Starting phenix.real_space_refine on Tue Aug 4 12:05:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28lo_56599/08_2026/28lo_56599.cif Found real_map, /net/cci-nas-00/data/ceres_data/28lo_56599/08_2026/28lo_56599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28lo_56599/08_2026/28lo_56599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28lo_56599/08_2026/28lo_56599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28lo_56599/08_2026/28lo_56599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28lo_56599/08_2026/28lo_56599.map" } resolution = 2.1 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1392 2.51 5 N 414 2.21 5 O 414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 2223 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 741 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Restraints were copied for chains: B, C Time building chain proxies: 0.60, per 1000 atoms: 0.27 Number of scatterers: 2223 At special positions: 0 Unit cell: (133.176, 65.472, 34.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 414 8.00 N 414 7.00 C 1392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 75.9 milliseconds 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 90.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 253 through 260 removed outlier: 6.440A pdb=" N LEU A 253 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL B 256 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN A 255 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N SER B 258 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 257 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE B 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS A 259 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.771A pdb=" N THR A 263 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU C 266 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN A 265 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS C 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS A 267 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 273 through 310 removed outlier: 6.582A pdb=" N LYS A 274 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ILE B 308 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 7.144A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.468A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.571A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 336 through 354 removed outlier: 9.088A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N GLU B 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N SER A 341 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LEU B 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE B 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASP B 348 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS A 347 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL B 350 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG A 349 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N SER B 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL C 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU A 338 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS A 340 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER C 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU A 342 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS C 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 362 removed outlier: 8.638A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP A 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN C 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 378 removed outlier: 7.052A pdb=" N LYS B 370 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.25 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 535 1.34 - 1.46: 546 1.46 - 1.58: 1172 1.58 - 1.69: 0 1.69 - 1.81: 3 Bond restraints: 2256 Sorted by residual: bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.329 0.025 1.10e-02 8.26e+03 5.26e+00 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.329 0.025 1.10e-02 8.26e+03 5.21e+00 bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.329 0.025 1.10e-02 8.26e+03 5.12e+00 bond pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 1.331 1.358 -0.027 1.31e-02 5.83e+03 4.36e+00 bond pdb=" C LYS A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 1.331 1.358 -0.027 1.31e-02 5.83e+03 4.35e+00 ... (remaining 2251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 1940 1.21 - 2.42: 778 2.42 - 3.63: 173 3.63 - 4.84: 97 4.84 - 6.05: 27 Bond angle restraints: 3015 Sorted by residual: angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 118.83 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 118.82 -5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 118.81 -5.01 1.00e+00 1.00e+00 2.51e+01 angle pdb=" CA ASP C 314 " pdb=" CB ASP C 314 " pdb=" CG ASP C 314 " ideal model delta sigma weight residual 112.60 117.53 -4.93 1.00e+00 1.00e+00 2.43e+01 angle pdb=" CA ASP A 314 " pdb=" CB ASP A 314 " pdb=" CG ASP A 314 " ideal model delta sigma weight residual 112.60 117.51 -4.91 1.00e+00 1.00e+00 2.41e+01 ... (remaining 3010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.01: 1266 14.01 - 28.03: 99 28.03 - 42.04: 18 42.04 - 56.05: 3 56.05 - 70.06: 3 Dihedral angle restraints: 1389 sinusoidal: 588 harmonic: 801 Sorted by residual: dihedral pdb=" C GLN A 269 " pdb=" N GLN A 269 " pdb=" CA GLN A 269 " pdb=" CB GLN A 269 " ideal model delta harmonic sigma weight residual -122.60 -132.95 10.35 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" C GLN B 269 " pdb=" N GLN B 269 " pdb=" CA GLN B 269 " pdb=" CB GLN B 269 " ideal model delta harmonic sigma weight residual -122.60 -132.95 10.35 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" C GLN C 269 " pdb=" N GLN C 269 " pdb=" CA GLN C 269 " pdb=" CB GLN C 269 " ideal model delta harmonic sigma weight residual -122.60 -132.92 10.32 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 1386 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.078: 204 0.078 - 0.154: 93 0.154 - 0.231: 24 0.231 - 0.308: 12 0.308 - 0.385: 6 Chirality restraints: 339 Sorted by residual: chirality pdb=" CA GLN B 269 " pdb=" N GLN B 269 " pdb=" C GLN B 269 " pdb=" CB GLN B 269 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA GLN A 269 " pdb=" N GLN A 269 " pdb=" C GLN A 269 " pdb=" CB GLN A 269 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA GLN C 269 " pdb=" N GLN C 269 " pdb=" C GLN C 269 " pdb=" CB GLN C 269 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 336 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 347 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C LYS B 347 " -0.022 2.00e-02 2.50e+03 pdb=" O LYS B 347 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP B 348 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 347 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C LYS A 347 " -0.022 2.00e-02 2.50e+03 pdb=" O LYS A 347 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 348 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 347 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C LYS C 347 " -0.022 2.00e-02 2.50e+03 pdb=" O LYS C 347 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP C 348 " 0.007 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.02: 972 3.02 - 3.49: 1983 3.49 - 3.96: 3156 3.96 - 4.43: 3271 4.43 - 4.90: 6252 Nonbonded interactions: 15634 Sorted by model distance: nonbonded pdb=" OG1 THR A 263 " pdb=" OG SER A 352 " model vdw 2.545 3.040 nonbonded pdb=" OG1 THR C 263 " pdb=" OG SER C 352 " model vdw 2.545 3.040 nonbonded pdb=" OG1 THR B 263 " pdb=" OG SER B 352 " model vdw 2.545 3.040 nonbonded pdb=" OD1 ASP B 345 " pdb=" NZ LYS B 347 " model vdw 2.657 3.120 nonbonded pdb=" OD1 ASP A 345 " pdb=" NZ LYS A 347 " model vdw 2.657 3.120 ... (remaining 15629 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.600 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 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 0.045 2256 Z= 0.588 Angle : 1.528 6.048 3015 Z= 0.963 Chirality : 0.107 0.385 339 Planarity : 0.005 0.023 384 Dihedral : 10.902 70.063 879 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.53 % Allowed : 0.00 % Favored : 96.47 % Cbeta Deviations : 1.18 % 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: -2.45 (0.34), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.26), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG A 379 TYR 0.012 0.006 TYR B 310 PHE 0.019 0.003 PHE B 346 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00952 / 0.59 ( 2256) covalent geometry : angle 1.52821 / 0.96 ( 3015) hydrogen bonds : bond 0.15855 / 10.63 ( 47) hydrogen bonds : angle 7.01273 / 4.73 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.053 Fit side-chains REVERT: A 254 LYS cc_start: 0.7130 (ttpt) cc_final: 0.6489 (mttp) REVERT: A 321 LYS cc_start: 0.8385 (mttt) cc_final: 0.7911 (tttt) REVERT: B 254 LYS cc_start: 0.7238 (ttpt) cc_final: 0.6542 (mttp) REVERT: B 266 LEU cc_start: 0.8754 (mp) cc_final: 0.8537 (tt) REVERT: B 321 LYS cc_start: 0.8492 (mttt) cc_final: 0.8103 (tttt) REVERT: C 321 LYS cc_start: 0.8419 (mttt) cc_final: 0.7928 (tttt) REVERT: C 375 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7316 (mptt) outliers start: 9 outliers final: 3 residues processed: 94 average time/residue: 0.3993 time to fit residues: 38.2259 Evaluate side-chains 63 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 375 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 307 GLN C 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.149575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.132238 restraints weight = 2265.861| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.70 r_work: 0.4020 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2256 Z= 0.097 Angle : 0.598 4.336 3015 Z= 0.306 Chirality : 0.050 0.136 339 Planarity : 0.002 0.008 384 Dihedral : 8.110 53.827 307 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.92 % Allowed : 15.29 % Favored : 80.78 % 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: -2.06 (0.38), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.29), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.004 0.001 TYR C 310 PHE 0.011 0.002 PHE C 378 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 2256) covalent geometry : angle 0.59797 / 0.31 ( 3015) hydrogen bonds : bond 0.02483 / 1.80 ( 47) hydrogen bonds : angle 5.83903 / 4.00 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.094 Fit side-chains REVERT: A 254 LYS cc_start: 0.7036 (ttpt) cc_final: 0.6719 (mttp) REVERT: A 321 LYS cc_start: 0.8273 (mttt) cc_final: 0.7862 (tttt) REVERT: A 360 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8249 (mt) REVERT: B 254 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6957 (mttp) REVERT: B 321 LYS cc_start: 0.8528 (mttt) cc_final: 0.8152 (tttt) REVERT: C 321 LYS cc_start: 0.8353 (mttt) cc_final: 0.8044 (tttt) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.4213 time to fit residues: 32.3566 Evaluate side-chains 69 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.145581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.128228 restraints weight = 2207.363| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.72 r_work: 0.3966 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2256 Z= 0.210 Angle : 0.764 5.523 3015 Z= 0.402 Chirality : 0.058 0.157 339 Planarity : 0.003 0.012 384 Dihedral : 8.330 58.941 303 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.71 % Allowed : 11.76 % Favored : 83.53 % 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: -1.97 (0.39), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.007 0.002 TYR C 310 PHE 0.009 0.002 PHE C 378 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.21 ( 2256) covalent geometry : angle 0.76432 / 0.40 ( 3015) hydrogen bonds : bond 0.03723 / 2.69 ( 47) hydrogen bonds : angle 5.99702 / 4.09 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.091 Fit side-chains REVERT: A 321 LYS cc_start: 0.8391 (mttt) cc_final: 0.7891 (tttt) REVERT: B 266 LEU cc_start: 0.8696 (mp) cc_final: 0.8488 (tt) REVERT: B 321 LYS cc_start: 0.8580 (mttt) cc_final: 0.8250 (mtpm) REVERT: C 321 LYS cc_start: 0.8455 (mttt) cc_final: 0.8029 (tttt) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.4346 time to fit residues: 26.6759 Evaluate side-chains 61 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 374 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.146415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.129327 restraints weight = 2214.772| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.70 r_work: 0.3984 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2256 Z= 0.158 Angle : 0.693 5.206 3015 Z= 0.360 Chirality : 0.055 0.145 339 Planarity : 0.002 0.013 384 Dihedral : 8.229 58.230 303 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.10 % Allowed : 12.55 % Favored : 82.35 % 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: -1.91 (0.40), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.007 0.002 TYR C 310 PHE 0.005 0.001 PHE C 378 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 2256) covalent geometry : angle 0.69270 / 0.36 ( 3015) hydrogen bonds : bond 0.03154 / 2.30 ( 47) hydrogen bonds : angle 5.75694 / 3.94 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.072 Fit side-chains REVERT: A 321 LYS cc_start: 0.8369 (mttt) cc_final: 0.7865 (tttt) REVERT: B 321 LYS cc_start: 0.8545 (mttt) cc_final: 0.8194 (mtpm) REVERT: C 321 LYS cc_start: 0.8474 (mttt) cc_final: 0.8047 (tttt) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.4593 time to fit residues: 29.5724 Evaluate side-chains 63 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.0010 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.147879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.130940 restraints weight = 2176.378| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.67 r_work: 0.4009 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2256 Z= 0.112 Angle : 0.608 4.613 3015 Z= 0.315 Chirality : 0.052 0.142 339 Planarity : 0.002 0.013 384 Dihedral : 8.062 59.418 303 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.10 % Allowed : 11.76 % Favored : 83.14 % 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: -1.84 (0.41), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 349 TYR 0.006 0.002 TYR C 310 PHE 0.004 0.001 PHE A 378 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 2256) covalent geometry : angle 0.60761 / 0.31 ( 3015) hydrogen bonds : bond 0.02578 / 1.89 ( 47) hydrogen bonds : angle 5.48588 / 3.76 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.075 Fit side-chains REVERT: A 264 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: A 321 LYS cc_start: 0.8328 (mttt) cc_final: 0.7830 (tttt) REVERT: A 360 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8217 (mt) REVERT: B 321 LYS cc_start: 0.8459 (mttt) cc_final: 0.8107 (mtpm) REVERT: C 321 LYS cc_start: 0.8408 (mttt) cc_final: 0.8032 (tttt) outliers start: 13 outliers final: 7 residues processed: 62 average time/residue: 0.4970 time to fit residues: 31.4394 Evaluate side-chains 62 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS 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 = 0.148349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.131323 restraints weight = 2169.496| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.68 r_work: 0.4007 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2256 Z= 0.128 Angle : 0.630 4.865 3015 Z= 0.327 Chirality : 0.053 0.142 339 Planarity : 0.002 0.013 384 Dihedral : 8.063 59.746 303 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.71 % Allowed : 11.76 % Favored : 83.53 % 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: -1.85 (0.41), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 349 TYR 0.007 0.002 TYR C 310 PHE 0.004 0.001 PHE A 378 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 2256) covalent geometry : angle 0.62961 / 0.33 ( 3015) hydrogen bonds : bond 0.02707 / 1.99 ( 47) hydrogen bonds : angle 5.47094 / 3.75 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.057 Fit side-chains REVERT: A 264 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: A 321 LYS cc_start: 0.8349 (mttt) cc_final: 0.7848 (tttt) REVERT: A 360 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8197 (mt) REVERT: B 321 LYS cc_start: 0.8443 (mttt) cc_final: 0.8065 (mtpm) REVERT: C 321 LYS cc_start: 0.8446 (mttt) cc_final: 0.8038 (tttt) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.3265 time to fit residues: 20.6783 Evaluate side-chains 64 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.148582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.131446 restraints weight = 2209.864| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.68 r_work: 0.4018 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2256 Z= 0.112 Angle : 0.599 4.902 3015 Z= 0.310 Chirality : 0.051 0.141 339 Planarity : 0.002 0.010 384 Dihedral : 7.812 57.681 303 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.49 % Allowed : 11.76 % Favored : 82.75 % 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: -1.79 (0.42), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 349 TYR 0.006 0.002 TYR C 310 PHE 0.003 0.001 PHE A 378 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 ( 2256) covalent geometry : angle 0.59936 / 0.31 ( 3015) hydrogen bonds : bond 0.02497 / 1.81 ( 47) hydrogen bonds : angle 5.34299 / 3.66 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.097 Fit side-chains REVERT: A 264 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: A 321 LYS cc_start: 0.8308 (mttt) cc_final: 0.7793 (tttt) REVERT: A 360 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8306 (mt) REVERT: B 321 LYS cc_start: 0.8455 (mttt) cc_final: 0.8064 (mtpm) REVERT: C 321 LYS cc_start: 0.8416 (mttt) cc_final: 0.8027 (tttt) outliers start: 14 outliers final: 8 residues processed: 62 average time/residue: 0.3626 time to fit residues: 22.9799 Evaluate side-chains 62 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.147278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.130144 restraints weight = 2191.135| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.69 r_work: 0.4001 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2256 Z= 0.156 Angle : 0.681 7.730 3015 Z= 0.351 Chirality : 0.054 0.145 339 Planarity : 0.002 0.011 384 Dihedral : 8.042 58.004 303 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.49 % Allowed : 12.55 % Favored : 81.96 % 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: -1.83 (0.42), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.008 0.002 TYR C 310 PHE 0.003 0.001 PHE A 378 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 2256) covalent geometry : angle 0.68086 / 0.35 ( 3015) hydrogen bonds : bond 0.03026 / 2.16 ( 47) hydrogen bonds : angle 5.57671 / 3.82 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.095 Fit side-chains REVERT: A 264 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: A 321 LYS cc_start: 0.8324 (mttt) cc_final: 0.7946 (mtpm) REVERT: B 321 LYS cc_start: 0.8522 (mttt) cc_final: 0.8146 (mtpm) REVERT: C 321 LYS cc_start: 0.8450 (mttt) cc_final: 0.8013 (tttt) outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 0.4097 time to fit residues: 25.0910 Evaluate side-chains 62 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.0770 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.146701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.129649 restraints weight = 2230.851| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.72 r_work: 0.3994 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2256 Z= 0.169 Angle : 0.702 7.614 3015 Z= 0.362 Chirality : 0.055 0.146 339 Planarity : 0.002 0.018 384 Dihedral : 8.178 57.276 303 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.71 % Allowed : 13.73 % Favored : 81.57 % 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: -1.85 (0.41), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 379 TYR 0.008 0.002 TYR C 310 PHE 0.004 0.001 PHE A 378 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 2256) covalent geometry : angle 0.70205 / 0.36 ( 3015) hydrogen bonds : bond 0.03175 / 2.28 ( 47) hydrogen bonds : angle 5.63449 / 3.86 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.055 Fit side-chains REVERT: A 264 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: A 321 LYS cc_start: 0.8316 (mttt) cc_final: 0.7937 (mtpm) REVERT: B 321 LYS cc_start: 0.8520 (mttt) cc_final: 0.8143 (mtpm) REVERT: C 321 LYS cc_start: 0.8440 (mttt) cc_final: 0.8019 (tttt) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.3818 time to fit residues: 22.5785 Evaluate side-chains 62 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 374 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.146854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.130352 restraints weight = 2307.311| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.65 r_work: 0.4043 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2256 Z= 0.087 Angle : 0.571 8.005 3015 Z= 0.284 Chirality : 0.049 0.138 339 Planarity : 0.002 0.010 384 Dihedral : 7.504 57.065 303 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.92 % Allowed : 15.29 % Favored : 80.78 % 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: -1.76 (0.42), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.004 0.001 TYR C 310 PHE 0.004 0.001 PHE A 378 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 2256) covalent geometry : angle 0.57121 / 0.28 ( 3015) hydrogen bonds : bond 0.02057 / 1.48 ( 47) hydrogen bonds : angle 5.14197 / 3.55 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.104 Fit side-chains REVERT: A 264 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: A 321 LYS cc_start: 0.8225 (mttt) cc_final: 0.7876 (mtpm) REVERT: B 321 LYS cc_start: 0.8437 (mttt) cc_final: 0.8077 (mtpm) REVERT: C 321 LYS cc_start: 0.8497 (mttt) cc_final: 0.8093 (tttt) outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.3473 time to fit residues: 22.3672 Evaluate side-chains 59 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.146827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.130221 restraints weight = 2306.170| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.65 r_work: 0.4042 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2256 Z= 0.094 Angle : 0.604 7.971 3015 Z= 0.296 Chirality : 0.050 0.138 339 Planarity : 0.003 0.041 384 Dihedral : 6.790 58.759 301 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.75 % Allowed : 15.29 % Favored : 81.96 % 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: -1.74 (0.42), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 379 TYR 0.005 0.001 TYR C 310 PHE 0.004 0.001 PHE C 378 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.09 ( 2256) covalent geometry : angle 0.60372 / 0.30 ( 3015) hydrogen bonds : bond 0.02064 / 1.46 ( 47) hydrogen bonds : angle 5.05789 / 3.49 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1179.99 seconds wall clock time: 20 minutes 52.27 seconds (1252.27 seconds total)