Starting phenix.real_space_refine on Sat May 10 16:08:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgw_37517/05_2025/8wgw_37517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgw_37517/05_2025/8wgw_37517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wgw_37517/05_2025/8wgw_37517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgw_37517/05_2025/8wgw_37517.map" model { file = "/net/cci-nas-00/data/ceres_data/8wgw_37517/05_2025/8wgw_37517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgw_37517/05_2025/8wgw_37517.cif" } resolution = 2.9 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= -0.005 sd= 0.079 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4199 2.51 5 N 1084 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6564 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Conformer: "B" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} bond proxies already assigned to first conformer: 1613 Chain: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 493 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 493 " occ=0.50 Time building chain proxies: 5.44, per 1000 atoms: 0.83 Number of scatterers: 6564 At special positions: 0 Unit cell: (82.016, 84.812, 119.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1243 8.00 N 1084 7.00 C 4199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B 701 " - " ASN B 322 " " NAG B 702 " - " ASN B 432 " " NAG B 703 " - " ASN B 103 " " NAG B 704 " - " ASN B 90 " " NAG B 705 " - " ASN B 53 " " NAG C 1 " - " ASN B 546 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 989.6 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 51.6% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.588A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.436A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.690A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 81 removed outlier: 3.613A pdb=" N GLN B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.533A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.670A pdb=" N ASN B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 176 through 194 removed outlier: 3.602A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.709A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.777A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 386 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.654A pdb=" N ALA B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.702A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 444 removed outlier: 3.968A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 505 through 509 removed outlier: 4.084A pdb=" N ASP B 509 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 532 removed outlier: 4.258A pdb=" N TYR B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.584A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 542' Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.794A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.757A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.820A pdb=" N LEU B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.928A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.052A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 831 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: 1.70 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2091 1.34 - 1.46: 1586 1.46 - 1.58: 3012 1.58 - 1.69: 1 1.69 - 1.81: 58 Bond restraints: 6748 Sorted by residual: bond pdb=" CB PRO B 289 " pdb=" CG PRO B 289 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" C1 NAG B 704 " pdb=" O5 NAG B 704 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" CA VAL B 339 " pdb=" CB VAL B 339 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.60e+00 bond pdb=" C2 NAG B 703 " pdb=" N2 NAG B 703 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.52e+00 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 9068 2.39 - 4.78: 91 4.78 - 7.16: 8 7.16 - 9.55: 2 9.55 - 11.94: 2 Bond angle restraints: 9171 Sorted by residual: angle pdb=" CA PRO B 289 " pdb=" N PRO B 289 " pdb=" CD PRO B 289 " ideal model delta sigma weight residual 112.00 100.06 11.94 1.40e+00 5.10e-01 7.27e+01 angle pdb=" N PRO B 289 " pdb=" CD PRO B 289 " pdb=" CG PRO B 289 " ideal model delta sigma weight residual 103.20 96.94 6.26 1.50e+00 4.44e-01 1.74e+01 angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 112.29 108.65 3.64 9.40e-01 1.13e+00 1.50e+01 angle pdb=" N GLY B 466 " pdb=" CA GLY B 466 " pdb=" C GLY B 466 " ideal model delta sigma weight residual 113.18 120.66 -7.48 2.37e+00 1.78e-01 9.96e+00 angle pdb=" N PRO B 289 " pdb=" CA PRO B 289 " pdb=" C PRO B 289 " ideal model delta sigma weight residual 111.03 115.70 -4.67 1.78e+00 3.16e-01 6.87e+00 ... (remaining 9166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 3683 21.43 - 42.85: 286 42.85 - 64.28: 52 64.28 - 85.70: 9 85.70 - 107.13: 42 Dihedral angle restraints: 4072 sinusoidal: 1737 harmonic: 2335 Sorted by residual: dihedral pdb=" CA ASN B 338 " pdb=" C ASN B 338 " pdb=" N VAL B 339 " pdb=" CA VAL B 339 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C2 NAG B 701 " pdb=" C3 NAG B 701 " pdb=" C4 NAG B 701 " pdb=" O4 NAG B 701 " ideal model delta sinusoidal sigma weight residual 175.11 67.98 107.13 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C2 NAG B 701 " pdb=" C3 NAG B 701 " pdb=" C4 NAG B 701 " pdb=" C5 NAG B 701 " ideal model delta sinusoidal sigma weight residual 53.78 -53.19 106.97 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 4069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 726 0.045 - 0.090: 195 0.090 - 0.135: 55 0.135 - 0.180: 2 0.180 - 0.225: 2 Chirality restraints: 980 Sorted by residual: chirality pdb=" CG LEU B 267 " pdb=" CB LEU B 267 " pdb=" CD1 LEU B 267 " pdb=" CD2 LEU B 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 432 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" C2 NAG B 703 " pdb=" C1 NAG B 703 " pdb=" C3 NAG B 703 " pdb=" N2 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 977 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 288 " -0.050 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO B 289 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 425 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.32e+00 pdb=" N PRO B 426 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 479 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.024 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 204 2.71 - 3.26: 6682 3.26 - 3.81: 10938 3.81 - 4.35: 13988 4.35 - 4.90: 23629 Nonbonded interactions: 55441 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.167 3.040 nonbonded pdb=" OE2 GLU B 166 " pdb=" OG SER B 170 " model vdw 2.167 3.040 nonbonded pdb=" O SER A 359 " pdb=" OG1 THR A 523 " model vdw 2.178 3.040 nonbonded pdb=" OG SER B 331 " pdb=" O ILE B 358 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASP B 382 " pdb=" OH TYR B 385 " model vdw 2.256 3.040 ... (remaining 55436 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=0.50 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: 3.410 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.670 Find NCS groups from input model: 0.050 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 : 0.004 0.163 6757 Z= 0.149 Angle : 0.597 11.938 9197 Z= 0.304 Chirality : 0.044 0.225 980 Planarity : 0.005 0.070 1179 Dihedral : 19.741 107.128 2571 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % 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: -0.16 (0.30), residues: 793 helix: 0.73 (0.27), residues: 372 sheet: -0.07 (0.73), residues: 57 loop : -0.96 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 566 HIS 0.004 0.001 HIS B 374 PHE 0.011 0.001 PHE B 369 TYR 0.022 0.001 TYR B 381 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 7) link_NAG-ASN : angle 1.34606 ( 21) link_BETA1-4 : bond 0.01854 ( 1) link_BETA1-4 : angle 2.53150 ( 3) hydrogen bonds : bond 0.14173 ( 289) hydrogen bonds : angle 6.12046 ( 831) SS BOND : bond 0.00093 ( 1) SS BOND : angle 0.08152 ( 2) covalent geometry : bond 0.00359 ( 6748) covalent geometry : angle 0.59242 ( 9171) *********************** 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 119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.720 Fit side-chains REVERT: A 444 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7801 (mtpm) REVERT: B 98 GLN cc_start: 0.7706 (tt0) cc_final: 0.7471 (tt0) REVERT: B 227 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 383 MET cc_start: 0.9016 (mtp) cc_final: 0.8801 (mtp) REVERT: B 597 ASP cc_start: 0.7476 (m-30) cc_final: 0.7135 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.2104 time to fit residues: 151.5553 Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 60 GLN B 578 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112615 restraints weight = 17711.919| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.23 r_work: 0.3131 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6757 Z= 0.214 Angle : 0.689 9.574 9197 Z= 0.331 Chirality : 0.049 0.286 980 Planarity : 0.005 0.051 1179 Dihedral : 13.740 81.655 1034 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.01 % Allowed : 11.33 % Favored : 86.66 % 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 (0.30), residues: 793 helix: 0.66 (0.27), residues: 382 sheet: -0.13 (0.73), residues: 57 loop : -1.06 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 165 HIS 0.007 0.001 HIS B 374 PHE 0.018 0.002 PHE B 400 TYR 0.042 0.002 TYR B 381 ARG 0.003 0.000 ARG B 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 7) link_NAG-ASN : angle 1.73219 ( 21) link_BETA1-4 : bond 0.02220 ( 1) link_BETA1-4 : angle 5.41974 ( 3) hydrogen bonds : bond 0.05194 ( 289) hydrogen bonds : angle 4.77393 ( 831) SS BOND : bond 0.00451 ( 1) SS BOND : angle 0.65620 ( 2) covalent geometry : bond 0.00506 ( 6748) covalent geometry : angle 0.67827 ( 9171) *********************** 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 108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.685 Fit side-chains REVERT: A 420 ASP cc_start: 0.8869 (m-30) cc_final: 0.8379 (m-30) REVERT: A 444 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7653 (mtpm) REVERT: B 98 GLN cc_start: 0.7724 (tt0) cc_final: 0.7440 (tt0) REVERT: B 217 TYR cc_start: 0.8861 (t80) cc_final: 0.8641 (t80) REVERT: B 227 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 383 MET cc_start: 0.8726 (mtp) cc_final: 0.8455 (mtp) REVERT: B 479 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7485 (mt-10) REVERT: B 571 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: B 597 ASP cc_start: 0.7542 (m-30) cc_final: 0.7024 (t0) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 1.1650 time to fit residues: 128.0900 Evaluate side-chains 99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.0030 chunk 54 optimal weight: 2.9990 overall best weight: 0.7290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 34 HIS B 159 ASN B 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.151804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115975 restraints weight = 14525.746| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.86 r_work: 0.3197 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6757 Z= 0.144 Angle : 0.606 9.678 9197 Z= 0.291 Chirality : 0.044 0.250 980 Planarity : 0.004 0.051 1179 Dihedral : 9.629 74.922 1034 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.01 % Allowed : 12.48 % Favored : 84.51 % 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: -0.15 (0.30), residues: 793 helix: 0.78 (0.27), residues: 377 sheet: -0.24 (0.73), residues: 57 loop : -0.98 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.011 0.001 PHE B 315 TYR 0.027 0.002 TYR B 381 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 7) link_NAG-ASN : angle 1.80004 ( 21) link_BETA1-4 : bond 0.01836 ( 1) link_BETA1-4 : angle 4.64453 ( 3) hydrogen bonds : bond 0.04607 ( 289) hydrogen bonds : angle 4.55455 ( 831) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.65792 ( 2) covalent geometry : bond 0.00335 ( 6748) covalent geometry : angle 0.59511 ( 9171) *********************** 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 116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.720 Fit side-chains REVERT: A 357 ARG cc_start: 0.8419 (ttt180) cc_final: 0.8112 (ttt-90) REVERT: A 420 ASP cc_start: 0.8816 (m-30) cc_final: 0.8355 (m-30) REVERT: A 444 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7668 (mtpm) REVERT: B 63 ASN cc_start: 0.8040 (m110) cc_final: 0.7722 (m110) REVERT: B 98 GLN cc_start: 0.7695 (tt0) cc_final: 0.7445 (tt0) REVERT: B 217 TYR cc_start: 0.8914 (t80) cc_final: 0.8672 (t80) REVERT: B 227 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 383 MET cc_start: 0.8693 (mtp) cc_final: 0.8450 (mtp) REVERT: B 479 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7464 (mt-10) REVERT: B 571 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: B 597 ASP cc_start: 0.7465 (m-30) cc_final: 0.6954 (t0) outliers start: 20 outliers final: 11 residues processed: 107 average time/residue: 1.0621 time to fit residues: 120.4369 Evaluate side-chains 103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114473 restraints weight = 21795.857| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.53 r_work: 0.3150 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6757 Z= 0.142 Angle : 0.589 9.691 9197 Z= 0.283 Chirality : 0.043 0.268 980 Planarity : 0.004 0.055 1179 Dihedral : 8.610 67.480 1034 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.01 % Allowed : 13.77 % Favored : 83.21 % 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: -0.12 (0.30), residues: 793 helix: 0.77 (0.27), residues: 381 sheet: -0.26 (0.73), residues: 57 loop : -0.95 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.011 0.001 PHE B 327 TYR 0.023 0.002 TYR B 385 ARG 0.002 0.000 ARG B 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 7) link_NAG-ASN : angle 1.98806 ( 21) link_BETA1-4 : bond 0.01692 ( 1) link_BETA1-4 : angle 4.66951 ( 3) hydrogen bonds : bond 0.04524 ( 289) hydrogen bonds : angle 4.47628 ( 831) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.61791 ( 2) covalent geometry : bond 0.00332 ( 6748) covalent geometry : angle 0.57574 ( 9171) *********************** 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 116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.756 Fit side-chains REVERT: A 420 ASP cc_start: 0.8874 (m-30) cc_final: 0.8427 (m-30) REVERT: A 444 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7724 (mtpm) REVERT: B 63 ASN cc_start: 0.8110 (m110) cc_final: 0.7753 (m110) REVERT: B 98 GLN cc_start: 0.7753 (tt0) cc_final: 0.7500 (tt0) REVERT: B 217 TYR cc_start: 0.9023 (t80) cc_final: 0.8789 (t80) REVERT: B 227 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7990 (mt-10) REVERT: B 479 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7550 (mt-10) REVERT: B 597 ASP cc_start: 0.7516 (m-30) cc_final: 0.6984 (t0) outliers start: 20 outliers final: 12 residues processed: 109 average time/residue: 1.0244 time to fit residues: 118.8708 Evaluate side-chains 101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114880 restraints weight = 24190.555| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 4.02 r_work: 0.3132 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6757 Z= 0.145 Angle : 0.595 9.675 9197 Z= 0.287 Chirality : 0.043 0.258 980 Planarity : 0.004 0.056 1179 Dihedral : 8.041 61.663 1034 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.30 % Allowed : 14.78 % Favored : 81.92 % 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: -0.10 (0.30), residues: 793 helix: 0.79 (0.27), residues: 381 sheet: -0.25 (0.73), residues: 57 loop : -0.93 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.010 0.001 PHE B 315 TYR 0.021 0.001 TYR B 385 ARG 0.002 0.000 ARG B 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 7) link_NAG-ASN : angle 1.86144 ( 21) link_BETA1-4 : bond 0.01832 ( 1) link_BETA1-4 : angle 4.76278 ( 3) hydrogen bonds : bond 0.04489 ( 289) hydrogen bonds : angle 4.44496 ( 831) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.59015 ( 2) covalent geometry : bond 0.00341 ( 6748) covalent geometry : angle 0.58253 ( 9171) *********************** 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 127 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.741 Fit side-chains REVERT: A 357 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8200 (ttt-90) REVERT: A 420 ASP cc_start: 0.8888 (m-30) cc_final: 0.8556 (m-30) REVERT: A 444 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7694 (mtpm) REVERT: B 63 ASN cc_start: 0.8113 (m110) cc_final: 0.7739 (m110) REVERT: B 98 GLN cc_start: 0.7705 (tt0) cc_final: 0.7450 (tt0) REVERT: B 217 TYR cc_start: 0.9006 (t80) cc_final: 0.8800 (t80) REVERT: B 227 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7943 (mt-10) REVERT: B 479 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7535 (mt-10) REVERT: B 571 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: B 597 ASP cc_start: 0.7480 (m-30) cc_final: 0.6936 (t0) outliers start: 22 outliers final: 15 residues processed: 117 average time/residue: 1.1193 time to fit residues: 138.6902 Evaluate side-chains 109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.0060 chunk 23 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 159 ASN B 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115205 restraints weight = 17312.006| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.22 r_work: 0.3171 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6757 Z= 0.131 Angle : 0.581 9.665 9197 Z= 0.281 Chirality : 0.043 0.250 980 Planarity : 0.004 0.060 1179 Dihedral : 7.521 57.228 1034 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.87 % Allowed : 14.63 % Favored : 81.49 % 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: -0.04 (0.31), residues: 793 helix: 0.80 (0.27), residues: 386 sheet: -0.24 (0.73), residues: 57 loop : -0.87 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.010 0.001 PHE B 327 TYR 0.020 0.001 TYR B 385 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 7) link_NAG-ASN : angle 1.83238 ( 21) link_BETA1-4 : bond 0.01746 ( 1) link_BETA1-4 : angle 4.93787 ( 3) hydrogen bonds : bond 0.04371 ( 289) hydrogen bonds : angle 4.42095 ( 831) SS BOND : bond 0.00231 ( 1) SS BOND : angle 0.56577 ( 2) covalent geometry : bond 0.00302 ( 6748) covalent geometry : angle 0.56767 ( 9171) *********************** 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 119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.687 Fit side-chains REVERT: A 420 ASP cc_start: 0.8840 (m-30) cc_final: 0.8512 (m-30) REVERT: A 428 ASP cc_start: 0.8078 (p0) cc_final: 0.7796 (p0) REVERT: A 444 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7696 (mtpm) REVERT: B 37 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6758 (mm-30) REVERT: B 63 ASN cc_start: 0.8103 (m110) cc_final: 0.7724 (m110) REVERT: B 98 GLN cc_start: 0.7626 (tt0) cc_final: 0.7385 (tt0) REVERT: B 217 TYR cc_start: 0.8970 (t80) cc_final: 0.8770 (t80) REVERT: B 227 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7886 (mt-10) REVERT: B 571 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: B 597 ASP cc_start: 0.7447 (m-30) cc_final: 0.6937 (t0) outliers start: 26 outliers final: 15 residues processed: 110 average time/residue: 1.0291 time to fit residues: 120.3889 Evaluate side-chains 105 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 159 ASN B 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117516 restraints weight = 14561.159| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.01 r_work: 0.3191 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6757 Z= 0.130 Angle : 0.584 9.645 9197 Z= 0.282 Chirality : 0.043 0.246 980 Planarity : 0.004 0.061 1179 Dihedral : 7.007 57.331 1034 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.44 % Allowed : 15.64 % Favored : 80.92 % 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: -0.01 (0.31), residues: 793 helix: 0.84 (0.27), residues: 386 sheet: -0.24 (0.72), residues: 57 loop : -0.87 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.010 0.001 PHE B 369 TYR 0.019 0.001 TYR B 385 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 7) link_NAG-ASN : angle 1.69894 ( 21) link_BETA1-4 : bond 0.01755 ( 1) link_BETA1-4 : angle 5.17536 ( 3) hydrogen bonds : bond 0.04327 ( 289) hydrogen bonds : angle 4.40648 ( 831) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.55653 ( 2) covalent geometry : bond 0.00302 ( 6748) covalent geometry : angle 0.57198 ( 9171) *********************** 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 121 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.680 Fit side-chains REVERT: A 420 ASP cc_start: 0.8827 (m-30) cc_final: 0.8535 (m-30) REVERT: A 444 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7754 (mtpm) REVERT: B 37 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6736 (mm-30) REVERT: B 63 ASN cc_start: 0.8102 (m110) cc_final: 0.7725 (m110) REVERT: B 98 GLN cc_start: 0.7615 (tt0) cc_final: 0.7387 (tt0) REVERT: B 171 GLU cc_start: 0.7671 (tt0) cc_final: 0.7180 (tt0) REVERT: B 227 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 571 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: B 597 ASP cc_start: 0.7287 (m-30) cc_final: 0.6862 (t0) outliers start: 23 outliers final: 16 residues processed: 113 average time/residue: 0.9804 time to fit residues: 117.8183 Evaluate side-chains 109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 14 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116759 restraints weight = 18078.661| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.36 r_work: 0.3173 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6757 Z= 0.125 Angle : 0.577 9.636 9197 Z= 0.280 Chirality : 0.042 0.246 980 Planarity : 0.004 0.064 1179 Dihedral : 6.720 57.248 1034 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.01 % Allowed : 16.21 % Favored : 80.77 % 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: -0.01 (0.31), residues: 793 helix: 0.83 (0.27), residues: 388 sheet: -0.25 (0.73), residues: 57 loop : -0.86 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.011 0.001 PHE A 338 TYR 0.019 0.001 TYR B 385 ARG 0.007 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 7) link_NAG-ASN : angle 1.61614 ( 21) link_BETA1-4 : bond 0.01699 ( 1) link_BETA1-4 : angle 5.29496 ( 3) hydrogen bonds : bond 0.04284 ( 289) hydrogen bonds : angle 4.39251 ( 831) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.56313 ( 2) covalent geometry : bond 0.00289 ( 6748) covalent geometry : angle 0.56402 ( 9171) *********************** 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 114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.693 Fit side-chains REVERT: A 357 ARG cc_start: 0.8373 (ttt180) cc_final: 0.8135 (ttt-90) REVERT: A 420 ASP cc_start: 0.8831 (m-30) cc_final: 0.8536 (m-30) REVERT: A 444 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7750 (mtpm) REVERT: B 63 ASN cc_start: 0.8104 (m110) cc_final: 0.7739 (m110) REVERT: B 98 GLN cc_start: 0.7590 (tt0) cc_final: 0.7388 (tt0) REVERT: B 227 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 571 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: B 597 ASP cc_start: 0.7278 (m-30) cc_final: 0.6840 (t0) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 1.0623 time to fit residues: 120.6713 Evaluate side-chains 105 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 overall best weight: 0.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118092 restraints weight = 18226.709| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.32 r_work: 0.3218 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6757 Z= 0.107 Angle : 0.550 9.582 9197 Z= 0.267 Chirality : 0.041 0.243 980 Planarity : 0.004 0.066 1179 Dihedral : 5.965 56.800 1034 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.58 % Allowed : 16.79 % Favored : 80.63 % 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: 0.15 (0.31), residues: 793 helix: 0.99 (0.28), residues: 384 sheet: -0.20 (0.73), residues: 57 loop : -0.80 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 165 HIS 0.004 0.001 HIS B 374 PHE 0.010 0.001 PHE A 338 TYR 0.018 0.001 TYR B 385 ARG 0.007 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 7) link_NAG-ASN : angle 1.38884 ( 21) link_BETA1-4 : bond 0.01784 ( 1) link_BETA1-4 : angle 5.53639 ( 3) hydrogen bonds : bond 0.03935 ( 289) hydrogen bonds : angle 4.27491 ( 831) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.41119 ( 2) covalent geometry : bond 0.00242 ( 6748) covalent geometry : angle 0.53730 ( 9171) *********************** 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 114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8800 (m-30) cc_final: 0.8493 (m-30) REVERT: A 428 ASP cc_start: 0.8083 (p0) cc_final: 0.7813 (p0) REVERT: A 444 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7743 (mtpm) REVERT: B 63 ASN cc_start: 0.8093 (m110) cc_final: 0.7734 (m110) REVERT: B 98 GLN cc_start: 0.7514 (tt0) cc_final: 0.7306 (tt0) REVERT: B 142 LEU cc_start: 0.7417 (mp) cc_final: 0.6631 (mt) REVERT: B 227 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7892 (mt-10) REVERT: B 574 VAL cc_start: 0.8936 (t) cc_final: 0.8656 (m) REVERT: B 597 ASP cc_start: 0.7187 (m-30) cc_final: 0.6854 (t0) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 1.0117 time to fit residues: 114.9032 Evaluate side-chains 101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118009 restraints weight = 18326.205| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.30 r_work: 0.3185 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6757 Z= 0.147 Angle : 0.579 9.558 9197 Z= 0.282 Chirality : 0.043 0.243 980 Planarity : 0.004 0.067 1179 Dihedral : 5.891 57.239 1034 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.15 % Allowed : 17.93 % Favored : 79.91 % 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: 0.11 (0.31), residues: 793 helix: 0.96 (0.27), residues: 387 sheet: -0.10 (0.73), residues: 57 loop : -0.86 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.011 0.001 PHE B 369 TYR 0.020 0.002 TYR B 385 ARG 0.007 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 7) link_NAG-ASN : angle 1.42942 ( 21) link_BETA1-4 : bond 0.01960 ( 1) link_BETA1-4 : angle 5.59954 ( 3) hydrogen bonds : bond 0.04325 ( 289) hydrogen bonds : angle 4.36683 ( 831) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.67675 ( 2) covalent geometry : bond 0.00349 ( 6748) covalent geometry : angle 0.56625 ( 9171) ********************** 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 106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.667 Fit side-chains REVERT: A 420 ASP cc_start: 0.8833 (m-30) cc_final: 0.8527 (m-30) REVERT: A 444 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7772 (mtpm) REVERT: B 63 ASN cc_start: 0.8071 (m110) cc_final: 0.7708 (m110) REVERT: B 171 GLU cc_start: 0.7627 (tt0) cc_final: 0.7032 (pt0) REVERT: B 227 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 597 ASP cc_start: 0.7269 (m-30) cc_final: 0.6899 (t0) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 1.0644 time to fit residues: 115.1001 Evaluate side-chains 101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114987 restraints weight = 18170.555| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.24 r_work: 0.3142 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6757 Z= 0.202 Angle : 0.629 9.642 9197 Z= 0.310 Chirality : 0.044 0.248 980 Planarity : 0.005 0.066 1179 Dihedral : 6.070 58.061 1034 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.15 % Allowed : 18.36 % Favored : 79.48 % 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: -0.05 (0.31), residues: 793 helix: 0.80 (0.27), residues: 388 sheet: -0.21 (0.73), residues: 57 loop : -0.91 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 165 HIS 0.007 0.001 HIS B 374 PHE 0.015 0.002 PHE A 338 TYR 0.021 0.002 TYR B 385 ARG 0.007 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 7) link_NAG-ASN : angle 1.59516 ( 21) link_BETA1-4 : bond 0.02120 ( 1) link_BETA1-4 : angle 5.72496 ( 3) hydrogen bonds : bond 0.04974 ( 289) hydrogen bonds : angle 4.54885 ( 831) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.76236 ( 2) covalent geometry : bond 0.00483 ( 6748) covalent geometry : angle 0.61625 ( 9171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5061.05 seconds wall clock time: 87 minutes 54.96 seconds (5274.96 seconds total)