Starting phenix.real_space_refine on Tue Aug 4 17:00:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29ou_57275/08_2026/29ou_57275.cif Found real_map, /net/cci-nas-00/data/ceres_data/29ou_57275/08_2026/29ou_57275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29ou_57275/08_2026/29ou_57275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29ou_57275/08_2026/29ou_57275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29ou_57275/08_2026/29ou_57275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29ou_57275/08_2026/29ou_57275.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 1521 2.51 5 N 453 2.21 5 O 459 1.98 5 H 2556 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4995 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1665 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1665 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1665 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 1.26, per 1000 atoms: 0.25 Number of scatterers: 4995 At special positions: 0 Unit cell: (110.416, 87.344, 36.256, 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 459 8.00 N 453 7.00 C 1521 6.00 H 2556 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: 0.43 Conformation dependent library (CDL) restraints added in 118.6 milliseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.845A 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 283 removed outlier: 6.425A pdb=" N LEU A 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AA4, first strand: chain 'B' and resid 305 through 310 removed outlier: 6.450A pdb=" N SER A 305 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ILE B 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 318 Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.953A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS B 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 removed outlier: 6.307A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 371 removed outlier: 6.419A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 374 through 375 removed outlier: 6.566A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.595A pdb=" N PHE A 378 " --> pdb=" O ARG C 379 " (cutoff:3.500A) 32 hydrogen bonds defined for protein. 96 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2550 1.12 - 1.29: 414 1.29 - 1.47: 786 1.47 - 1.64: 1272 1.64 - 1.81: 6 Bond restraints: 5028 Sorted by residual: bond pdb=" NE2 HIS C 362 " pdb=" HE2 HIS C 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY B 335 " pdb=" H GLY B 335 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 HIS B 374 " pdb=" HD2 HIS B 374 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL C 337 " pdb=" H VAL C 337 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS B 343 " pdb=" H LYS B 343 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 5023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 7432 2.52 - 5.05: 1333 5.05 - 7.57: 385 7.57 - 10.09: 21 10.09 - 12.61: 9 Bond angle restraints: 9180 Sorted by residual: angle pdb=" CA HIS C 330 " pdb=" C HIS C 330 " pdb=" N LYS C 331 " ideal model delta sigma weight residual 116.23 127.64 -11.41 1.37e+00 5.33e-01 6.94e+01 angle pdb=" CA HIS C 330 " pdb=" C HIS C 330 " pdb=" O HIS C 330 " ideal model delta sigma weight residual 120.70 114.09 6.61 1.14e+00 7.69e-01 3.36e+01 angle pdb=" N ASP C 314 " pdb=" CA ASP C 314 " pdb=" CB ASP C 314 " ideal model delta sigma weight residual 111.13 100.76 10.37 1.79e+00 3.12e-01 3.35e+01 angle pdb=" N ASP C 314 " pdb=" CA ASP C 314 " pdb=" C ASP C 314 " ideal model delta sigma weight residual 109.06 118.67 -9.61 1.70e+00 3.46e-01 3.20e+01 angle pdb=" CA ASP C 314 " pdb=" CB ASP C 314 " pdb=" CG ASP C 314 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.12e+01 ... (remaining 9175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 1950 13.63 - 27.26: 186 27.26 - 40.89: 51 40.89 - 54.51: 47 54.51 - 68.14: 73 Dihedral angle restraints: 2307 sinusoidal: 1335 harmonic: 972 Sorted by residual: dihedral pdb=" CA VAL A 287 " pdb=" C VAL A 287 " pdb=" N GLN A 288 " pdb=" CA GLN A 288 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" C LYS C 331 " pdb=" N LYS C 331 " pdb=" CA LYS C 331 " pdb=" CB LYS C 331 " ideal model delta harmonic sigma weight residual -122.60 -136.07 13.47 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" C LYS C 347 " pdb=" N LYS C 347 " pdb=" CA LYS C 347 " pdb=" CB LYS C 347 " ideal model delta harmonic sigma weight residual -122.60 -135.25 12.65 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 2304 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.104: 250 0.104 - 0.207: 106 0.207 - 0.310: 12 0.310 - 0.413: 2 0.413 - 0.516: 2 Chirality restraints: 372 Sorted by residual: chirality pdb=" CA LYS C 331 " pdb=" N LYS C 331 " pdb=" C LYS C 331 " pdb=" CB LYS C 331 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" CA LYS A 331 " pdb=" N LYS A 331 " pdb=" C LYS A 331 " pdb=" CB LYS A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 369 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 299 " -0.107 2.00e-02 2.50e+03 6.50e-02 9.50e+01 pdb=" CG HIS A 299 " 0.079 2.00e-02 2.50e+03 pdb=" ND1 HIS A 299 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 HIS A 299 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 HIS A 299 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS A 299 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 HIS A 299 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 HIS A 299 " -0.068 2.00e-02 2.50e+03 pdb=" HE2 HIS A 299 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 329 " 0.104 2.00e-02 2.50e+03 5.79e-02 7.53e+01 pdb=" CG HIS C 329 " -0.106 2.00e-02 2.50e+03 pdb=" ND1 HIS C 329 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS C 329 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 HIS C 329 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS C 329 " -0.012 2.00e-02 2.50e+03 pdb=" HD2 HIS C 329 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 HIS C 329 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 HIS C 329 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 296 " -0.072 2.00e-02 2.50e+03 6.84e-02 7.03e+01 pdb=" CG ASN C 296 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN C 296 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN C 296 " 0.081 2.00e-02 2.50e+03 pdb="HD21 ASN C 296 " 0.038 2.00e-02 2.50e+03 pdb="HD22 ASN C 296 " -0.113 2.00e-02 2.50e+03 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 604 2.26 - 2.85: 10235 2.85 - 3.43: 12389 3.43 - 4.02: 16089 4.02 - 4.60: 23152 Nonbonded interactions: 62469 Sorted by model distance: nonbonded pdb=" O LYS A 290 " pdb=" HG SER A 293 " model vdw 1.679 2.450 nonbonded pdb=" O LYS C 290 " pdb=" HG SER C 293 " model vdw 1.688 2.450 nonbonded pdb=" O LYS B 340 " pdb=" HG SER B 341 " model vdw 1.700 2.450 nonbonded pdb=" HZ2 LYS C 298 " pdb=" OD2 ASP C 358 " model vdw 1.702 2.450 nonbonded pdb=" O LYS C 340 " pdb=" HG SER C 341 " model vdw 1.710 2.450 ... (remaining 62464 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 'B' selection = chain 'C' } 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: 0.680 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: 0.040 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.910 Find NCS groups from input model: 0.070 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 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 : 0.011 0.037 2472 Z= 0.708 Angle : 2.162 11.411 3303 Z= 1.421 Chirality : 0.110 0.516 372 Planarity : 0.012 0.065 423 Dihedral : 13.419 68.143 963 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.32), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.25), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG B 349 TYR 0.079 0.023 TYR A 310 PHE 0.073 0.016 PHE C 346 HIS 0.016 0.004 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.01082 / 0.71 ( 2472) covalent geometry : angle 2.16200 / 1.42 ( 3303) hydrogen bonds : bond 0.10870 / 7.36 ( 32) hydrogen bonds : angle 6.36021 / 4.59 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 316 SER cc_start: 0.8232 (t) cc_final: 0.7718 (m) REVERT: B 372 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7549 (mp0) REVERT: B 379 ARG cc_start: 0.7282 (tmt170) cc_final: 0.6467 (pmt-80) REVERT: C 377 THR cc_start: 0.8163 (t) cc_final: 0.7731 (p) REVERT: C 378 PHE cc_start: 0.8087 (t80) cc_final: 0.7740 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1750 time to fit residues: 14.4653 Evaluate side-chains 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 329 HIS B 374 HIS C 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.135017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.115401 restraints weight = 12650.545| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.82 r_work: 0.3989 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2472 Z= 0.142 Angle : 0.631 5.783 3303 Z= 0.331 Chirality : 0.052 0.148 372 Planarity : 0.003 0.018 423 Dihedral : 6.938 20.339 327 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.33), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.25), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 349 TYR 0.003 0.001 TYR B 310 PHE 0.007 0.002 PHE C 378 HIS 0.013 0.003 HIS C 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 2472) covalent geometry : angle 0.63098 / 0.33 ( 3303) hydrogen bonds : bond 0.02099 / 1.24 ( 32) hydrogen bonds : angle 4.31486 / 3.05 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 316 SER cc_start: 0.8167 (t) cc_final: 0.7473 (m) REVERT: A 359 ASN cc_start: 0.7859 (t0) cc_final: 0.7602 (m-40) REVERT: A 380 GLU cc_start: 0.7473 (tt0) cc_final: 0.7114 (tm-30) REVERT: B 316 SER cc_start: 0.7695 (t) cc_final: 0.7294 (m) REVERT: B 331 LYS cc_start: 0.8889 (pttt) cc_final: 0.8588 (ptpt) REVERT: B 368 ASN cc_start: 0.8340 (m-40) cc_final: 0.8073 (m110) REVERT: B 372 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8183 (mp0) REVERT: B 379 ARG cc_start: 0.7256 (tmt170) cc_final: 0.6170 (pmt-80) REVERT: C 283 ASP cc_start: 0.7671 (t0) cc_final: 0.7466 (t0) REVERT: C 286 ASN cc_start: 0.8297 (m-40) cc_final: 0.8083 (m-40) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1205 time to fit residues: 8.5316 Evaluate side-chains 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.0030 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 overall best weight: 1.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.136775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.117628 restraints weight = 12616.797| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.79 r_work: 0.4007 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2472 Z= 0.104 Angle : 0.544 4.275 3303 Z= 0.285 Chirality : 0.050 0.137 372 Planarity : 0.003 0.017 423 Dihedral : 6.054 18.584 327 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.06 % Allowed : 7.45 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.003 0.001 TYR A 310 PHE 0.005 0.001 PHE C 378 HIS 0.010 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 2472) covalent geometry : angle 0.54379 / 0.28 ( 3303) hydrogen bonds : bond 0.01969 / 1.13 ( 32) hydrogen bonds : angle 4.22868 / 3.00 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 316 SER cc_start: 0.8084 (t) cc_final: 0.7358 (m) REVERT: A 359 ASN cc_start: 0.7908 (t0) cc_final: 0.7657 (m-40) REVERT: A 373 THR cc_start: 0.7150 (m) cc_final: 0.6846 (t) REVERT: A 380 GLU cc_start: 0.7446 (tt0) cc_final: 0.7204 (tm-30) REVERT: B 314 ASP cc_start: 0.7611 (t0) cc_final: 0.7135 (m-30) REVERT: B 316 SER cc_start: 0.7830 (t) cc_final: 0.7480 (m) REVERT: B 331 LYS cc_start: 0.8917 (pttt) cc_final: 0.8612 (ptpt) REVERT: B 343 LYS cc_start: 0.9361 (mttt) cc_final: 0.8616 (pttm) REVERT: B 368 ASN cc_start: 0.8330 (m-40) cc_final: 0.8028 (m110) REVERT: B 372 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8331 (mp0) REVERT: B 379 ARG cc_start: 0.6818 (tmt170) cc_final: 0.5853 (pmt-80) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.1268 time to fit residues: 8.4608 Evaluate side-chains 50 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 285 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.0298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 HIS ** C 288 GLN ** 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 = 0.4548 r_free = 0.4548 target = 0.137846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.118764 restraints weight = 12594.093| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.83 r_work: 0.3994 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2472 Z= 0.089 Angle : 0.498 4.438 3303 Z= 0.262 Chirality : 0.050 0.132 372 Planarity : 0.003 0.026 423 Dihedral : 5.551 17.700 327 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.35 % Allowed : 9.93 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.002 0.001 TYR B 310 PHE 0.004 0.001 PHE C 378 HIS 0.009 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 2472) covalent geometry : angle 0.49841 / 0.26 ( 3303) hydrogen bonds : bond 0.01693 / 0.95 ( 32) hydrogen bonds : angle 4.18190 / 2.95 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.084 Fit side-chains REVERT: A 316 SER cc_start: 0.8094 (t) cc_final: 0.7372 (m) REVERT: A 359 ASN cc_start: 0.8257 (t0) cc_final: 0.7776 (m-40) REVERT: A 373 THR cc_start: 0.7453 (m) cc_final: 0.7249 (t) REVERT: B 314 ASP cc_start: 0.7752 (t0) cc_final: 0.7179 (m-30) REVERT: B 316 SER cc_start: 0.7788 (t) cc_final: 0.7450 (m) REVERT: B 331 LYS cc_start: 0.8934 (pttt) cc_final: 0.8640 (ptpt) REVERT: B 343 LYS cc_start: 0.9501 (mttt) cc_final: 0.8786 (pttm) REVERT: B 368 ASN cc_start: 0.8438 (m-40) cc_final: 0.8148 (m110) REVERT: B 372 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8322 (mp0) REVERT: B 379 ARG cc_start: 0.6793 (tmt170) cc_final: 0.5862 (pmt-80) outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.1114 time to fit residues: 7.3653 Evaluate side-chains 50 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 285 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 288 GLN ** 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 = 0.4539 r_free = 0.4539 target = 0.136745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.117465 restraints weight = 12795.496| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.93 r_work: 0.3987 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2472 Z= 0.105 Angle : 0.489 3.480 3303 Z= 0.261 Chirality : 0.049 0.130 372 Planarity : 0.003 0.029 423 Dihedral : 5.348 17.980 327 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.71 % Allowed : 10.99 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.36), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.28), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.003 0.001 TYR C 310 PHE 0.006 0.001 PHE C 378 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 2472) covalent geometry : angle 0.48931 / 0.26 ( 3303) hydrogen bonds : bond 0.01573 / 0.94 ( 32) hydrogen bonds : angle 4.24987 / 2.97 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8478 (p0) cc_final: 0.8082 (p0) REVERT: A 316 SER cc_start: 0.8102 (t) cc_final: 0.7380 (m) REVERT: A 359 ASN cc_start: 0.8191 (t0) cc_final: 0.7761 (m-40) REVERT: B 314 ASP cc_start: 0.7798 (t0) cc_final: 0.7258 (m-30) REVERT: B 316 SER cc_start: 0.7795 (t) cc_final: 0.7457 (m) REVERT: B 331 LYS cc_start: 0.8881 (pttt) cc_final: 0.8650 (ptpt) REVERT: B 342 GLU cc_start: 0.3589 (pm20) cc_final: 0.3371 (pm20) REVERT: B 368 ASN cc_start: 0.8431 (m-40) cc_final: 0.8119 (m110) REVERT: B 372 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8369 (mp0) REVERT: B 379 ARG cc_start: 0.6806 (tmt170) cc_final: 0.6074 (pmt-80) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.1052 time to fit residues: 7.2546 Evaluate side-chains 52 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.4323 r_free = 0.4323 target = 0.114523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.095219 restraints weight = 13124.420| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.99 r_work: 0.4090 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2472 Z= 0.154 Angle : 0.513 3.872 3303 Z= 0.275 Chirality : 0.050 0.133 372 Planarity : 0.003 0.029 423 Dihedral : 5.426 18.728 327 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.13 % Allowed : 10.99 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 349 TYR 0.005 0.001 TYR C 310 PHE 0.009 0.002 PHE B 378 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 2472) covalent geometry : angle 0.51304 / 0.28 ( 3303) hydrogen bonds : bond 0.02106 / 1.28 ( 32) hydrogen bonds : angle 4.27904 / 3.02 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 295 ASP cc_start: 0.8657 (p0) cc_final: 0.8424 (p0) REVERT: A 316 SER cc_start: 0.8369 (t) cc_final: 0.7756 (m) REVERT: A 359 ASN cc_start: 0.8428 (t0) cc_final: 0.8067 (m-40) REVERT: B 314 ASP cc_start: 0.8198 (t0) cc_final: 0.7592 (m-30) REVERT: B 316 SER cc_start: 0.8141 (t) cc_final: 0.7795 (m) REVERT: B 343 LYS cc_start: 0.9395 (mttt) cc_final: 0.8571 (pttm) REVERT: B 368 ASN cc_start: 0.8595 (m-40) cc_final: 0.8049 (m110) REVERT: B 372 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8465 (mp0) REVERT: B 379 ARG cc_start: 0.6907 (tmt170) cc_final: 0.6182 (pmt-80) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.1122 time to fit residues: 7.4775 Evaluate side-chains 54 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.4332 r_free = 0.4332 target = 0.115601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.096089 restraints weight = 12630.632| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.98 r_work: 0.4110 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2472 Z= 0.103 Angle : 0.489 3.648 3303 Z= 0.260 Chirality : 0.050 0.128 372 Planarity : 0.003 0.031 423 Dihedral : 5.182 17.596 327 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.71 % Allowed : 14.54 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.36), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.002 0.001 TYR C 310 PHE 0.005 0.001 PHE C 378 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 2472) covalent geometry : angle 0.48863 / 0.26 ( 3303) hydrogen bonds : bond 0.01677 / 1.01 ( 32) hydrogen bonds : angle 4.21237 / 2.99 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 316 SER cc_start: 0.8301 (t) cc_final: 0.7688 (m) REVERT: B 314 ASP cc_start: 0.8247 (t0) cc_final: 0.7555 (m-30) REVERT: B 316 SER cc_start: 0.8015 (t) cc_final: 0.7687 (m) REVERT: B 343 LYS cc_start: 0.9398 (mttt) cc_final: 0.8443 (pttm) REVERT: B 368 ASN cc_start: 0.8636 (m-40) cc_final: 0.8355 (m110) REVERT: B 372 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8429 (mp0) REVERT: B 379 ARG cc_start: 0.6921 (tmt170) cc_final: 0.6190 (pmt-80) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.1166 time to fit residues: 7.0781 Evaluate side-chains 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain C residue 285 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.4296 r_free = 0.4296 target = 0.113608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.094284 restraints weight = 12995.543| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 3.98 r_work: 0.3911 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2472 Z= 0.166 Angle : 0.526 3.901 3303 Z= 0.283 Chirality : 0.049 0.130 372 Planarity : 0.003 0.031 423 Dihedral : 5.322 18.691 327 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.77 % Allowed : 14.18 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 349 TYR 0.005 0.001 TYR C 310 PHE 0.010 0.002 PHE C 378 HIS 0.006 0.002 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 2472) covalent geometry : angle 0.52590 / 0.28 ( 3303) hydrogen bonds : bond 0.02240 / 1.40 ( 32) hydrogen bonds : angle 4.28945 / 3.05 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 285 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8090 (m) REVERT: A 316 SER cc_start: 0.8162 (t) cc_final: 0.7446 (m) REVERT: B 314 ASP cc_start: 0.7960 (t0) cc_final: 0.7314 (m-30) REVERT: B 316 SER cc_start: 0.7902 (t) cc_final: 0.7532 (m) REVERT: B 343 LYS cc_start: 0.9410 (mttt) cc_final: 0.8270 (pttm) REVERT: B 368 ASN cc_start: 0.8350 (m-40) cc_final: 0.7798 (m110) REVERT: B 372 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8455 (mp0) REVERT: B 379 ARG cc_start: 0.6828 (tmt170) cc_final: 0.6112 (pmt-80) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.1096 time to fit residues: 6.9501 Evaluate side-chains 53 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 285 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.4342 r_free = 0.4342 target = 0.116562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.096778 restraints weight = 12561.453| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 4.10 r_work: 0.4103 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2472 Z= 0.090 Angle : 0.485 3.892 3303 Z= 0.257 Chirality : 0.049 0.128 372 Planarity : 0.003 0.034 423 Dihedral : 4.990 16.774 327 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.71 % Allowed : 15.25 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.36), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.002 0.000 TYR A 310 PHE 0.005 0.001 PHE C 346 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 2472) covalent geometry : angle 0.48454 / 0.26 ( 3303) hydrogen bonds : bond 0.01598 / 0.95 ( 32) hydrogen bonds : angle 4.17356 / 2.94 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 SER cc_start: 0.8920 (p) cc_final: 0.8288 (m) REVERT: A 316 SER cc_start: 0.8291 (t) cc_final: 0.7716 (m) REVERT: B 314 ASP cc_start: 0.8325 (t0) cc_final: 0.7645 (m-30) REVERT: B 316 SER cc_start: 0.7982 (t) cc_final: 0.7679 (m) REVERT: B 343 LYS cc_start: 0.9341 (mttt) cc_final: 0.8420 (pttm) REVERT: B 379 ARG cc_start: 0.6947 (tmt170) cc_final: 0.6226 (pmt-80) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.1141 time to fit residues: 6.8024 Evaluate side-chains 48 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain C residue 285 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** C 288 GLN ** 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 = 0.4334 r_free = 0.4334 target = 0.116366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.096606 restraints weight = 12771.755| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 4.05 r_work: 0.3946 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2472 Z= 0.104 Angle : 0.487 3.979 3303 Z= 0.259 Chirality : 0.049 0.129 372 Planarity : 0.003 0.033 423 Dihedral : 4.953 16.929 327 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.06 % Allowed : 15.25 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.36), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.003 0.001 TYR C 310 PHE 0.006 0.001 PHE C 378 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 2472) covalent geometry : angle 0.48677 / 0.26 ( 3303) hydrogen bonds : bond 0.01662 / 1.04 ( 32) hydrogen bonds : angle 4.14315 / 2.92 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 SER cc_start: 0.8764 (p) cc_final: 0.8070 (m) REVERT: A 316 SER cc_start: 0.8193 (t) cc_final: 0.7554 (m) REVERT: B 314 ASP cc_start: 0.7947 (t0) cc_final: 0.7237 (m-30) REVERT: B 316 SER cc_start: 0.7713 (t) cc_final: 0.7392 (m) REVERT: B 343 LYS cc_start: 0.9402 (mttt) cc_final: 0.8250 (pttm) REVERT: B 379 ARG cc_start: 0.6808 (tmt170) cc_final: 0.6099 (pmt-80) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.1068 time to fit residues: 6.4510 Evaluate side-chains 50 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain C residue 285 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** C 288 GLN ** 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 = 0.4340 r_free = 0.4340 target = 0.116736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.096935 restraints weight = 12803.744| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 4.05 r_work: 0.3945 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2472 Z= 0.101 Angle : 0.487 3.986 3303 Z= 0.259 Chirality : 0.049 0.128 372 Planarity : 0.003 0.034 423 Dihedral : 4.891 16.762 327 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.71 % Allowed : 15.25 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.36), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.002 0.001 TYR C 310 PHE 0.006 0.001 PHE C 378 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 2472) covalent geometry : angle 0.48691 / 0.26 ( 3303) hydrogen bonds : bond 0.01669 / 1.02 ( 32) hydrogen bonds : angle 4.13061 / 2.90 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.09 seconds wall clock time: 31 minutes 19.71 seconds (1879.71 seconds total)