Starting phenix.real_space_refine on Tue Feb 11 22:40:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozl_17313/02_2025/8ozl_17313.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozl_17313/02_2025/8ozl_17313.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozl_17313/02_2025/8ozl_17313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozl_17313/02_2025/8ozl_17313.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozl_17313/02_2025/8ozl_17313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozl_17313/02_2025/8ozl_17313.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 25 5.16 5 C 4220 2.51 5 N 1205 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6675 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1335 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Restraints were copied for chains: C, B, E, D Time building chain proxies: 3.25, per 1000 atoms: 0.49 Number of scatterers: 6675 At special positions: 0 Unit cell: (111.24, 110.16, 51.84, 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 25 16.00 O 1225 8.00 N 1205 7.00 C 4220 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: 1.44 Conformation dependent library (CDL) restraints added in 879.9 milliseconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.760A pdb=" N ILE A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 323 through 339 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 343 through 355 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.077A pdb=" N LEU A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 386 through 389 removed outlier: 3.566A pdb=" N HIS A 389 " --> pdb=" O PHE A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.541A pdb=" N ASP A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 418 through 430 removed outlier: 3.692A pdb=" N GLY A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.706A pdb=" N VAL A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.760A pdb=" N ILE B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 323 through 339 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 343 through 355 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.077A pdb=" N LEU B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 386 through 389 removed outlier: 3.566A pdb=" N HIS B 389 " --> pdb=" O PHE B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.542A pdb=" N ASP B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 Processing helix chain 'B' and resid 418 through 430 removed outlier: 3.691A pdb=" N GLY B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.706A pdb=" N VAL B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.760A pdb=" N ILE C 310 " --> pdb=" O PRO C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 322 No H-bonds generated for 'chain 'C' and resid 320 through 322' Processing helix chain 'C' and resid 323 through 339 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.078A pdb=" N LEU C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 386 through 389 removed outlier: 3.566A pdb=" N HIS C 389 " --> pdb=" O PHE C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 390 through 402 removed outlier: 3.541A pdb=" N ASP C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 Processing helix chain 'C' and resid 418 through 430 removed outlier: 3.692A pdb=" N GLY C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 446 removed outlier: 3.706A pdb=" N VAL C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.760A pdb=" N ILE D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 323 through 339 Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 343 through 355 Processing helix chain 'D' and resid 364 through 369 removed outlier: 4.078A pdb=" N LEU D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 383 Processing helix chain 'D' and resid 386 through 389 removed outlier: 3.566A pdb=" N HIS D 389 " --> pdb=" O PHE D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 389' Processing helix chain 'D' and resid 390 through 402 removed outlier: 3.542A pdb=" N ASP D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 418 through 430 removed outlier: 3.691A pdb=" N GLY D 428 " --> pdb=" O GLY D 424 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR D 429 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 446 removed outlier: 3.706A pdb=" N VAL D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.760A pdb=" N ILE E 310 " --> pdb=" O PRO E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 323 through 339 Proline residue: E 333 - end of helix Processing helix chain 'E' and resid 343 through 355 Processing helix chain 'E' and resid 364 through 369 removed outlier: 4.078A pdb=" N LEU E 369 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 386 through 389 removed outlier: 3.566A pdb=" N HIS E 389 " --> pdb=" O PHE E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 389' Processing helix chain 'E' and resid 390 through 402 removed outlier: 3.542A pdb=" N ASP E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 415 Processing helix chain 'E' and resid 418 through 430 removed outlier: 3.691A pdb=" N GLY E 428 " --> pdb=" O GLY E 424 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR E 429 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 446 removed outlier: 3.706A pdb=" N VAL E 436 " --> pdb=" O GLY E 432 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 455 Processing helix chain 'E' and resid 455 through 467 410 hydrogen bonds defined for protein. 1200 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: 1.53 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1366 1.33 - 1.45: 1444 1.45 - 1.57: 3955 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 6805 Sorted by residual: bond pdb=" C PRO B 317 " pdb=" O PRO B 317 " ideal model delta sigma weight residual 1.246 1.208 0.038 8.50e-03 1.38e+04 1.99e+01 bond pdb=" C PRO A 317 " pdb=" O PRO A 317 " ideal model delta sigma weight residual 1.246 1.208 0.037 8.50e-03 1.38e+04 1.94e+01 bond pdb=" C PRO E 317 " pdb=" O PRO E 317 " ideal model delta sigma weight residual 1.246 1.208 0.037 8.50e-03 1.38e+04 1.93e+01 bond pdb=" C PRO D 317 " pdb=" O PRO D 317 " ideal model delta sigma weight residual 1.246 1.208 0.037 8.50e-03 1.38e+04 1.91e+01 bond pdb=" C PRO C 317 " pdb=" O PRO C 317 " ideal model delta sigma weight residual 1.246 1.209 0.037 8.50e-03 1.38e+04 1.90e+01 ... (remaining 6800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 4806 1.03 - 2.05: 2739 2.05 - 3.08: 1355 3.08 - 4.11: 315 4.11 - 5.13: 65 Bond angle restraints: 9280 Sorted by residual: angle pdb=" C PRO A 431 " pdb=" CA PRO A 431 " pdb=" CB PRO A 431 " ideal model delta sigma weight residual 111.87 107.00 4.87 8.40e-01 1.42e+00 3.37e+01 angle pdb=" C PRO B 431 " pdb=" CA PRO B 431 " pdb=" CB PRO B 431 " ideal model delta sigma weight residual 111.87 107.00 4.87 8.40e-01 1.42e+00 3.36e+01 angle pdb=" C PRO D 431 " pdb=" CA PRO D 431 " pdb=" CB PRO D 431 " ideal model delta sigma weight residual 111.87 107.03 4.84 8.40e-01 1.42e+00 3.32e+01 angle pdb=" C PRO E 431 " pdb=" CA PRO E 431 " pdb=" CB PRO E 431 " ideal model delta sigma weight residual 111.87 107.03 4.84 8.40e-01 1.42e+00 3.32e+01 angle pdb=" C PRO C 431 " pdb=" CA PRO C 431 " pdb=" CB PRO C 431 " ideal model delta sigma weight residual 111.87 107.05 4.82 8.40e-01 1.42e+00 3.29e+01 ... (remaining 9275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.61: 3455 9.61 - 19.22: 396 19.22 - 28.83: 134 28.83 - 38.44: 55 38.44 - 48.05: 30 Dihedral angle restraints: 4070 sinusoidal: 1625 harmonic: 2445 Sorted by residual: dihedral pdb=" N GLN D 308 " pdb=" C GLN D 308 " pdb=" CA GLN D 308 " pdb=" CB GLN D 308 " ideal model delta harmonic sigma weight residual 122.80 130.47 -7.67 0 2.50e+00 1.60e-01 9.41e+00 dihedral pdb=" N GLN C 308 " pdb=" C GLN C 308 " pdb=" CA GLN C 308 " pdb=" CB GLN C 308 " ideal model delta harmonic sigma weight residual 122.80 130.47 -7.67 0 2.50e+00 1.60e-01 9.41e+00 dihedral pdb=" N GLN A 308 " pdb=" C GLN A 308 " pdb=" CA GLN A 308 " pdb=" CB GLN A 308 " ideal model delta harmonic sigma weight residual 122.80 130.47 -7.67 0 2.50e+00 1.60e-01 9.40e+00 ... (remaining 4067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 415 0.054 - 0.108: 326 0.108 - 0.162: 287 0.162 - 0.216: 40 0.216 - 0.270: 17 Chirality restraints: 1085 Sorted by residual: chirality pdb=" CA GLN D 308 " pdb=" N GLN D 308 " pdb=" C GLN D 308 " pdb=" CB GLN D 308 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA GLN B 308 " pdb=" N GLN B 308 " pdb=" C GLN B 308 " pdb=" CB GLN B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA GLN A 308 " pdb=" N GLN A 308 " pdb=" C GLN A 308 " pdb=" CB GLN A 308 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1082 not shown) Planarity restraints: 1220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 310 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C ILE C 310 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE C 310 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG C 311 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 310 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C ILE E 310 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE E 310 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG E 311 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 310 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C ILE A 310 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE A 310 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 311 " 0.007 2.00e-02 2.50e+03 ... (remaining 1217 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 3716 3.04 - 3.50: 6788 3.50 - 3.97: 10310 3.97 - 4.43: 10865 4.43 - 4.90: 19040 Nonbonded interactions: 50719 Sorted by model distance: nonbonded pdb=" O THR E 364 " pdb=" OD1 ASP E 367 " model vdw 2.574 3.040 nonbonded pdb=" O THR C 364 " pdb=" OD1 ASP C 367 " model vdw 2.574 3.040 nonbonded pdb=" O THR A 364 " pdb=" OD1 ASP A 367 " model vdw 2.574 3.040 nonbonded pdb=" O THR B 364 " pdb=" OD1 ASP B 367 " model vdw 2.574 3.040 nonbonded pdb=" O THR D 364 " pdb=" OD1 ASP D 367 " model vdw 2.575 3.040 ... (remaining 50714 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 15.970 Find NCS groups from input model: 0.120 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 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 : 0.012 0.042 6805 Z= 0.826 Angle : 1.519 5.132 9280 Z= 1.240 Chirality : 0.097 0.270 1085 Planarity : 0.005 0.019 1220 Dihedral : 10.880 48.048 2510 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.27), residues: 860 helix: 1.83 (0.19), residues: 610 sheet: None (None), residues: 0 loop : 1.07 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 327 HIS 0.005 0.002 HIS E 459 PHE 0.011 0.002 PHE D 456 TYR 0.008 0.002 TYR E 429 ARG 0.006 0.001 ARG E 477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.710 Fit side-chains REVERT: C 412 MET cc_start: 0.7114 (mtp) cc_final: 0.6796 (mmm) REVERT: D 412 MET cc_start: 0.7158 (mtp) cc_final: 0.6858 (mtp) REVERT: E 412 MET cc_start: 0.7100 (mtp) cc_final: 0.6823 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2848 time to fit residues: 29.5048 Evaluate side-chains 79 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 HIS A 474 GLN B 389 HIS B 474 GLN C 389 HIS C 474 GLN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 HIS D 474 GLN E 389 HIS E 474 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.107434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.097597 restraints weight = 7829.184| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.01 r_work: 0.2804 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6805 Z= 0.208 Angle : 0.547 4.948 9280 Z= 0.308 Chirality : 0.043 0.131 1085 Planarity : 0.005 0.031 1220 Dihedral : 3.795 10.717 945 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.42 % Allowed : 7.92 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 860 helix: 1.55 (0.19), residues: 620 sheet: None (None), residues: 0 loop : 1.02 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 327 HIS 0.001 0.000 HIS A 309 PHE 0.008 0.001 PHE A 379 TYR 0.009 0.001 TYR E 419 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.741 Fit side-chains REVERT: A 396 LYS cc_start: 0.8626 (tttt) cc_final: 0.8169 (tptt) REVERT: D 354 ILE cc_start: 0.8189 (mt) cc_final: 0.7936 (mm) outliers start: 3 outliers final: 2 residues processed: 99 average time/residue: 0.1879 time to fit residues: 25.0628 Evaluate side-chains 96 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 362 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 = 0.2953 r_free = 0.2953 target = 0.100799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.092794 restraints weight = 8279.899| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 0.85 r_work: 0.2729 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 6805 Z= 0.353 Angle : 0.579 5.216 9280 Z= 0.311 Chirality : 0.044 0.130 1085 Planarity : 0.004 0.033 1220 Dihedral : 3.879 11.928 945 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.11 % Allowed : 10.00 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.27), residues: 860 helix: 1.45 (0.20), residues: 620 sheet: None (None), residues: 0 loop : 0.73 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 327 HIS 0.003 0.001 HIS A 383 PHE 0.012 0.002 PHE A 456 TYR 0.011 0.002 TYR E 419 ARG 0.004 0.000 ARG E 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.788 Fit side-chains REVERT: A 396 LYS cc_start: 0.8748 (tttt) cc_final: 0.8405 (tptt) REVERT: E 319 ARG cc_start: 0.8594 (tpp-160) cc_final: 0.8264 (tpp-160) outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 0.2479 time to fit residues: 33.0788 Evaluate side-chains 106 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 323 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 = 0.3021 r_free = 0.3021 target = 0.105959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.098318 restraints weight = 8086.283| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 0.79 r_work: 0.2813 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6805 Z= 0.158 Angle : 0.460 4.902 9280 Z= 0.243 Chirality : 0.040 0.127 1085 Planarity : 0.004 0.031 1220 Dihedral : 3.660 13.185 945 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.97 % Allowed : 9.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.28), residues: 860 helix: 1.81 (0.20), residues: 615 sheet: None (None), residues: 0 loop : 0.82 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.000 HIS A 383 PHE 0.003 0.001 PHE A 379 TYR 0.007 0.001 TYR B 419 ARG 0.001 0.000 ARG E 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.745 Fit side-chains REVERT: A 396 LYS cc_start: 0.8703 (tttt) cc_final: 0.8374 (tptt) outliers start: 7 outliers final: 3 residues processed: 109 average time/residue: 0.2227 time to fit residues: 31.4184 Evaluate side-chains 104 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain E residue 388 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 GLN ** E 308 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 = 0.2971 r_free = 0.2971 target = 0.102448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.092371 restraints weight = 8202.476| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.06 r_work: 0.2735 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6805 Z= 0.208 Angle : 0.485 5.028 9280 Z= 0.253 Chirality : 0.040 0.127 1085 Planarity : 0.004 0.030 1220 Dihedral : 3.619 12.921 945 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.11 % Allowed : 10.00 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.28), residues: 860 helix: 1.78 (0.20), residues: 620 sheet: None (None), residues: 0 loop : 0.79 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.002 0.000 HIS D 383 PHE 0.006 0.001 PHE A 456 TYR 0.008 0.001 TYR E 419 ARG 0.001 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.771 Fit side-chains REVERT: A 396 LYS cc_start: 0.8697 (tttt) cc_final: 0.8282 (tptt) REVERT: E 319 ARG cc_start: 0.8529 (tpp-160) cc_final: 0.8175 (tpp-160) REVERT: E 445 GLN cc_start: 0.8157 (mt0) cc_final: 0.7957 (mt0) outliers start: 8 outliers final: 6 residues processed: 100 average time/residue: 0.2279 time to fit residues: 29.3995 Evaluate side-chains 102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 323 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 = 0.2984 r_free = 0.2984 target = 0.103513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.093720 restraints weight = 8212.116| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.02 r_work: 0.2771 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6805 Z= 0.179 Angle : 0.462 4.952 9280 Z= 0.240 Chirality : 0.040 0.126 1085 Planarity : 0.004 0.028 1220 Dihedral : 3.558 13.169 945 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.11 % Allowed : 10.28 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.28), residues: 860 helix: 1.87 (0.20), residues: 620 sheet: None (None), residues: 0 loop : 0.76 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.000 HIS D 383 PHE 0.003 0.001 PHE D 456 TYR 0.008 0.001 TYR E 419 ARG 0.001 0.000 ARG E 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.666 Fit side-chains REVERT: A 396 LYS cc_start: 0.8666 (tttt) cc_final: 0.8257 (tptt) REVERT: E 319 ARG cc_start: 0.8708 (tpp-160) cc_final: 0.8330 (tpp-160) outliers start: 8 outliers final: 7 residues processed: 96 average time/residue: 0.2063 time to fit residues: 25.9006 Evaluate side-chains 99 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 388 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.0020 chunk 18 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 = 0.2992 r_free = 0.2992 target = 0.104119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.094530 restraints weight = 8175.526| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.00 r_work: 0.2767 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6805 Z= 0.167 Angle : 0.453 4.949 9280 Z= 0.234 Chirality : 0.039 0.126 1085 Planarity : 0.003 0.028 1220 Dihedral : 3.477 13.082 945 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.11 % Allowed : 10.56 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.28), residues: 860 helix: 1.95 (0.20), residues: 620 sheet: None (None), residues: 0 loop : 0.82 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.000 HIS D 383 PHE 0.004 0.001 PHE D 456 TYR 0.008 0.001 TYR E 419 ARG 0.001 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.754 Fit side-chains REVERT: A 396 LYS cc_start: 0.8669 (tttt) cc_final: 0.8212 (tptt) REVERT: E 319 ARG cc_start: 0.8625 (tpp-160) cc_final: 0.8262 (tpp-160) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.2280 time to fit residues: 29.2003 Evaluate side-chains 102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 388 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 = 0.2996 r_free = 0.2996 target = 0.104158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.094490 restraints weight = 8245.315| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.00 r_work: 0.2756 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6805 Z= 0.184 Angle : 0.461 4.973 9280 Z= 0.237 Chirality : 0.039 0.126 1085 Planarity : 0.003 0.027 1220 Dihedral : 3.479 13.022 945 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.11 % Allowed : 10.56 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.28), residues: 860 helix: 1.96 (0.21), residues: 620 sheet: None (None), residues: 0 loop : 0.75 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.000 HIS D 383 PHE 0.004 0.001 PHE D 456 TYR 0.008 0.001 TYR E 419 ARG 0.001 0.000 ARG C 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.713 Fit side-chains REVERT: A 396 LYS cc_start: 0.8672 (tttt) cc_final: 0.8190 (tptt) REVERT: E 319 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8212 (tpp-160) outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.2114 time to fit residues: 26.1665 Evaluate side-chains 99 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 388 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 = 0.2998 r_free = 0.2998 target = 0.104500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.094661 restraints weight = 8234.950| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.02 r_work: 0.2775 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6805 Z= 0.165 Angle : 0.449 4.954 9280 Z= 0.230 Chirality : 0.039 0.126 1085 Planarity : 0.003 0.027 1220 Dihedral : 3.437 13.174 945 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.97 % Allowed : 10.83 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.28), residues: 860 helix: 2.00 (0.21), residues: 620 sheet: None (None), residues: 0 loop : 0.76 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.000 HIS D 383 PHE 0.003 0.001 PHE D 456 TYR 0.008 0.001 TYR E 419 ARG 0.001 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.778 Fit side-chains REVERT: A 396 LYS cc_start: 0.8691 (tttt) cc_final: 0.8246 (tptt) REVERT: E 319 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.8290 (tpp-160) outliers start: 7 outliers final: 7 residues processed: 97 average time/residue: 0.2164 time to fit residues: 27.2691 Evaluate side-chains 100 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 388 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 = 0.2999 r_free = 0.2999 target = 0.104516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.094649 restraints weight = 8285.805| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.03 r_work: 0.2765 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6805 Z= 0.162 Angle : 0.449 4.950 9280 Z= 0.230 Chirality : 0.039 0.125 1085 Planarity : 0.003 0.027 1220 Dihedral : 3.400 13.062 945 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.97 % Allowed : 11.11 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.28), residues: 860 helix: 2.05 (0.21), residues: 620 sheet: None (None), residues: 0 loop : 0.79 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.000 HIS D 383 PHE 0.003 0.001 PHE D 456 TYR 0.008 0.001 TYR B 419 ARG 0.001 0.000 ARG C 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.742 Fit side-chains REVERT: A 396 LYS cc_start: 0.8682 (tttt) cc_final: 0.8232 (tptt) REVERT: D 396 LYS cc_start: 0.8609 (tttt) cc_final: 0.8073 (tptt) REVERT: E 319 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8216 (tpp-160) outliers start: 7 outliers final: 7 residues processed: 95 average time/residue: 0.2387 time to fit residues: 29.0317 Evaluate side-chains 99 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 388 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 = 0.2994 r_free = 0.2994 target = 0.104069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.094391 restraints weight = 8275.918| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.01 r_work: 0.2760 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6805 Z= 0.170 Angle : 0.451 4.963 9280 Z= 0.231 Chirality : 0.039 0.126 1085 Planarity : 0.003 0.027 1220 Dihedral : 3.413 13.011 945 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.97 % Allowed : 10.97 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.28), residues: 860 helix: 2.05 (0.21), residues: 620 sheet: None (None), residues: 0 loop : 0.73 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.000 HIS D 383 PHE 0.004 0.001 PHE D 456 TYR 0.008 0.001 TYR E 419 ARG 0.001 0.000 ARG E 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2842.21 seconds wall clock time: 51 minutes 21.88 seconds (3081.88 seconds total)