Starting phenix.real_space_refine on Thu Jul 2 04:42:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dlv_27517/07_2026/8dlv_27517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlv_27517/07_2026/8dlv_27517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2026/8dlv_27517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2026/8dlv_27517.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2026/8dlv_27517.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2026/8dlv_27517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2026/8dlv_27517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2026/8dlv_27517.map" } resolution = 3.11 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= 0.028 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 4186 2.51 5 N 1081 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6553 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 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: {'PTRANS': 27, '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: 1.34, per 1000 atoms: 0.20 Number of scatterers: 6553 At special positions: 0 Unit cell: (81, 83, 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 1249 8.00 N 1081 7.00 C 4186 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=2.04 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=2.02 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: 0.51 Conformation dependent library (CDL) restraints added in 386.6 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: 40 helices and 6 sheets defined 58.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.358A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.448A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.667A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.004A pdb=" N ASN E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.611A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) 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: 3.721A 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: 4.033A 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 143 through 155 removed outlier: 3.881A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.718A 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 218 through 252 removed outlier: 3.764A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.784A 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: 3.632A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.671A 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: 4.197A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.527A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.320A 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: 3.595A 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 512 through 533 removed outlier: 4.474A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.902A 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: 3.995A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.803A 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 262 through 263 removed outlier: 6.092A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.075A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.70 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: 2088 1.35 - 1.47: 1815 1.47 - 1.60: 2774 1.60 - 1.73: 0 1.73 - 1.85: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.38e-02 5.25e+03 5.31e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 8761 2.01 - 4.02: 349 4.02 - 6.03: 30 6.03 - 8.04: 11 8.04 - 10.04: 1 Bond angle restraints: 9152 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 122.36 128.16 -5.80 1.42e+00 4.96e-01 1.67e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 116.24 -3.64 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 120.12 -6.22 1.80e+00 3.09e-01 1.20e+01 angle pdb=" CA CYS E 133 " pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " ideal model delta sigma weight residual 114.40 122.20 -7.80 2.30e+00 1.89e-01 1.15e+01 angle pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 112.60 115.95 -3.35 1.00e+00 1.00e+00 1.12e+01 ... (remaining 9147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 3552 17.07 - 34.14: 297 34.14 - 51.21: 50 51.21 - 68.27: 12 68.27 - 85.34: 10 Dihedral angle restraints: 3921 sinusoidal: 1583 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 -51.15 -34.85 1 1.00e+01 1.00e-02 1.72e+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 15.84 63.16 1 2.00e+01 2.50e-03 1.32e+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 -131.24 8.64 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 3918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 711 0.055 - 0.110: 198 0.110 - 0.165: 56 0.165 - 0.220: 10 0.220 - 0.275: 2 Chirality restraints: 977 Sorted by residual: 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 0.28 2.00e-01 2.50e+01 1.89e+00 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 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASN E 437 " pdb=" N ASN E 437 " pdb=" C ASN E 437 " pdb=" CB ASN E 437 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 974 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO E 590 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 41 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.61e+00 pdb=" C TYR E 41 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR E 41 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN E 42 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.047 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO E 500 " 0.122 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 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2049 2.83 - 3.35: 5939 3.35 - 3.86: 11341 3.86 - 4.38: 12913 4.38 - 4.90: 22190 Nonbonded interactions: 54432 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.311 3.040 nonbonded pdb=" O ASP E 367 " pdb=" OG1 THR E 371 " model vdw 2.367 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.369 3.120 nonbonded pdb=" OH TYR E 237 " pdb=" O VAL E 485 " model vdw 2.374 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.406 3.040 ... (remaining 54427 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 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: 5.200 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.430 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 : 0.006 0.070 6748 Z= 0.259 Angle : 0.914 12.322 9185 Z= 0.508 Chirality : 0.058 0.275 977 Planarity : 0.008 0.075 1178 Dihedral : 13.454 85.343 2403 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.29 % Allowed : 4.29 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 793 helix: 0.20 (0.22), residues: 393 sheet: 1.13 (0.73), residues: 43 loop : -0.64 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 460 TYR 0.033 0.002 TYR B 495 PHE 0.028 0.003 PHE E 369 TRP 0.021 0.002 TRP E 69 HIS 0.005 0.001 HIS E 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.26 ( 6735) covalent geometry : angle 0.88417 / 0.50 ( 9152) SS BOND : bond 0.00660 / 0.36 ( 6) SS BOND : angle 2.32356 / 1.34 ( 12) hydrogen bonds : bond 0.14584 / 9.92 ( 321) hydrogen bonds : angle 6.23743 / 4.44 ( 912) link_NAG-ASN : bond 0.00762 / 0.40 ( 7) link_NAG-ASN : angle 4.64038 / 3.46 ( 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 121 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8498 (m-30) cc_final: 0.8282 (m-30) REVERT: E 367 ASP cc_start: 0.8696 (m-30) cc_final: 0.8448 (p0) outliers start: 2 outliers final: 1 residues processed: 121 average time/residue: 0.1074 time to fit residues: 16.4367 Evaluate side-chains 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 HIS 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: 0.0980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN B 437 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 HIS E 374 HIS E 552 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.056118 restraints weight = 18792.692| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.28 r_work: 0.2773 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6748 Z= 0.136 Angle : 0.578 7.440 9185 Z= 0.291 Chirality : 0.041 0.145 977 Planarity : 0.005 0.043 1178 Dihedral : 4.268 32.297 868 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.86 % Allowed : 8.14 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.28), residues: 793 helix: 1.24 (0.25), residues: 404 sheet: 1.09 (0.72), residues: 42 loop : -0.34 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.017 0.001 TYR B 369 PHE 0.017 0.001 PHE E 369 TRP 0.016 0.001 TRP E 165 HIS 0.004 0.001 HIS E 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 6735) covalent geometry : angle 0.55848 / 0.29 ( 9152) SS BOND : bond 0.00327 / 0.19 ( 6) SS BOND : angle 1.54896 / 0.86 ( 12) hydrogen bonds : bond 0.04531 / 3.09 ( 321) hydrogen bonds : angle 4.68643 / 3.37 ( 912) link_NAG-ASN : bond 0.00461 / 0.23 ( 7) link_NAG-ASN : angle 3.00263 / 2.23 ( 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 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8775 (mm-30) REVERT: E 367 ASP cc_start: 0.9128 (m-30) cc_final: 0.8731 (p0) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.0856 time to fit residues: 8.0749 Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3207 r_free = 0.3207 target = 0.068081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.054066 restraints weight = 18643.583| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.24 r_work: 0.2729 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6748 Z= 0.151 Angle : 0.538 6.396 9185 Z= 0.273 Chirality : 0.040 0.138 977 Planarity : 0.004 0.041 1178 Dihedral : 3.981 15.230 866 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.14 % Allowed : 8.86 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.29), residues: 793 helix: 1.64 (0.26), residues: 402 sheet: 0.97 (0.75), residues: 43 loop : 0.01 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.014 0.001 TYR B 495 PHE 0.016 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6735) covalent geometry : angle 0.52472 / 0.27 ( 9152) SS BOND : bond 0.00295 / 0.17 ( 6) SS BOND : angle 1.26882 / 0.71 ( 12) hydrogen bonds : bond 0.04325 / 2.95 ( 321) hydrogen bonds : angle 4.45939 / 3.20 ( 912) link_NAG-ASN : bond 0.00404 / 0.21 ( 7) link_NAG-ASN : angle 2.36500 / 1.77 ( 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: 8 poor density : 61 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 403 ARG cc_start: 0.8991 (mtm110) cc_final: 0.8687 (mtm110) REVERT: B 458 LYS cc_start: 0.9402 (mppt) cc_final: 0.9143 (mmtm) REVERT: E 182 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8777 (mm-30) REVERT: E 270 MET cc_start: 0.9249 (tpt) cc_final: 0.8409 (tpp) REVERT: E 291 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8146 (mm) REVERT: E 325 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8260 (mm-40) REVERT: E 367 ASP cc_start: 0.9137 (m-30) cc_final: 0.8722 (p0) REVERT: E 435 GLU cc_start: 0.8630 (mp0) cc_final: 0.8263 (mp0) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.0854 time to fit residues: 7.5806 Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3207 r_free = 0.3207 target = 0.068034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.054000 restraints weight = 18957.773| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.23 r_work: 0.2730 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6748 Z= 0.139 Angle : 0.507 5.428 9185 Z= 0.259 Chirality : 0.040 0.155 977 Planarity : 0.004 0.037 1178 Dihedral : 3.912 15.109 866 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.43 % Allowed : 10.14 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.29), residues: 793 helix: 1.78 (0.26), residues: 398 sheet: 1.08 (0.78), residues: 42 loop : 0.07 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.019 0.001 TYR E 613 PHE 0.016 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 6735) covalent geometry : angle 0.49644 / 0.26 ( 9152) SS BOND : bond 0.00263 / 0.16 ( 6) SS BOND : angle 1.16346 / 0.65 ( 12) hydrogen bonds : bond 0.04145 / 2.84 ( 321) hydrogen bonds : angle 4.38459 / 3.15 ( 912) link_NAG-ASN : bond 0.00336 / 0.18 ( 7) link_NAG-ASN : angle 2.07048 / 1.55 ( 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 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 458 LYS cc_start: 0.9408 (mppt) cc_final: 0.9139 (mmtm) REVERT: E 182 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8754 (mm-30) REVERT: E 270 MET cc_start: 0.9214 (tpt) cc_final: 0.8402 (tpp) REVERT: E 291 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8129 (mm) REVERT: E 367 ASP cc_start: 0.9156 (m-30) cc_final: 0.8754 (p0) REVERT: E 435 GLU cc_start: 0.8608 (mp0) cc_final: 0.8191 (mp0) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.0975 time to fit residues: 8.9416 Evaluate side-chains 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3154 r_free = 0.3154 target = 0.065413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.051332 restraints weight = 19307.387| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.21 r_work: 0.2661 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6748 Z= 0.218 Angle : 0.567 5.804 9185 Z= 0.290 Chirality : 0.042 0.151 977 Planarity : 0.004 0.033 1178 Dihedral : 4.064 15.315 866 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 11.14 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.29), residues: 793 helix: 1.86 (0.26), residues: 391 sheet: 1.04 (0.78), residues: 42 loop : 0.20 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.017 0.001 TYR B 495 PHE 0.018 0.001 PHE E 369 TRP 0.015 0.001 TRP E 165 HIS 0.005 0.001 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 6735) covalent geometry : angle 0.55780 / 0.29 ( 9152) SS BOND : bond 0.00291 / 0.18 ( 6) SS BOND : angle 1.11495 / 0.63 ( 12) hydrogen bonds : bond 0.04536 / 3.10 ( 321) hydrogen bonds : angle 4.51232 / 3.24 ( 912) link_NAG-ASN : bond 0.00297 / 0.17 ( 7) link_NAG-ASN : angle 2.08816 / 1.53 ( 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 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8782 (mm-30) REVERT: E 291 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8214 (mm) REVERT: E 367 ASP cc_start: 0.9145 (m-30) cc_final: 0.8753 (p0) REVERT: E 435 GLU cc_start: 0.8567 (mp0) cc_final: 0.8164 (mp0) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.0961 time to fit residues: 8.7280 Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3180 r_free = 0.3180 target = 0.066717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.052845 restraints weight = 19150.700| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.19 r_work: 0.2690 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6748 Z= 0.150 Angle : 0.510 5.384 9185 Z= 0.261 Chirality : 0.040 0.156 977 Planarity : 0.004 0.034 1178 Dihedral : 3.919 14.784 866 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.71 % Allowed : 11.86 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.30), residues: 793 helix: 1.88 (0.26), residues: 397 sheet: 0.99 (0.78), residues: 42 loop : 0.25 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.031 0.001 TYR E 613 PHE 0.016 0.001 PHE E 369 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6735) covalent geometry : angle 0.50068 / 0.26 ( 9152) SS BOND : bond 0.00297 / 0.18 ( 6) SS BOND : angle 1.18567 / 0.67 ( 12) hydrogen bonds : bond 0.04157 / 2.84 ( 321) hydrogen bonds : angle 4.41936 / 3.18 ( 912) link_NAG-ASN : bond 0.00303 / 0.16 ( 7) link_NAG-ASN : angle 1.91826 / 1.41 ( 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 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8764 (mm-30) REVERT: E 291 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8223 (mm) REVERT: E 367 ASP cc_start: 0.9135 (m-30) cc_final: 0.8753 (p0) REVERT: E 435 GLU cc_start: 0.8587 (mp0) cc_final: 0.8184 (mp0) REVERT: E 474 MET cc_start: 0.8973 (mmp) cc_final: 0.8604 (mmm) REVERT: E 613 TYR cc_start: 0.6952 (t80) cc_final: 0.6726 (t80) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.0896 time to fit residues: 8.1077 Evaluate side-chains 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 75 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3197 r_free = 0.3197 target = 0.067452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.053569 restraints weight = 18999.437| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.21 r_work: 0.2711 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6748 Z= 0.126 Angle : 0.491 5.361 9185 Z= 0.251 Chirality : 0.040 0.153 977 Planarity : 0.003 0.036 1178 Dihedral : 3.820 14.381 866 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.57 % Allowed : 12.57 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.30), residues: 793 helix: 1.92 (0.26), residues: 394 sheet: 0.86 (0.80), residues: 42 loop : 0.29 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.022 0.001 TYR E 613 PHE 0.014 0.001 PHE E 369 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 6735) covalent geometry : angle 0.48248 / 0.25 ( 9152) SS BOND : bond 0.00275 / 0.16 ( 6) SS BOND : angle 1.15493 / 0.65 ( 12) hydrogen bonds : bond 0.03956 / 2.71 ( 321) hydrogen bonds : angle 4.36636 / 3.15 ( 912) link_NAG-ASN : bond 0.00281 / 0.15 ( 7) link_NAG-ASN : angle 1.80401 / 1.33 ( 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 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.275 Fit side-chains REVERT: E 182 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8763 (mm-30) REVERT: E 291 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8212 (mm) REVERT: E 367 ASP cc_start: 0.9147 (m-30) cc_final: 0.8739 (p0) REVERT: E 435 GLU cc_start: 0.8549 (mp0) cc_final: 0.8166 (mp0) REVERT: E 474 MET cc_start: 0.9005 (mmp) cc_final: 0.8569 (mmm) REVERT: E 613 TYR cc_start: 0.7001 (t80) cc_final: 0.6617 (t80) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.0843 time to fit residues: 7.2806 Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3189 r_free = 0.3189 target = 0.067145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.052941 restraints weight = 18960.028| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.24 r_work: 0.2707 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6748 Z= 0.128 Angle : 0.498 5.365 9185 Z= 0.253 Chirality : 0.040 0.157 977 Planarity : 0.003 0.035 1178 Dihedral : 3.821 14.356 866 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.43 % Allowed : 12.71 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.30), residues: 793 helix: 1.95 (0.26), residues: 394 sheet: 0.81 (0.79), residues: 42 loop : 0.33 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.017 0.001 TYR E 613 PHE 0.014 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 6735) covalent geometry : angle 0.49113 / 0.25 ( 9152) SS BOND : bond 0.00197 / 0.13 ( 6) SS BOND : angle 0.75636 / 0.43 ( 12) hydrogen bonds : bond 0.03935 / 2.70 ( 321) hydrogen bonds : angle 4.33343 / 3.12 ( 912) link_NAG-ASN : bond 0.00268 / 0.15 ( 7) link_NAG-ASN : angle 1.76778 / 1.30 ( 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 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.186 Fit side-chains REVERT: E 182 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8764 (mm-30) REVERT: E 291 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8210 (mm) REVERT: E 367 ASP cc_start: 0.9164 (m-30) cc_final: 0.8734 (p0) REVERT: E 435 GLU cc_start: 0.8545 (mp0) cc_final: 0.8159 (mp0) REVERT: E 474 MET cc_start: 0.9016 (mmp) cc_final: 0.8684 (mmm) REVERT: E 613 TYR cc_start: 0.7034 (t80) cc_final: 0.6597 (t80) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.0698 time to fit residues: 6.1421 Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 48 optimal weight: 0.0980 chunk 39 optimal weight: 0.0030 chunk 46 optimal weight: 0.0010 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3232 r_free = 0.3232 target = 0.069208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.055139 restraints weight = 18941.476| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.25 r_work: 0.2762 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6748 Z= 0.094 Angle : 0.476 5.316 9185 Z= 0.241 Chirality : 0.039 0.157 977 Planarity : 0.003 0.038 1178 Dihedral : 3.649 13.596 866 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.14 % Allowed : 13.14 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.30), residues: 793 helix: 1.98 (0.26), residues: 394 sheet: 0.82 (0.81), residues: 42 loop : 0.34 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.015 0.001 TYR E 613 PHE 0.012 0.001 PHE E 369 TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 6735) covalent geometry : angle 0.46844 / 0.24 ( 9152) SS BOND : bond 0.00143 / 0.10 ( 6) SS BOND : angle 0.86351 / 0.50 ( 12) hydrogen bonds : bond 0.03586 / 2.47 ( 321) hydrogen bonds : angle 4.26526 / 3.08 ( 912) link_NAG-ASN : bond 0.00280 / 0.15 ( 7) link_NAG-ASN : angle 1.69728 / 1.25 ( 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 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.270 Fit side-chains REVERT: E 182 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8730 (mm-30) REVERT: E 367 ASP cc_start: 0.9111 (m-30) cc_final: 0.8699 (p0) REVERT: E 435 GLU cc_start: 0.8552 (mp0) cc_final: 0.8189 (mp0) REVERT: E 467 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8538 (mt-10) REVERT: E 613 TYR cc_start: 0.6926 (t80) cc_final: 0.6395 (t80) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.0925 time to fit residues: 7.9076 Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3191 r_free = 0.3191 target = 0.067239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.053073 restraints weight = 18859.271| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.21 r_work: 0.2710 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6748 Z= 0.144 Angle : 0.519 7.779 9185 Z= 0.263 Chirality : 0.040 0.154 977 Planarity : 0.004 0.037 1178 Dihedral : 3.754 14.114 866 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.14 % Allowed : 13.29 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.30), residues: 793 helix: 2.06 (0.26), residues: 395 sheet: 0.78 (0.80), residues: 42 loop : 0.40 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.014 0.001 TYR E 613 PHE 0.015 0.001 PHE E 369 TRP 0.016 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6735) covalent geometry : angle 0.51292 / 0.26 ( 9152) SS BOND : bond 0.00205 / 0.14 ( 6) SS BOND : angle 0.75604 / 0.44 ( 12) hydrogen bonds : bond 0.03955 / 2.70 ( 321) hydrogen bonds : angle 4.30494 / 3.10 ( 912) link_NAG-ASN : bond 0.00237 / 0.13 ( 7) link_NAG-ASN : angle 1.74045 / 1.28 ( 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 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.275 Fit side-chains REVERT: E 182 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8773 (mm-30) REVERT: E 367 ASP cc_start: 0.9144 (m-30) cc_final: 0.8704 (p0) REVERT: E 435 GLU cc_start: 0.8551 (mp0) cc_final: 0.8180 (mp0) REVERT: E 467 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8554 (mt-10) REVERT: E 613 TYR cc_start: 0.7062 (t80) cc_final: 0.6656 (t80) outliers start: 8 outliers final: 8 residues processed: 63 average time/residue: 0.0774 time to fit residues: 6.6749 Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 0.0370 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3231 r_free = 0.3231 target = 0.069082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055117 restraints weight = 18867.408| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.21 r_work: 0.2748 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6748 Z= 0.103 Angle : 0.508 8.183 9185 Z= 0.254 Chirality : 0.040 0.156 977 Planarity : 0.003 0.039 1178 Dihedral : 3.657 13.621 866 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.14 % Allowed : 13.71 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.30), residues: 793 helix: 2.01 (0.26), residues: 395 sheet: 0.86 (0.81), residues: 42 loop : 0.38 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.014 0.001 TYR E 613 PHE 0.012 0.001 PHE E 369 TRP 0.026 0.001 TRP E 168 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6735) covalent geometry : angle 0.50152 / 0.25 ( 9152) SS BOND : bond 0.00166 / 0.11 ( 6) SS BOND : angle 0.91293 / 0.53 ( 12) hydrogen bonds : bond 0.03754 / 2.59 ( 321) hydrogen bonds : angle 4.28028 / 3.08 ( 912) link_NAG-ASN : bond 0.00272 / 0.14 ( 7) link_NAG-ASN : angle 1.67552 / 1.24 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.69 seconds wall clock time: 27 minutes 54.60 seconds (1674.60 seconds total)