Starting phenix.real_space_refine on Sat May 10 18:32:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlv_27517/05_2025/8dlv_27517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlv_27517/05_2025/8dlv_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_27517/05_2025/8dlv_27517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlv_27517/05_2025/8dlv_27517.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlv_27517/05_2025/8dlv_27517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlv_27517/05_2025/8dlv_27517.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.77, per 1000 atoms: 0.73 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: 1.64 Conformation dependent library (CDL) restraints added in 849.2 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: 0.78 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: 1.75 Time building geometry restraints manager: 1.93 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.002 TRP E 69 HIS 0.005 0.001 HIS E 378 PHE 0.028 0.003 PHE E 369 TYR 0.033 0.002 TYR B 495 ARG 0.014 0.001 ARG E 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 7) link_NAG-ASN : angle 4.64038 ( 21) hydrogen bonds : bond 0.14584 ( 321) hydrogen bonds : angle 6.23743 ( 912) SS BOND : bond 0.00660 ( 6) SS BOND : angle 2.32356 ( 12) covalent geometry : bond 0.00564 ( 6735) covalent geometry : angle 0.88417 ( 9152) *********************** 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 : 0.791 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: 0.2580 time to fit residues: 38.9891 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 : 0.786 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.070051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055964 restraints weight = 18661.361| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.27 r_work: 0.2773 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1994 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= 0.129 Angle : 0.574 7.308 9185 Z= 0.288 Chirality : 0.040 0.143 977 Planarity : 0.005 0.042 1178 Dihedral : 5.370 52.518 1015 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.86 % Allowed : 7.86 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 793 helix: 1.25 (0.25), residues: 404 sheet: 1.09 (0.72), residues: 42 loop : -0.32 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 165 HIS 0.004 0.001 HIS E 345 PHE 0.016 0.001 PHE E 369 TYR 0.017 0.001 TYR B 495 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 7) link_NAG-ASN : angle 3.00550 ( 21) hydrogen bonds : bond 0.04444 ( 321) hydrogen bonds : angle 4.67075 ( 912) SS BOND : bond 0.00302 ( 6) SS BOND : angle 1.59103 ( 12) covalent geometry : bond 0.00280 ( 6735) covalent geometry : angle 0.55420 ( 9152) *********************** 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 : 0.778 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8774 (mm-30) REVERT: E 367 ASP cc_start: 0.9129 (m-30) cc_final: 0.8732 (p0) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2093 time to fit residues: 19.8999 Evaluate side-chains 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 28 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.068212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054306 restraints weight = 18824.989| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.21 r_work: 0.2732 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.152 Angle : 0.542 6.372 9185 Z= 0.274 Chirality : 0.040 0.142 977 Planarity : 0.004 0.044 1178 Dihedral : 4.798 53.924 1013 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.14 % Allowed : 8.43 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 793 helix: 1.65 (0.26), residues: 402 sheet: 0.95 (0.75), residues: 43 loop : 0.03 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.003 0.001 HIS E 239 PHE 0.016 0.001 PHE E 369 TYR 0.013 0.001 TYR B 495 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 7) link_NAG-ASN : angle 2.53972 ( 21) hydrogen bonds : bond 0.04337 ( 321) hydrogen bonds : angle 4.46355 ( 912) SS BOND : bond 0.00302 ( 6) SS BOND : angle 1.33922 ( 12) covalent geometry : bond 0.00336 ( 6735) covalent geometry : angle 0.52646 ( 9152) *********************** 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 67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8763 (mm-30) REVERT: E 270 MET cc_start: 0.9372 (tpt) cc_final: 0.8585 (tpp) REVERT: E 291 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8142 (mm) REVERT: E 325 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8292 (mm-40) REVERT: E 367 ASP cc_start: 0.9125 (m-30) cc_final: 0.8713 (p0) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.2093 time to fit residues: 18.2550 Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 63 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.067598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.053648 restraints weight = 19054.841| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.22 r_work: 0.2716 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2618 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= 0.151 Angle : 0.517 5.467 9185 Z= 0.263 Chirality : 0.040 0.155 977 Planarity : 0.004 0.039 1178 Dihedral : 4.645 54.784 1013 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.71 % Allowed : 9.14 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 793 helix: 1.77 (0.26), residues: 399 sheet: 1.11 (0.78), residues: 42 loop : 0.07 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.018 0.001 TYR E 613 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 7) link_NAG-ASN : angle 2.24231 ( 21) hydrogen bonds : bond 0.04207 ( 321) hydrogen bonds : angle 4.40510 ( 912) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.17863 ( 12) covalent geometry : bond 0.00335 ( 6735) covalent geometry : angle 0.50514 ( 9152) *********************** 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: 12 poor density : 60 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: B 403 ARG cc_start: 0.8961 (mtm110) cc_final: 0.8728 (mtm110) REVERT: B 458 LYS cc_start: 0.9422 (mppt) cc_final: 0.9163 (mmtm) REVERT: E 182 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8760 (mm-30) REVERT: E 270 MET cc_start: 0.9347 (tpt) cc_final: 0.8581 (tpp) REVERT: E 291 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8106 (mm) REVERT: E 367 ASP cc_start: 0.9160 (m-30) cc_final: 0.8758 (p0) outliers start: 12 outliers final: 8 residues processed: 70 average time/residue: 0.2197 time to fit residues: 20.2205 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 : 0.777 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.067994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.054112 restraints weight = 18775.837| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.18 r_work: 0.2736 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2781 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 : 0.501 5.999 9185 Z= 0.255 Chirality : 0.040 0.155 977 Planarity : 0.004 0.037 1178 Dihedral : 4.480 55.101 1013 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.29 % Allowed : 11.43 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 793 helix: 1.85 (0.26), residues: 398 sheet: 1.13 (0.79), residues: 42 loop : 0.16 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 PHE 0.014 0.001 PHE E 369 TYR 0.010 0.001 TYR E 385 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 7) link_NAG-ASN : angle 2.04013 ( 21) hydrogen bonds : bond 0.04003 ( 321) hydrogen bonds : angle 4.37343 ( 912) SS BOND : bond 0.00256 ( 6) SS BOND : angle 1.18241 ( 12) covalent geometry : bond 0.00279 ( 6735) covalent geometry : angle 0.49094 ( 9152) *********************** 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 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: B 458 LYS cc_start: 0.9399 (mppt) cc_final: 0.9120 (mmtm) REVERT: E 55 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8006 (p) REVERT: E 182 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8743 (mm-30) REVERT: E 270 MET cc_start: 0.9297 (tpt) cc_final: 0.8353 (tpp) REVERT: E 291 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8187 (mm) REVERT: E 367 ASP cc_start: 0.9151 (m-30) cc_final: 0.8753 (p0) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.2247 time to fit residues: 19.4846 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 : 0.774 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3176 r_free = 0.3176 target = 0.066505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.052503 restraints weight = 18698.653| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.17 r_work: 0.2697 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6748 Z= 0.163 Angle : 0.520 5.413 9185 Z= 0.266 Chirality : 0.041 0.155 977 Planarity : 0.004 0.035 1178 Dihedral : 4.531 55.569 1013 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.57 % Allowed : 12.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.30), residues: 793 helix: 1.90 (0.26), residues: 398 sheet: 0.99 (0.77), residues: 42 loop : 0.26 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.013 0.001 TYR B 495 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 7) link_NAG-ASN : angle 2.01725 ( 21) hydrogen bonds : bond 0.04207 ( 321) hydrogen bonds : angle 4.38558 ( 912) SS BOND : bond 0.00287 ( 6) SS BOND : angle 1.07773 ( 12) covalent geometry : bond 0.00368 ( 6735) covalent geometry : angle 0.51000 ( 9152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.811 Fit side-chains REVERT: E 182 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8757 (mm-30) REVERT: E 270 MET cc_start: 0.9346 (tpt) cc_final: 0.8639 (tpp) REVERT: E 291 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8203 (mm) REVERT: E 367 ASP cc_start: 0.9155 (m-30) cc_final: 0.8761 (p0) REVERT: E 613 TYR cc_start: 0.7015 (t80) cc_final: 0.6780 (t80) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.2104 time to fit residues: 17.6655 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 : 0.823 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.066963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053019 restraints weight = 18764.496| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.18 r_work: 0.2700 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3028 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= 0.155 Angle : 0.518 6.384 9185 Z= 0.262 Chirality : 0.040 0.154 977 Planarity : 0.004 0.035 1178 Dihedral : 4.534 55.890 1013 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.29 % Allowed : 12.57 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.30), residues: 793 helix: 1.94 (0.26), residues: 397 sheet: 0.91 (0.78), residues: 42 loop : 0.28 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.013 0.001 TYR B 495 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 7) link_NAG-ASN : angle 1.99100 ( 21) hydrogen bonds : bond 0.04123 ( 321) hydrogen bonds : angle 4.38763 ( 912) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.68672 ( 12) covalent geometry : bond 0.00348 ( 6735) covalent geometry : angle 0.50934 ( 9152) *********************** 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 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.720 Fit side-chains REVERT: E 182 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8763 (mm-30) REVERT: E 270 MET cc_start: 0.9341 (tpt) cc_final: 0.8646 (tpp) REVERT: E 291 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8195 (mm) REVERT: E 367 ASP cc_start: 0.9160 (m-30) cc_final: 0.8756 (p0) REVERT: E 474 MET cc_start: 0.8836 (mmp) cc_final: 0.8594 (mmm) REVERT: E 613 TYR cc_start: 0.7049 (t80) cc_final: 0.6543 (t80) outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.2062 time to fit residues: 16.8083 Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.067123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.053226 restraints weight = 18838.279| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.19 r_work: 0.2703 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3110 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= 0.144 Angle : 0.502 5.979 9185 Z= 0.255 Chirality : 0.040 0.153 977 Planarity : 0.003 0.036 1178 Dihedral : 4.504 56.110 1013 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.29 % Allowed : 12.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.30), residues: 793 helix: 1.93 (0.26), residues: 397 sheet: 0.83 (0.79), residues: 42 loop : 0.29 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.015 0.001 PHE E 369 TYR 0.011 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 7) link_NAG-ASN : angle 1.96543 ( 21) hydrogen bonds : bond 0.04047 ( 321) hydrogen bonds : angle 4.35633 ( 912) SS BOND : bond 0.00217 ( 6) SS BOND : angle 0.87334 ( 12) covalent geometry : bond 0.00322 ( 6735) covalent geometry : angle 0.49333 ( 9152) *********************** 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 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.796 Fit side-chains REVERT: E 182 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8757 (mm-30) REVERT: E 291 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8215 (mm) REVERT: E 367 ASP cc_start: 0.9154 (m-30) cc_final: 0.8754 (p0) REVERT: E 474 MET cc_start: 0.8837 (mmp) cc_final: 0.8611 (mmm) REVERT: E 613 TYR cc_start: 0.7040 (t80) cc_final: 0.6524 (t80) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.1942 time to fit residues: 16.2882 Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.067259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.053394 restraints weight = 18940.537| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.19 r_work: 0.2706 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3162 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= 0.139 Angle : 0.501 5.831 9185 Z= 0.254 Chirality : 0.040 0.154 977 Planarity : 0.003 0.035 1178 Dihedral : 4.492 56.200 1013 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.29 % Allowed : 12.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.30), residues: 793 helix: 1.99 (0.26), residues: 394 sheet: 0.78 (0.80), residues: 42 loop : 0.36 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.015 0.001 PHE E 369 TYR 0.013 0.001 TYR B 495 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 7) link_NAG-ASN : angle 1.97533 ( 21) hydrogen bonds : bond 0.04014 ( 321) hydrogen bonds : angle 4.36955 ( 912) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.85200 ( 12) covalent geometry : bond 0.00311 ( 6735) covalent geometry : angle 0.49163 ( 9152) *********************** 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 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.737 Fit side-chains REVERT: E 182 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8762 (mm-30) REVERT: E 291 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8331 (mm) REVERT: E 367 ASP cc_start: 0.9144 (m-30) cc_final: 0.8746 (p0) REVERT: E 474 MET cc_start: 0.8822 (mmp) cc_final: 0.8613 (mmm) REVERT: E 613 TYR cc_start: 0.7002 (t80) cc_final: 0.6432 (t80) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.2019 time to fit residues: 17.0487 Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.0040 chunk 16 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.068404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.054483 restraints weight = 18946.270| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.19 r_work: 0.2739 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 : 0.002 0.023 6748 Z= 0.106 Angle : 0.481 5.799 9185 Z= 0.244 Chirality : 0.039 0.155 977 Planarity : 0.003 0.037 1178 Dihedral : 4.369 56.526 1013 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.86 % Allowed : 13.00 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.30), residues: 793 helix: 1.99 (0.26), residues: 393 sheet: 0.77 (0.80), residues: 42 loop : 0.36 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.013 0.001 PHE E 369 TYR 0.010 0.001 TYR B 495 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 7) link_NAG-ASN : angle 1.92196 ( 21) hydrogen bonds : bond 0.03780 ( 321) hydrogen bonds : angle 4.31150 ( 912) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.88434 ( 12) covalent geometry : bond 0.00232 ( 6735) covalent geometry : angle 0.47222 ( 9152) ********************** 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 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.790 Fit side-chains REVERT: E 182 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8751 (mm-30) REVERT: E 367 ASP cc_start: 0.9148 (m-30) cc_final: 0.8713 (p0) REVERT: E 467 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8521 (mt-10) REVERT: E 613 TYR cc_start: 0.6916 (t80) cc_final: 0.6297 (t80) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.2142 time to fit residues: 17.1132 Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 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 = 0.3204 r_free = 0.3204 target = 0.067688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.053769 restraints weight = 19159.779| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.21 r_work: 0.2716 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3238 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= 0.130 Angle : 0.491 5.360 9185 Z= 0.250 Chirality : 0.040 0.154 977 Planarity : 0.003 0.037 1178 Dihedral : 4.406 56.221 1013 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.00 % Allowed : 12.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.30), residues: 793 helix: 2.04 (0.26), residues: 394 sheet: 0.80 (0.80), residues: 42 loop : 0.39 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.014 0.001 PHE E 369 TYR 0.012 0.001 TYR B 495 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.92602 ( 21) hydrogen bonds : bond 0.03938 ( 321) hydrogen bonds : angle 4.33137 ( 912) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.81911 ( 12) covalent geometry : bond 0.00290 ( 6735) covalent geometry : angle 0.48219 ( 9152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3068.67 seconds wall clock time: 54 minutes 5.58 seconds (3245.58 seconds total)