 6861.612| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.86 r_work: 0.3937 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1965 Z= 0.208 Angle : 0.493 3.598 2628 Z= 0.255 Chirality : 0.051 0.123 300 Planarity : 0.003 0.027 336 Dihedral : 5.351 15.316 261 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.63 % Allowed : 20.18 % Favored : 77.19 % 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: -2.89 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLN cc_start: 0.8514 (mt0) cc_final: 0.8185 (tt0) REVERT: A 340 LYS cc_start: 0.8706 (mttt) cc_final: 0.8387 (mtpp) REVERT: A 349 ARG cc_start: 0.8202 (mtt180) cc_final: 0.6122 (mmp-170) REVERT: C 338 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7929 (mp0) REVERT: C 340 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8560 (mtpm) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 1.5322 time to fit residues: 85.2219 Evaluate side-chains 54 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.142900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.124499 restraints weight = 6806.882| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.90 r_work: 0.3985 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1965 Z= 0.143 Angle : 0.464 3.509 2628 Z= 0.238 Chirality : 0.051 0.123 300 Planarity : 0.003 0.025 336 Dihedral : 5.032 14.785 261 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.19 % Allowed : 21.05 % Favored : 76.75 % 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 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.002 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) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.9181 (mt) cc_final: 0.8929 (mt) REVERT: A 336 GLN cc_start: 0.8553 (mt0) cc_final: 0.8232 (tt0) REVERT: A 340 LYS cc_start: 0.8723 (mttt) cc_final: 0.8393 (mtpp) REVERT: A 349 ARG cc_start: 0.8195 (mtt180) cc_final: 0.6134 (mmp-170) REVERT: C 338 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7918 (mp0) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 1.4815 time to fit residues: 74.7821 Evaluate side-chains 48 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.141741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.124280 restraints weight = 7083.789| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.84 r_work: 0.3982 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1965 Z= 0.167 Angle : 0.474 3.606 2628 Z= 0.243 Chirality : 0.051 0.122 300 Planarity : 0.003 0.025 336 Dihedral : 5.012 14.935 261 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.75 % Allowed : 21.93 % Favored : 76.32 % 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: -2.89 (0.42), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.9225 (mt) cc_final: 0.8970 (mt) REVERT: A 336 GLN cc_start: 0.8552 (mt0) cc_final: 0.8257 (tt0) REVERT: A 340 LYS cc_start: 0.8731 (mttt) cc_final: 0.8416 (mtpp) REVERT: A 349 ARG cc_start: 0.8233 (mtt180) cc_final: 0.6072 (mmp-170) REVERT: C 338 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7926 (mp0) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 1.7485 time to fit residues: 85.0489 Evaluate side-chains 48 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.141181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.123588 restraints weight = 7097.020| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.86 r_work: 0.3985 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1965 Z= 0.165 Angle : 0.469 3.790 2628 Z= 0.240 Chirality : 0.051 0.122 300 Planarity : 0.003 0.024 336 Dihedral : 4.979 15.103 261 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.75 % Allowed : 21.49 % Favored : 76.75 % 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: -2.90 (0.42), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLN cc_start: 0.8542 (mt0) cc_final: 0.8260 (tt0) REVERT: A 340 LYS cc_start: 0.8743 (mttt) cc_final: 0.8434 (mtpp) REVERT: A 349 ARG cc_start: 0.8238 (mtt180) cc_final: 0.6183 (mmp-170) REVERT: C 338 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7918 (mp0) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 1.4387 time to fit residues: 71.3033 Evaluate side-chains 48 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 21 optimal weight: 0.0060 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.143239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.125720 restraints weight = 7015.402| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.87 r_work: 0.4007 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1965 Z= 0.147 Angle : 0.464 3.935 2628 Z= 0.236 Chirality : 0.051 0.122 300 Planarity : 0.003 0.026 336 Dihedral : 4.829 14.716 261 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 21.05 % Favored : 78.07 % 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: -2.92 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.003 0.001 TYR C 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLN cc_start: 0.8517 (mt0) cc_final: 0.8231 (tt0) REVERT: A 340 LYS cc_start: 0.8769 (mttt) cc_final: 0.8460 (mtpp) REVERT: A 349 ARG cc_start: 0.8203 (mtt180) cc_final: 0.6045 (mmp-170) REVERT: C 338 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7889 (mp0) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 1.5536 time to fit residues: 76.7398 Evaluate side-chains 49 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.142361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.124765 restraints weight = 6984.014| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.86 r_work: 0.4000 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1965 Z= 0.152 Angle : 0.457 3.520 2628 Z= 0.234 Chirality : 0.051 0.121 300 Planarity : 0.003 0.025 336 Dihedral : 4.874 14.740 261 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 21.49 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.003 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: 4514.07 seconds wall clock time: 79 minutes 46.99 seconds (4786.99 seconds total)