Starting phenix.real_space_refine on Thu Nov 14 16:24:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozl_17313/11_2024/8ozl_17313.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozl_17313/11_2024/8ozl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozl_17313/11_2024/8ozl_17313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozl_17313/11_2024/8ozl_17313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozl_17313/11_2024/8ozl_17313.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozl_17313/11_2024/8ozl_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-5513/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: 3.41, per 1000 atoms: 0.51 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: 1.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.75 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: 1.59 Time building geometry restraints manager: 1.84 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.180 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- 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 : 0.789 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: 0.2860 time to fit residues: 29.9696 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 : 0.784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 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 : 0.846 Fit side-chains REVERT: A 396 LYS cc_start: 0.6661 (tttt) cc_final: 0.6411 (tptt) outliers start: 3 outliers final: 2 residues processed: 99 average time/residue: 0.1823 time to fit residues: 24.6255 Evaluate side-chains 95 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 42 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6805 Z= 0.265 Angle : 0.536 5.080 9280 Z= 0.286 Chirality : 0.043 0.131 1085 Planarity : 0.004 0.032 1220 Dihedral : 3.777 12.142 945 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.25 % Allowed : 9.58 % Favored : 89.17 % 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: 2.00 (0.27), residues: 860 helix: 1.58 (0.20), residues: 620 sheet: None (None), residues: 0 loop : 0.89 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 327 HIS 0.002 0.001 HIS A 383 PHE 0.009 0.001 PHE A 456 TYR 0.010 0.001 TYR E 419 ARG 0.003 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 111 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.769 Fit side-chains REVERT: A 396 LYS cc_start: 0.6724 (tttt) cc_final: 0.6454 (tptt) outliers start: 9 outliers final: 6 residues processed: 107 average time/residue: 0.2475 time to fit residues: 33.3056 Evaluate side-chains 105 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 E residue 323 GLU Chi-restraints excluded: chain E residue 388 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6805 Z= 0.138 Angle : 0.446 4.892 9280 Z= 0.233 Chirality : 0.039 0.127 1085 Planarity : 0.004 0.030 1220 Dihedral : 3.588 12.398 945 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.83 % Allowed : 9.58 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.28), residues: 860 helix: 1.89 (0.20), residues: 620 sheet: None (None), residues: 0 loop : 1.14 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 327 HIS 0.001 0.000 HIS E 383 PHE 0.003 0.001 PHE A 379 TYR 0.006 0.001 TYR E 419 ARG 0.002 0.000 ARG A 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 112 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.740 Fit side-chains REVERT: A 396 LYS cc_start: 0.6766 (tttt) cc_final: 0.6464 (tptt) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.2235 time to fit residues: 30.9726 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 : 0.817 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6805 Z= 0.162 Angle : 0.453 4.951 9280 Z= 0.234 Chirality : 0.039 0.127 1085 Planarity : 0.003 0.029 1220 Dihedral : 3.463 12.204 945 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.83 % Allowed : 10.28 % 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: 2.51 (0.28), residues: 860 helix: 1.97 (0.20), residues: 620 sheet: None (None), residues: 0 loop : 1.04 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.001 0.000 HIS A 383 PHE 0.004 0.001 PHE A 456 TYR 0.007 0.001 TYR E 419 ARG 0.002 0.000 ARG C 319 *********************** 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: 6 poor density : 99 time to evaluate : 0.737 Fit side-chains REVERT: A 396 LYS cc_start: 0.6761 (tttt) cc_final: 0.6463 (tptt) outliers start: 6 outliers final: 6 residues processed: 101 average time/residue: 0.2040 time to fit residues: 27.0419 Evaluate side-chains 103 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 E residue 323 GLU Chi-restraints excluded: chain E residue 388 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6805 Z= 0.162 Angle : 0.448 4.934 9280 Z= 0.231 Chirality : 0.039 0.126 1085 Planarity : 0.003 0.028 1220 Dihedral : 3.430 12.137 945 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.83 % Allowed : 10.42 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.28), residues: 860 helix: 1.98 (0.20), residues: 620 sheet: None (None), residues: 0 loop : 0.87 (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 A 456 TYR 0.007 0.001 TYR E 419 ARG 0.001 0.000 ARG A 381 *********************** 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 102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.678 Fit side-chains REVERT: A 396 LYS cc_start: 0.6715 (tttt) cc_final: 0.6392 (tptt) outliers start: 6 outliers final: 6 residues processed: 98 average time/residue: 0.2309 time to fit residues: 29.3904 Evaluate side-chains 101 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 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 0.022 6805 Z= 0.145 Angle : 0.436 4.905 9280 Z= 0.224 Chirality : 0.039 0.127 1085 Planarity : 0.003 0.027 1220 Dihedral : 3.360 12.195 945 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.97 % Allowed : 10.00 % Favored : 89.03 % 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: 1.98 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.99 (0.41), residues: 235 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 0.006 0.001 TYR E 419 ARG 0.001 0.000 ARG D 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 102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.833 Fit side-chains REVERT: A 396 LYS cc_start: 0.6407 (tttt) cc_final: 0.6089 (tptt) REVERT: D 396 LYS cc_start: 0.6454 (tttt) cc_final: 0.6173 (tptt) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.2159 time to fit residues: 27.3377 Evaluate side-chains 100 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6805 Z= 0.148 Angle : 0.438 4.921 9280 Z= 0.223 Chirality : 0.039 0.126 1085 Planarity : 0.003 0.026 1220 Dihedral : 3.323 12.048 945 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.97 % Allowed : 10.56 % Favored : 88.47 % 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: 2.54 (0.28), residues: 860 helix: 2.02 (0.21), residues: 625 sheet: None (None), residues: 0 loop : 0.96 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.001 0.000 HIS D 383 PHE 0.003 0.001 PHE D 456 TYR 0.007 0.001 TYR B 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: 7 poor density : 93 time to evaluate : 0.772 Fit side-chains REVERT: A 396 LYS cc_start: 0.6537 (tttt) cc_final: 0.6224 (tptt) REVERT: D 396 LYS cc_start: 0.6452 (tttt) cc_final: 0.6171 (tptt) outliers start: 7 outliers final: 7 residues processed: 95 average time/residue: 0.2105 time to fit residues: 26.2091 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 : 0.738 ------------------------------------------------------------------------------- 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 C residue 472 ARG 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 71 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6805 Z= 0.146 Angle : 0.435 4.915 9280 Z= 0.222 Chirality : 0.038 0.126 1085 Planarity : 0.003 0.026 1220 Dihedral : 3.308 12.067 945 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.83 % Allowed : 10.97 % 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: 2.58 (0.28), residues: 860 helix: 2.04 (0.21), residues: 625 sheet: None (None), residues: 0 loop : 0.98 (0.41), residues: 235 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 0.007 0.001 TYR E 419 ARG 0.001 0.000 ARG D 311 *********************** 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 98 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.771 Fit side-chains REVERT: A 396 LYS cc_start: 0.6400 (tttt) cc_final: 0.6081 (tptt) REVERT: D 396 LYS cc_start: 0.6450 (tttt) cc_final: 0.6168 (tptt) outliers start: 6 outliers final: 6 residues processed: 94 average time/residue: 0.2080 time to fit residues: 25.5838 Evaluate side-chains 98 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 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 C residue 323 GLU Chi-restraints excluded: chain C residue 388 MET 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 49 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6805 Z= 0.141 Angle : 0.431 4.901 9280 Z= 0.219 Chirality : 0.038 0.126 1085 Planarity : 0.003 0.025 1220 Dihedral : 3.275 12.035 945 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 2.64 (0.28), residues: 860 helix: 2.08 (0.21), residues: 625 sheet: None (None), residues: 0 loop : 1.02 (0.41), residues: 235 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 0.007 0.001 TYR B 419 ARG 0.001 0.000 ARG D 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 100 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.654 Fit side-chains REVERT: A 396 LYS cc_start: 0.6534 (tttt) cc_final: 0.6217 (tptt) REVERT: D 396 LYS cc_start: 0.6501 (tttt) cc_final: 0.6213 (tptt) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2280 time to fit residues: 28.1115 Evaluate side-chains 98 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 388 MET 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 20 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.0000 chunk 67 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.0070 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.7406 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.105177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.095405 restraints weight = 8073.541| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.01 r_work: 0.2783 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6805 Z= 0.162 Angle : 0.443 4.937 9280 Z= 0.226 Chirality : 0.039 0.126 1085 Planarity : 0.003 0.026 1220 Dihedral : 3.308 11.879 945 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.83 % Allowed : 10.97 % 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: 2.57 (0.28), residues: 860 helix: 2.04 (0.21), residues: 625 sheet: None (None), residues: 0 loop : 0.95 (0.41), residues: 235 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 B 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1634.55 seconds wall clock time: 30 minutes 14.85 seconds (1814.85 seconds total)