Starting phenix.real_space_refine on Tue Mar 3 15:43:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlv_27517/03_2026/8dlv_27517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlv_27517/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlv_27517/03_2026/8dlv_27517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlv_27517/03_2026/8dlv_27517.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlv_27517/03_2026/8dlv_27517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlv_27517/03_2026/8dlv_27517.cif" } 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-5986/lib/python3.9/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 dihedrals: 3 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.54, per 1000 atoms: 0.24 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: 0.67 Conformation dependent library (CDL) restraints added in 238.3 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: 1.00 Time building geometry restraints manager: 0.85 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: 3687 17.07 - 34.14: 301 34.14 - 51.21: 56 51.21 - 68.27: 14 68.27 - 85.34: 10 Dihedral angle restraints: 4068 sinusoidal: 1730 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 4065 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 13.400 85.343 2550 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 covalent geometry : bond 0.00564 ( 6735) covalent geometry : angle 0.88417 ( 9152) SS BOND : bond 0.00660 ( 6) SS BOND : angle 2.32356 ( 12) hydrogen bonds : bond 0.14584 ( 321) hydrogen bonds : angle 6.23743 ( 912) link_NAG-ASN : bond 0.00762 ( 7) link_NAG-ASN : angle 4.64038 ( 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 : 0.245 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: 0.1083 time to fit residues: 16.3947 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 : 0.256 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3249 r_free = 0.3249 target = 0.070008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055896 restraints weight = 18794.362| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.29 r_work: 0.2769 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6748 Z= 0.130 Angle : 0.575 7.230 9185 Z= 0.288 Chirality : 0.040 0.143 977 Planarity : 0.005 0.042 1178 Dihedral : 5.389 52.527 1015 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.86 % Allowed : 8.00 % Favored : 91.14 % 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: 0.80 (0.28), residues: 793 helix: 1.25 (0.25), residues: 404 sheet: 1.08 (0.72), residues: 42 loop : -0.33 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 219 TYR 0.018 0.001 TYR B 369 PHE 0.016 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 covalent geometry : bond 0.00283 ( 6735) covalent geometry : angle 0.55473 ( 9152) SS BOND : bond 0.00271 ( 6) SS BOND : angle 1.59140 ( 12) hydrogen bonds : bond 0.04460 ( 321) hydrogen bonds : angle 4.67004 ( 912) link_NAG-ASN : bond 0.00475 ( 7) link_NAG-ASN : angle 3.02416 ( 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 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8781 (mm-30) REVERT: E 367 ASP cc_start: 0.9121 (m-30) cc_final: 0.8720 (p0) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.0902 time to fit residues: 8.5017 Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3175 r_free = 0.3175 target = 0.066495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.052623 restraints weight = 18741.766| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.17 r_work: 0.2693 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6748 Z= 0.195 Angle : 0.571 6.503 9185 Z= 0.291 Chirality : 0.041 0.142 977 Planarity : 0.004 0.042 1178 Dihedral : 4.875 54.012 1013 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.29 % Allowed : 9.43 % Favored : 89.29 % 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: 1.28 (0.29), residues: 793 helix: 1.69 (0.26), residues: 391 sheet: 0.91 (0.75), residues: 43 loop : -0.04 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.015 0.001 TYR B 495 PHE 0.018 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6735) covalent geometry : angle 0.55713 ( 9152) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.25262 ( 12) hydrogen bonds : bond 0.04591 ( 321) hydrogen bonds : angle 4.51836 ( 912) link_NAG-ASN : bond 0.00402 ( 7) link_NAG-ASN : angle 2.53568 ( 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 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8803 (mm-30) REVERT: E 270 MET cc_start: 0.9245 (tpt) cc_final: 0.8414 (tpp) REVERT: E 291 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8195 (mt) REVERT: E 367 ASP cc_start: 0.9169 (m-30) cc_final: 0.8769 (p0) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0914 time to fit residues: 8.0579 Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3159 r_free = 0.3159 target = 0.065615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.051604 restraints weight = 19147.606| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.21 r_work: 0.2667 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6748 Z= 0.211 Angle : 0.554 5.528 9185 Z= 0.283 Chirality : 0.041 0.145 977 Planarity : 0.004 0.035 1178 Dihedral : 4.847 54.799 1013 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.00 % Allowed : 10.14 % Favored : 87.86 % 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: 1.48 (0.29), residues: 793 helix: 1.85 (0.26), residues: 389 sheet: 0.95 (0.77), residues: 42 loop : 0.09 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.021 0.001 TYR E 613 PHE 0.019 0.001 PHE E 369 TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 6735) covalent geometry : angle 0.54184 ( 9152) SS BOND : bond 0.00315 ( 6) SS BOND : angle 1.17031 ( 12) hydrogen bonds : bond 0.04540 ( 321) hydrogen bonds : angle 4.53576 ( 912) link_NAG-ASN : bond 0.00349 ( 7) link_NAG-ASN : angle 2.30179 ( 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 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8786 (mm-30) REVERT: E 270 MET cc_start: 0.9259 (tpt) cc_final: 0.8396 (tpp) REVERT: E 291 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8171 (mm) REVERT: E 367 ASP cc_start: 0.9195 (m-30) cc_final: 0.8789 (p0) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.0888 time to fit residues: 8.3415 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 : 0.276 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.067311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.053401 restraints weight = 19070.587| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.22 r_work: 0.2708 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2905 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= 0.128 Angle : 0.502 5.383 9185 Z= 0.255 Chirality : 0.040 0.155 977 Planarity : 0.004 0.038 1178 Dihedral : 4.572 55.451 1013 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 10.86 % Favored : 87.43 % 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: 1.54 (0.30), residues: 793 helix: 1.85 (0.26), residues: 396 sheet: 0.95 (0.79), residues: 42 loop : 0.16 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.010 0.001 TYR E 385 PHE 0.015 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 covalent geometry : bond 0.00281 ( 6735) covalent geometry : angle 0.49101 ( 9152) SS BOND : bond 0.00284 ( 6) SS BOND : angle 1.17239 ( 12) hydrogen bonds : bond 0.04076 ( 321) hydrogen bonds : angle 4.42069 ( 912) link_NAG-ASN : bond 0.00316 ( 7) link_NAG-ASN : angle 2.09288 ( 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 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8768 (mm-30) REVERT: E 270 MET cc_start: 0.9315 (tpt) cc_final: 0.8580 (tpp) REVERT: E 291 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8264 (mm) REVERT: E 367 ASP cc_start: 0.9155 (m-30) cc_final: 0.8761 (p0) REVERT: E 474 MET cc_start: 0.8688 (mmp) cc_final: 0.8411 (mmm) REVERT: E 613 TYR cc_start: 0.6951 (t80) cc_final: 0.6629 (t80) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.0790 time to fit residues: 7.4218 Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3178 r_free = 0.3178 target = 0.066491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.052447 restraints weight = 19200.887| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.23 r_work: 0.2690 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6748 Z= 0.159 Angle : 0.516 5.422 9185 Z= 0.264 Chirality : 0.040 0.154 977 Planarity : 0.004 0.036 1178 Dihedral : 4.593 55.814 1013 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.29 % Allowed : 12.43 % Favored : 86.29 % 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: 1.63 (0.30), residues: 793 helix: 1.94 (0.26), residues: 396 sheet: 0.95 (0.79), residues: 42 loop : 0.19 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.010 0.001 TYR E 385 PHE 0.016 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6735) covalent geometry : angle 0.50669 ( 9152) SS BOND : bond 0.00241 ( 6) SS BOND : angle 0.76485 ( 12) hydrogen bonds : bond 0.04162 ( 321) hydrogen bonds : angle 4.42537 ( 912) link_NAG-ASN : bond 0.00289 ( 7) link_NAG-ASN : angle 2.02966 ( 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 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8790 (mm-30) REVERT: E 270 MET cc_start: 0.9313 (tpt) cc_final: 0.8596 (tpp) REVERT: E 291 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8199 (mm) REVERT: E 367 ASP cc_start: 0.9167 (m-30) cc_final: 0.8772 (p0) REVERT: E 474 MET cc_start: 0.8824 (mmp) cc_final: 0.8553 (mmm) REVERT: E 613 TYR cc_start: 0.7109 (t80) cc_final: 0.6656 (t80) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.0800 time to fit residues: 6.5876 Evaluate side-chains 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3188 r_free = 0.3188 target = 0.067010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053013 restraints weight = 19037.159| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.20 r_work: 0.2706 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6748 Z= 0.129 Angle : 0.488 5.357 9185 Z= 0.250 Chirality : 0.040 0.154 977 Planarity : 0.003 0.037 1178 Dihedral : 4.479 56.087 1013 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.57 % Allowed : 12.71 % 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: 1.70 (0.30), residues: 793 helix: 1.99 (0.26), residues: 394 sheet: 0.86 (0.80), residues: 42 loop : 0.27 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.009 0.001 TYR E 385 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 covalent geometry : bond 0.00287 ( 6735) covalent geometry : angle 0.47859 ( 9152) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.96384 ( 12) hydrogen bonds : bond 0.03967 ( 321) hydrogen bonds : angle 4.37110 ( 912) link_NAG-ASN : bond 0.00282 ( 7) link_NAG-ASN : angle 1.94294 ( 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 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8775 (mm-30) REVERT: E 270 MET cc_start: 0.9300 (tpt) cc_final: 0.8604 (tpp) REVERT: E 291 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8228 (mm) REVERT: E 367 ASP cc_start: 0.9134 (m-30) cc_final: 0.8732 (p0) REVERT: E 474 MET cc_start: 0.8837 (mmp) cc_final: 0.8593 (mmm) REVERT: E 613 TYR cc_start: 0.6944 (t80) cc_final: 0.6393 (t80) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.0732 time to fit residues: 6.4619 Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3177 r_free = 0.3177 target = 0.066449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.052385 restraints weight = 18956.669| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.22 r_work: 0.2688 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6748 Z= 0.154 Angle : 0.507 5.410 9185 Z= 0.260 Chirality : 0.040 0.153 977 Planarity : 0.004 0.035 1178 Dihedral : 4.532 56.433 1013 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.43 % Allowed : 13.00 % 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: 1.71 (0.30), residues: 793 helix: 1.97 (0.26), residues: 394 sheet: 0.87 (0.79), residues: 42 loop : 0.31 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.010 0.001 TYR E 385 PHE 0.015 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 covalent geometry : bond 0.00347 ( 6735) covalent geometry : angle 0.49862 ( 9152) SS BOND : bond 0.00246 ( 6) SS BOND : angle 0.91611 ( 12) hydrogen bonds : bond 0.04105 ( 321) hydrogen bonds : angle 4.40790 ( 912) link_NAG-ASN : bond 0.00273 ( 7) link_NAG-ASN : angle 1.95323 ( 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 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8787 (mm-30) REVERT: E 270 MET cc_start: 0.9287 (tpt) cc_final: 0.8582 (tpp) REVERT: E 291 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8242 (mm) REVERT: E 367 ASP cc_start: 0.9153 (m-30) cc_final: 0.8752 (p0) REVERT: E 474 MET cc_start: 0.8928 (mmp) cc_final: 0.8716 (mmm) REVERT: E 613 TYR cc_start: 0.7142 (t80) cc_final: 0.6545 (t80) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.0773 time to fit residues: 6.7623 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 : 0.157 ------------------------------------------------------------------------------- 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: 0.7980 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3192 r_free = 0.3192 target = 0.067142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.053046 restraints weight = 19044.009| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.24 r_work: 0.2704 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3210 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= 0.132 Angle : 0.499 5.397 9185 Z= 0.254 Chirality : 0.040 0.154 977 Planarity : 0.003 0.035 1178 Dihedral : 4.476 56.383 1013 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.43 % Allowed : 13.43 % 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: 1.69 (0.30), residues: 793 helix: 1.94 (0.26), residues: 394 sheet: 0.84 (0.80), residues: 42 loop : 0.33 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.009 0.001 TYR E 516 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 covalent geometry : bond 0.00295 ( 6735) covalent geometry : angle 0.48993 ( 9152) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.94601 ( 12) hydrogen bonds : bond 0.03998 ( 321) hydrogen bonds : angle 4.39134 ( 912) link_NAG-ASN : bond 0.00268 ( 7) link_NAG-ASN : angle 1.93042 ( 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 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8772 (mm-30) REVERT: E 270 MET cc_start: 0.9292 (tpt) cc_final: 0.8609 (tpp) REVERT: E 291 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8193 (mm) REVERT: E 367 ASP cc_start: 0.9130 (m-30) cc_final: 0.8703 (p0) REVERT: E 613 TYR cc_start: 0.7013 (t80) cc_final: 0.6382 (t80) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.0801 time to fit residues: 6.7083 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 : 0.186 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3142 r_free = 0.3142 target = 0.064838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.050864 restraints weight = 19019.422| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.19 r_work: 0.2649 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6748 Z= 0.227 Angle : 0.572 7.477 9185 Z= 0.293 Chirality : 0.042 0.152 977 Planarity : 0.004 0.032 1178 Dihedral : 4.784 56.529 1013 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.57 % Allowed : 13.29 % 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: 1.58 (0.30), residues: 793 helix: 1.84 (0.26), residues: 397 sheet: 0.74 (0.79), residues: 42 loop : 0.28 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.013 0.001 TYR E 385 PHE 0.018 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 493 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 6735) covalent geometry : angle 0.56352 ( 9152) SS BOND : bond 0.00300 ( 6) SS BOND : angle 0.86855 ( 12) hydrogen bonds : bond 0.04509 ( 321) hydrogen bonds : angle 4.50231 ( 912) link_NAG-ASN : bond 0.00295 ( 7) link_NAG-ASN : angle 2.07820 ( 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: 11 poor density : 54 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8831 (mm-30) REVERT: E 270 MET cc_start: 0.9349 (tpt) cc_final: 0.9041 (tpt) REVERT: E 291 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8229 (mm) REVERT: E 332 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8133 (ptm) REVERT: E 367 ASP cc_start: 0.9165 (m-30) cc_final: 0.8765 (p0) REVERT: E 613 TYR cc_start: 0.7245 (t80) cc_final: 0.6559 (t80) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.0866 time to fit residues: 7.2914 Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 332 MET Chi-restraints excluded: chain E residue 506 VAL 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: 0.6980 chunk 56 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3188 r_free = 0.3188 target = 0.066945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.052943 restraints weight = 18892.047| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.22 r_work: 0.2701 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6748 Z= 0.127 Angle : 0.525 8.581 9185 Z= 0.265 Chirality : 0.040 0.155 977 Planarity : 0.004 0.036 1178 Dihedral : 4.576 56.855 1013 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.71 % Allowed : 13.57 % Favored : 84.71 % 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: 1.65 (0.30), residues: 793 helix: 1.89 (0.26), residues: 393 sheet: 0.67 (0.80), residues: 42 loop : 0.36 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.009 0.001 TYR B 495 PHE 0.014 0.001 PHE E 369 TRP 0.027 0.001 TRP E 168 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6735) covalent geometry : angle 0.51562 ( 9152) SS BOND : bond 0.00252 ( 6) SS BOND : angle 1.05614 ( 12) hydrogen bonds : bond 0.04112 ( 321) hydrogen bonds : angle 4.44509 ( 912) link_NAG-ASN : bond 0.00297 ( 7) link_NAG-ASN : angle 1.99692 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1520.00 seconds wall clock time: 26 minutes 45.28 seconds (1605.28 seconds total)