Starting phenix.real_space_refine on Thu Jul 2 04:46:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tew_25853/07_2026/7tew_25853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tew_25853/07_2026/7tew_25853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tew_25853/07_2026/7tew_25853.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tew_25853/07_2026/7tew_25853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tew_25853/07_2026/7tew_25853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tew_25853/07_2026/7tew_25853.map" model { file = "/net/cci-nas-00/data/ceres_data/7tew_25853/07_2026/7tew_25853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tew_25853/07_2026/7tew_25853.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.013 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 37 5.16 5 C 4188 2.51 5 N 1082 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6555 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.38, per 1000 atoms: 0.21 Number of scatterers: 6555 At special positions: 0 Unit cell: (80, 86, 122, 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 37 16.00 O 1248 8.00 N 1082 7.00 C 4188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 372.6 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.752A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.114A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.753A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.041A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 4.045A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.697A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.928A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.811A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.521A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.689A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.289A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.511A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.328A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.648A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.614A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.896A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.002A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.774A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.158A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.347A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 915 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: 1.04 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2087 1.35 - 1.47: 1795 1.47 - 1.60: 2797 1.60 - 1.73: 0 1.73 - 1.85: 58 Bond restraints: 6737 Sorted by residual: bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.22e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.15e+00 ... (remaining 6732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8757 1.91 - 3.82: 350 3.82 - 5.73: 34 5.73 - 7.63: 8 7.63 - 9.54: 4 Bond angle restraints: 9153 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.24 -5.88 1.42e+00 4.96e-01 1.71e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 122.95 -8.55 2.30e+00 1.89e-01 1.38e+01 angle pdb=" C HIS E 34 " pdb=" N GLU E 35 " pdb=" CA GLU E 35 " ideal model delta sigma weight residual 122.38 115.72 6.66 1.81e+00 3.05e-01 1.35e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.25 -3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA LYS E 31 " pdb=" CB LYS E 31 " pdb=" CG LYS E 31 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 ... (remaining 9148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 3554 16.87 - 33.74: 302 33.74 - 50.61: 46 50.61 - 67.47: 10 67.47 - 84.34: 12 Dihedral angle restraints: 3924 sinusoidal: 1586 harmonic: 2338 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -47.25 -38.75 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 14.06 64.94 1 2.00e+01 2.50e-03 1.38e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.88 8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 3921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 729 0.056 - 0.111: 186 0.111 - 0.166: 51 0.166 - 0.222: 8 0.222 - 0.277: 2 Chirality restraints: 976 Sorted by residual: chirality pdb=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 103 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 973 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO E 590 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.048 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO E 500 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.021 2.00e-02 2.50e+03 1.86e-02 6.95e+00 pdb=" CG TYR B 495 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.003 2.00e-02 2.50e+03 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 2224 2.86 - 3.37: 5996 3.37 - 3.88: 11266 3.88 - 4.39: 12492 4.39 - 4.90: 21655 Nonbonded interactions: 53633 Sorted by model distance: nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.344 3.120 nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.346 3.040 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.365 3.040 nonbonded pdb=" O SER E 47 " pdb=" ND2 ASN E 51 " model vdw 2.374 3.120 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.387 3.120 ... (remaining 53628 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 6.700 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.005 0.064 6750 Z= 0.234 Angle : 0.878 11.268 9186 Z= 0.493 Chirality : 0.057 0.277 976 Planarity : 0.008 0.078 1178 Dihedral : 13.324 84.341 2406 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.25), residues: 793 helix: 0.53 (0.22), residues: 392 sheet: 0.98 (0.72), residues: 43 loop : -0.64 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 460 TYR 0.045 0.003 TYR B 495 PHE 0.027 0.003 PHE E 369 TRP 0.020 0.002 TRP E 69 HIS 0.011 0.002 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 ( 6737) covalent geometry : angle 0.85235 / 0.49 ( 9153) SS BOND : bond 0.00530 / 0.32 ( 6) SS BOND : angle 2.60855 / 1.46 ( 12) hydrogen bonds : bond 0.14790 / 10.16 ( 322) hydrogen bonds : angle 6.02989 / 4.17 ( 915) link_NAG-ASN : bond 0.00675 / 0.31 ( 7) link_NAG-ASN : angle 4.09989 / 3.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8482 (ttpt) REVERT: B 424 LYS cc_start: 0.8692 (tptt) cc_final: 0.8170 (tppt) REVERT: B 448 ASN cc_start: 0.9203 (t0) cc_final: 0.8699 (t0) REVERT: B 458 LYS cc_start: 0.9307 (mtmt) cc_final: 0.9071 (mtmm) REVERT: B 467 ASP cc_start: 0.8431 (t0) cc_final: 0.8106 (t0) REVERT: B 473 TYR cc_start: 0.9316 (t80) cc_final: 0.9062 (t80) REVERT: B 474 GLN cc_start: 0.8885 (tt0) cc_final: 0.8616 (tt0) REVERT: E 108 LEU cc_start: 0.8613 (tp) cc_final: 0.8360 (tp) REVERT: E 249 MET cc_start: 0.8484 (ttm) cc_final: 0.8082 (mtp) REVERT: E 297 MET cc_start: 0.9202 (mtm) cc_final: 0.8995 (mtm) REVERT: E 302 TRP cc_start: 0.8366 (m-10) cc_final: 0.7320 (m100) REVERT: E 498 CYS cc_start: 0.8204 (t) cc_final: 0.7637 (t) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.0979 time to fit residues: 16.5027 Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.052794 restraints weight = 26597.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054884 restraints weight = 13056.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056268 restraints weight = 8261.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057197 restraints weight = 6056.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057774 restraints weight = 4876.905| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6750 Z= 0.138 Angle : 0.576 6.401 9186 Z= 0.298 Chirality : 0.041 0.141 976 Planarity : 0.005 0.049 1178 Dihedral : 4.058 15.151 866 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.71 % Allowed : 8.43 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.28), residues: 793 helix: 1.44 (0.25), residues: 406 sheet: 1.12 (0.76), residues: 42 loop : -0.13 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.013 0.001 TYR B 453 PHE 0.015 0.001 PHE E 428 TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 6737) covalent geometry : angle 0.55968 / 0.29 ( 9153) SS BOND : bond 0.00387 / 0.23 ( 6) SS BOND : angle 1.87509 / 1.06 ( 12) hydrogen bonds : bond 0.04286 / 2.81 ( 322) hydrogen bonds : angle 4.58255 / 3.17 ( 915) link_NAG-ASN : bond 0.00346 / 0.17 ( 7) link_NAG-ASN : angle 2.54851 / 2.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.8709 (tptt) cc_final: 0.8318 (tppt) REVERT: B 448 ASN cc_start: 0.9181 (t0) cc_final: 0.8802 (t0) REVERT: B 458 LYS cc_start: 0.9298 (mtmt) cc_final: 0.9064 (mtmm) REVERT: B 467 ASP cc_start: 0.8208 (t0) cc_final: 0.7906 (t0) REVERT: E 108 LEU cc_start: 0.8518 (tp) cc_final: 0.8143 (tp) REVERT: E 190 MET cc_start: 0.9005 (tmm) cc_final: 0.8747 (tmm) REVERT: E 232 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8808 (mp0) REVERT: E 302 TRP cc_start: 0.8429 (m-10) cc_final: 0.7631 (m100) REVERT: E 366 MET cc_start: 0.8957 (mtp) cc_final: 0.8677 (mtm) REVERT: E 498 CYS cc_start: 0.8445 (t) cc_final: 0.8085 (t) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 0.0853 time to fit residues: 9.2201 Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 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 = 0.3212 r_free = 0.3212 target = 0.062862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.049510 restraints weight = 26661.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051464 restraints weight = 13259.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052723 restraints weight = 8517.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.053545 restraints weight = 6338.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054144 restraints weight = 5200.063| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6750 Z= 0.182 Angle : 0.573 8.498 9186 Z= 0.293 Chirality : 0.041 0.149 976 Planarity : 0.004 0.047 1178 Dihedral : 4.118 16.269 866 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.86 % Allowed : 9.00 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.29), residues: 793 helix: 1.63 (0.26), residues: 412 sheet: 0.46 (0.67), residues: 51 loop : 0.22 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.020 0.001 TYR E 613 PHE 0.016 0.002 PHE E 369 TRP 0.015 0.002 TRP E 165 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 6737) covalent geometry : angle 0.56284 / 0.29 ( 9153) SS BOND : bond 0.00494 / 0.30 ( 6) SS BOND : angle 1.78969 / 1.04 ( 12) hydrogen bonds : bond 0.04105 / 2.68 ( 322) hydrogen bonds : angle 4.51549 / 3.13 ( 915) link_NAG-ASN : bond 0.00298 / 0.15 ( 7) link_NAG-ASN : angle 1.97909 / 1.57 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9300 (mt0) cc_final: 0.8916 (tt0) REVERT: B 448 ASN cc_start: 0.9237 (t0) cc_final: 0.8822 (t0) REVERT: B 467 ASP cc_start: 0.8259 (t0) cc_final: 0.7973 (t0) REVERT: E 62 MET cc_start: 0.9518 (ttp) cc_final: 0.9236 (mtm) REVERT: E 142 LEU cc_start: 0.8054 (tp) cc_final: 0.7851 (tp) REVERT: E 366 MET cc_start: 0.8998 (mtp) cc_final: 0.8680 (mtm) REVERT: E 435 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8780 (mp0) REVERT: E 498 CYS cc_start: 0.8826 (t) cc_final: 0.8472 (t) outliers start: 13 outliers final: 9 residues processed: 68 average time/residue: 0.0657 time to fit residues: 6.3118 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.048058 restraints weight = 27163.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.049985 restraints weight = 13642.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051244 restraints weight = 8783.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.052050 restraints weight = 6530.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052651 restraints weight = 5370.714| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6750 Z= 0.206 Angle : 0.570 5.899 9186 Z= 0.292 Chirality : 0.041 0.147 976 Planarity : 0.004 0.045 1178 Dihedral : 4.179 16.729 866 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.29 % Allowed : 10.29 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.30), residues: 793 helix: 1.62 (0.26), residues: 416 sheet: 0.31 (0.67), residues: 51 loop : 0.26 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 403 TYR 0.016 0.001 TYR B 453 PHE 0.016 0.002 PHE E 369 TRP 0.016 0.002 TRP E 165 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 ( 6737) covalent geometry : angle 0.56095 / 0.29 ( 9153) SS BOND : bond 0.00499 / 0.30 ( 6) SS BOND : angle 1.66723 / 0.98 ( 12) hydrogen bonds : bond 0.04100 / 2.65 ( 322) hydrogen bonds : angle 4.48208 / 3.12 ( 915) link_NAG-ASN : bond 0.00311 / 0.16 ( 7) link_NAG-ASN : angle 1.77882 / 1.41 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9275 (mt0) cc_final: 0.8961 (mt0) REVERT: B 448 ASN cc_start: 0.9247 (t0) cc_final: 0.8826 (t0) REVERT: B 467 ASP cc_start: 0.8171 (t0) cc_final: 0.7848 (t0) REVERT: E 208 GLU cc_start: 0.8762 (tt0) cc_final: 0.8449 (tm-30) REVERT: E 277 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8513 (t0) REVERT: E 366 MET cc_start: 0.9002 (mtp) cc_final: 0.8685 (mtp) REVERT: E 435 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: E 498 CYS cc_start: 0.9124 (t) cc_final: 0.8849 (t) outliers start: 16 outliers final: 10 residues processed: 64 average time/residue: 0.0725 time to fit residues: 6.4490 Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048398 restraints weight = 27594.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050348 restraints weight = 13417.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.051606 restraints weight = 8532.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052477 restraints weight = 6296.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053016 restraints weight = 5112.257| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6750 Z= 0.163 Angle : 0.536 5.706 9186 Z= 0.275 Chirality : 0.041 0.143 976 Planarity : 0.004 0.043 1178 Dihedral : 4.074 16.364 866 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.43 % Allowed : 11.00 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.30), residues: 793 helix: 1.62 (0.26), residues: 415 sheet: 0.27 (0.68), residues: 51 loop : 0.25 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.013 0.001 TYR B 453 PHE 0.015 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 6737) covalent geometry : angle 0.52860 / 0.27 ( 9153) SS BOND : bond 0.00423 / 0.26 ( 6) SS BOND : angle 1.53685 / 0.90 ( 12) hydrogen bonds : bond 0.03917 / 2.53 ( 322) hydrogen bonds : angle 4.41552 / 3.08 ( 915) link_NAG-ASN : bond 0.00272 / 0.14 ( 7) link_NAG-ASN : angle 1.63038 / 1.29 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9301 (mt0) cc_final: 0.8979 (mt0) REVERT: B 424 LYS cc_start: 0.8844 (tptt) cc_final: 0.8421 (tppt) REVERT: B 448 ASN cc_start: 0.9214 (t0) cc_final: 0.8812 (t0) REVERT: B 467 ASP cc_start: 0.8096 (t0) cc_final: 0.7745 (t0) REVERT: E 22 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8592 (mm-30) REVERT: E 62 MET cc_start: 0.9505 (ttp) cc_final: 0.9238 (mtm) REVERT: E 190 MET cc_start: 0.9282 (ppp) cc_final: 0.8996 (ppp) REVERT: E 208 GLU cc_start: 0.8779 (tt0) cc_final: 0.8513 (tm-30) REVERT: E 277 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8655 (t0) REVERT: E 366 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8715 (mtp) REVERT: E 435 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: E 498 CYS cc_start: 0.9130 (t) cc_final: 0.8717 (t) outliers start: 17 outliers final: 10 residues processed: 64 average time/residue: 0.0825 time to fit residues: 7.2863 Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.047959 restraints weight = 27568.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.049894 restraints weight = 13365.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.051147 restraints weight = 8473.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051980 restraints weight = 6260.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052391 restraints weight = 5087.964| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6750 Z= 0.173 Angle : 0.543 5.677 9186 Z= 0.278 Chirality : 0.041 0.139 976 Planarity : 0.004 0.041 1178 Dihedral : 4.063 16.394 866 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 12.29 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.30), residues: 793 helix: 1.62 (0.26), residues: 415 sheet: 0.17 (0.68), residues: 51 loop : 0.28 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.013 0.001 TYR B 453 PHE 0.015 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 6737) covalent geometry : angle 0.53579 / 0.28 ( 9153) SS BOND : bond 0.00476 / 0.31 ( 6) SS BOND : angle 1.45697 / 0.86 ( 12) hydrogen bonds : bond 0.03891 / 2.51 ( 322) hydrogen bonds : angle 4.41483 / 3.09 ( 915) link_NAG-ASN : bond 0.00260 / 0.14 ( 7) link_NAG-ASN : angle 1.59640 / 1.25 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9315 (mt0) cc_final: 0.9048 (mt0) REVERT: B 424 LYS cc_start: 0.8870 (tptt) cc_final: 0.8476 (tppt) REVERT: B 444 LYS cc_start: 0.9122 (ptpp) cc_final: 0.8919 (ptpp) REVERT: B 467 ASP cc_start: 0.8062 (t0) cc_final: 0.7717 (t0) REVERT: E 22 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8598 (mm-30) REVERT: E 190 MET cc_start: 0.9334 (ppp) cc_final: 0.9122 (ppp) REVERT: E 208 GLU cc_start: 0.8810 (tt0) cc_final: 0.8558 (tm-30) REVERT: E 277 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8808 (t0) REVERT: E 366 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8683 (mtp) REVERT: E 455 MET cc_start: 0.8893 (ttp) cc_final: 0.8363 (ttt) REVERT: E 498 CYS cc_start: 0.9202 (t) cc_final: 0.8894 (t) outliers start: 15 outliers final: 10 residues processed: 62 average time/residue: 0.0762 time to fit residues: 6.4194 Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.048542 restraints weight = 26930.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.050419 restraints weight = 13561.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051675 restraints weight = 8816.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052527 restraints weight = 6590.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053071 restraints weight = 5383.916| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6750 Z= 0.131 Angle : 0.521 5.890 9186 Z= 0.267 Chirality : 0.040 0.134 976 Planarity : 0.004 0.040 1178 Dihedral : 3.964 16.653 866 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.86 % Allowed : 13.29 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.30), residues: 793 helix: 1.63 (0.26), residues: 415 sheet: 0.18 (0.69), residues: 51 loop : 0.38 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.021 0.001 TYR B 473 PHE 0.012 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6737) covalent geometry : angle 0.51343 / 0.26 ( 9153) SS BOND : bond 0.00419 / 0.26 ( 6) SS BOND : angle 1.54099 / 0.89 ( 12) hydrogen bonds : bond 0.03673 / 2.37 ( 322) hydrogen bonds : angle 4.33285 / 3.03 ( 915) link_NAG-ASN : bond 0.00249 / 0.13 ( 7) link_NAG-ASN : angle 1.53553 / 1.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9347 (mt0) cc_final: 0.9073 (mt0) REVERT: B 424 LYS cc_start: 0.8853 (tptt) cc_final: 0.8414 (tppt) REVERT: B 467 ASP cc_start: 0.7988 (t0) cc_final: 0.7704 (t0) REVERT: E 22 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8685 (mm-30) REVERT: E 62 MET cc_start: 0.9499 (ttp) cc_final: 0.9254 (mtm) REVERT: E 190 MET cc_start: 0.9346 (ppp) cc_final: 0.9087 (ppp) REVERT: E 208 GLU cc_start: 0.8800 (tt0) cc_final: 0.8548 (tm-30) REVERT: E 455 MET cc_start: 0.8887 (ttp) cc_final: 0.8395 (ttt) REVERT: E 498 CYS cc_start: 0.9179 (t) cc_final: 0.8727 (t) outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.0870 time to fit residues: 7.2357 Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.048153 restraints weight = 27338.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.050046 restraints weight = 13876.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051330 restraints weight = 9051.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.052136 restraints weight = 6764.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.052722 restraints weight = 5579.902| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6750 Z= 0.143 Angle : 0.532 6.641 9186 Z= 0.271 Chirality : 0.040 0.134 976 Planarity : 0.004 0.040 1178 Dihedral : 3.930 16.633 866 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.00 % Allowed : 13.71 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.30), residues: 793 helix: 1.66 (0.26), residues: 415 sheet: 0.17 (0.69), residues: 51 loop : 0.45 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.011 0.001 TYR B 453 PHE 0.013 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6737) covalent geometry : angle 0.52470 / 0.27 ( 9153) SS BOND : bond 0.00436 / 0.27 ( 6) SS BOND : angle 1.47264 / 0.86 ( 12) hydrogen bonds : bond 0.03659 / 2.36 ( 322) hydrogen bonds : angle 4.28902 / 3.00 ( 915) link_NAG-ASN : bond 0.00230 / 0.12 ( 7) link_NAG-ASN : angle 1.54693 / 1.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9352 (mt0) cc_final: 0.9069 (mt0) REVERT: B 424 LYS cc_start: 0.8866 (tptt) cc_final: 0.8454 (tppt) REVERT: B 467 ASP cc_start: 0.8003 (t0) cc_final: 0.7743 (t0) REVERT: E 22 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8640 (mm-30) REVERT: E 62 MET cc_start: 0.9496 (ttp) cc_final: 0.9139 (mtm) REVERT: E 190 MET cc_start: 0.9358 (ppp) cc_final: 0.9112 (ppp) REVERT: E 208 GLU cc_start: 0.8825 (tt0) cc_final: 0.8559 (tm-30) REVERT: E 277 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8876 (t0) REVERT: E 435 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: E 455 MET cc_start: 0.8894 (ttp) cc_final: 0.8410 (ttt) REVERT: E 498 CYS cc_start: 0.9220 (t) cc_final: 0.8831 (t) outliers start: 14 outliers final: 8 residues processed: 62 average time/residue: 0.0843 time to fit residues: 7.1434 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.0030 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 ASN E 277 ASN E 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.046425 restraints weight = 27949.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.048314 restraints weight = 13711.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.049542 restraints weight = 8796.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050341 restraints weight = 6536.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050904 restraints weight = 5364.804| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6750 Z= 0.229 Angle : 0.599 6.756 9186 Z= 0.306 Chirality : 0.042 0.143 976 Planarity : 0.004 0.041 1178 Dihedral : 4.167 17.167 866 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.00 % Allowed : 14.43 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.30), residues: 793 helix: 1.60 (0.26), residues: 414 sheet: -0.09 (0.67), residues: 51 loop : 0.43 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.016 0.001 TYR B 453 PHE 0.016 0.002 PHE E 369 TRP 0.015 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 ( 6737) covalent geometry : angle 0.59236 / 0.30 ( 9153) SS BOND : bond 0.00478 / 0.30 ( 6) SS BOND : angle 1.41070 / 0.83 ( 12) hydrogen bonds : bond 0.04030 / 2.60 ( 322) hydrogen bonds : angle 4.48287 / 3.14 ( 915) link_NAG-ASN : bond 0.00287 / 0.15 ( 7) link_NAG-ASN : angle 1.70584 / 1.31 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9315 (mt0) cc_final: 0.8944 (mt0) REVERT: B 424 LYS cc_start: 0.8909 (tptt) cc_final: 0.8508 (tppt) REVERT: B 467 ASP cc_start: 0.8097 (t0) cc_final: 0.7846 (t0) REVERT: E 62 MET cc_start: 0.9473 (ttp) cc_final: 0.9067 (mtm) REVERT: E 208 GLU cc_start: 0.8858 (tt0) cc_final: 0.8632 (tm-30) REVERT: E 277 ASN cc_start: 0.9329 (OUTLIER) cc_final: 0.8874 (t0) outliers start: 14 outliers final: 11 residues processed: 61 average time/residue: 0.0834 time to fit residues: 6.8920 Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.0030 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048808 restraints weight = 27090.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050722 restraints weight = 13760.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051964 restraints weight = 8971.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052821 restraints weight = 6734.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053335 restraints weight = 5524.414| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6750 Z= 0.109 Angle : 0.537 7.437 9186 Z= 0.272 Chirality : 0.040 0.149 976 Planarity : 0.004 0.040 1178 Dihedral : 3.916 16.625 866 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.29 % Allowed : 15.00 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.30), residues: 793 helix: 1.65 (0.26), residues: 414 sheet: 0.11 (0.71), residues: 51 loop : 0.51 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.009 0.001 TYR E 385 PHE 0.011 0.001 PHE E 369 TRP 0.010 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6737) covalent geometry : angle 0.53021 / 0.27 ( 9153) SS BOND : bond 0.00302 / 0.18 ( 6) SS BOND : angle 1.43944 / 0.83 ( 12) hydrogen bonds : bond 0.03548 / 2.29 ( 322) hydrogen bonds : angle 4.27063 / 2.98 ( 915) link_NAG-ASN : bond 0.00278 / 0.14 ( 7) link_NAG-ASN : angle 1.53183 / 1.20 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 409 GLN cc_start: 0.9358 (mt0) cc_final: 0.9080 (mt0) REVERT: B 424 LYS cc_start: 0.8876 (tptt) cc_final: 0.8469 (tppt) REVERT: B 467 ASP cc_start: 0.8009 (t0) cc_final: 0.7732 (t0) REVERT: E 22 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8671 (mm-30) REVERT: E 62 MET cc_start: 0.9495 (ttp) cc_final: 0.9198 (mtm) REVERT: E 190 MET cc_start: 0.9191 (ppp) cc_final: 0.8856 (ppp) REVERT: E 208 GLU cc_start: 0.8834 (tt0) cc_final: 0.8598 (tm-30) REVERT: E 249 MET cc_start: 0.8759 (mtp) cc_final: 0.8167 (mtm) REVERT: E 455 MET cc_start: 0.8817 (ttp) cc_final: 0.8334 (ttt) REVERT: E 498 CYS cc_start: 0.9205 (t) cc_final: 0.8681 (t) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.0845 time to fit residues: 6.5251 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 62 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.048170 restraints weight = 27378.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.050078 restraints weight = 13882.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.051328 restraints weight = 9042.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052128 restraints weight = 6776.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.052728 restraints weight = 5593.747| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6750 Z= 0.136 Angle : 0.535 7.434 9186 Z= 0.274 Chirality : 0.040 0.169 976 Planarity : 0.004 0.041 1178 Dihedral : 3.903 17.154 866 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.00 % Allowed : 15.14 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.30), residues: 793 helix: 1.65 (0.26), residues: 415 sheet: 0.13 (0.71), residues: 51 loop : 0.52 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.010 0.001 TYR B 453 PHE 0.013 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6737) covalent geometry : angle 0.52816 / 0.27 ( 9153) SS BOND : bond 0.00363 / 0.23 ( 6) SS BOND : angle 1.37386 / 0.80 ( 12) hydrogen bonds : bond 0.03576 / 2.31 ( 322) hydrogen bonds : angle 4.30871 / 3.00 ( 915) link_NAG-ASN : bond 0.00227 / 0.12 ( 7) link_NAG-ASN : angle 1.60131 / 1.25 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1232.26 seconds wall clock time: 22 minutes 8.45 seconds (1328.45 seconds total)