Starting phenix.real_space_refine on Wed Sep 17 21:40:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wbl_32405/09_2025/7wbl_32405.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wbl_32405/09_2025/7wbl_32405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wbl_32405/09_2025/7wbl_32405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wbl_32405/09_2025/7wbl_32405.map" model { file = "/net/cci-nas-00/data/ceres_data/7wbl_32405/09_2025/7wbl_32405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wbl_32405/09_2025/7wbl_32405.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6402 atoms to isotropic. 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 4152 2.51 5 N 1073 2.21 5 O 1221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6484 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.61, per 1000 atoms: 0.25 Number of scatterers: 6484 At special positions: 0 Unit cell: (75.71, 86.43, 123.28, 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 1221 8.00 N 1073 7.00 C 4152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 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=2.05 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 A 801 " - " ASN A 103 " " NAG A 802 " - " ASN A 53 " " NAG A 803 " - " ASN A 90 " " NAG A 804 " - " ASN A 322 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 324.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 374 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 56.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.952A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.588A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.925A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.092A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.690A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.576A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.545A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.684A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.818A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.820A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.579A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.710A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.525A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 4.051A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.633A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.733A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.938A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.816A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.893A 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: 3.563A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.143A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.299A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.563A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2094 1.35 - 1.48: 1774 1.48 - 1.61: 2741 1.61 - 1.74: 0 1.74 - 1.87: 58 Bond restraints: 6667 Sorted by residual: bond pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 1.334 1.505 -0.171 2.34e-02 1.83e+03 5.36e+01 bond pdb=" N GLY A 352 " pdb=" CA GLY A 352 " ideal model delta sigma weight residual 1.448 1.475 -0.027 9.00e-03 1.23e+04 8.81e+00 bond pdb=" N ARG B 498 " pdb=" CA ARG B 498 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.50e-02 4.44e+03 7.56e+00 bond pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.19e-02 7.06e+03 6.98e+00 bond pdb=" N GLU A 35 " pdb=" CA GLU A 35 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.28e-02 6.10e+03 6.30e+00 ... (remaining 6662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 8969 2.49 - 4.97: 82 4.97 - 7.46: 7 7.46 - 9.94: 3 9.94 - 12.43: 2 Bond angle restraints: 9063 Sorted by residual: angle pdb=" C ARG B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.84 132.27 -12.43 1.25e+00 6.40e-01 9.88e+01 angle pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" O GLY A 352 " ideal model delta sigma weight residual 122.45 118.18 4.27 7.20e-01 1.93e+00 3.51e+01 angle pdb=" CA ARG B 498 " pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 117.93 126.11 -8.18 1.42e+00 4.96e-01 3.32e+01 angle pdb=" CA CYS B 379 " pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 114.40 126.48 -12.08 2.30e+00 1.89e-01 2.76e+01 angle pdb=" O ARG B 498 " pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 121.72 117.79 3.93 9.80e-01 1.04e+00 1.61e+01 ... (remaining 9058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 3467 16.79 - 33.57: 396 33.57 - 50.36: 90 50.36 - 67.14: 29 67.14 - 83.93: 8 Dihedral angle restraints: 3990 sinusoidal: 1664 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 45.60 47.40 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 56.80 36.20 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -114.71 28.71 1 1.00e+01 1.00e-02 1.18e+01 ... (remaining 3987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 798 0.055 - 0.110: 141 0.110 - 0.164: 17 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 959 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ARG B 498 " pdb=" N ARG B 498 " pdb=" C ARG B 498 " pdb=" CB ARG B 498 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 956 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 497 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C PHE B 497 " 0.069 2.00e-02 2.50e+03 pdb=" O PHE B 497 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG B 498 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 478 " 0.013 2.00e-02 2.50e+03 1.17e-02 3.44e+00 pdb=" CG TRP A 478 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 478 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 478 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 478 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 478 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 478 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 478 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO A 583 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.020 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 156 2.71 - 3.26: 6280 3.26 - 3.80: 9928 3.80 - 4.35: 12420 4.35 - 4.90: 21633 Nonbonded interactions: 50417 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 805 " model vdw 2.158 2.230 nonbonded pdb=" O SER B 496 " pdb=" OH TYR B 501 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.235 3.040 nonbonded pdb=" O MET A 152 " pdb=" NH1 ARG A 161 " model vdw 2.302 3.120 ... (remaining 50412 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.960 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 0.171 6680 Z= 0.208 Angle : 0.609 12.427 9089 Z= 0.344 Chirality : 0.044 0.274 959 Planarity : 0.004 0.040 1170 Dihedral : 15.429 83.928 2475 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.56 % Favored : 96.06 % Rotamer: Outliers : 0.72 % Allowed : 0.86 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.30), residues: 787 helix: 1.27 (0.27), residues: 379 sheet: 0.20 (0.74), residues: 46 loop : -0.59 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.017 0.001 TYR B 501 PHE 0.009 0.001 PHE A 308 TRP 0.031 0.001 TRP A 478 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6667) covalent geometry : angle 0.59533 ( 9063) SS BOND : bond 0.01108 ( 7) SS BOND : angle 1.91911 ( 14) hydrogen bonds : bond 0.14089 ( 302) hydrogen bonds : angle 5.84379 ( 846) metal coordination : bond 0.00198 ( 2) link_NAG-ASN : bond 0.00729 ( 4) link_NAG-ASN : angle 2.97912 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.254 Fit side-chains REVERT: A 159 ASN cc_start: 0.6522 (m-40) cc_final: 0.6261 (m-40) REVERT: A 269 ASP cc_start: 0.7718 (p0) cc_final: 0.7295 (p0) REVERT: B 472 ILE cc_start: 0.7817 (mp) cc_final: 0.7548 (tp) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.0722 time to fit residues: 10.1691 Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 6.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.194307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.156502 restraints weight = 7545.725| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.13 r_work: 0.3538 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6680 Z= 0.135 Angle : 0.534 10.476 9089 Z= 0.275 Chirality : 0.042 0.258 959 Planarity : 0.004 0.038 1170 Dihedral : 5.818 56.703 947 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 1.58 % Allowed : 7.61 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.30), residues: 787 helix: 1.36 (0.27), residues: 383 sheet: 0.12 (0.73), residues: 46 loop : -0.60 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.018 0.002 TYR B 501 PHE 0.011 0.001 PHE A 308 TRP 0.018 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6667) covalent geometry : angle 0.52269 ( 9063) SS BOND : bond 0.00547 ( 7) SS BOND : angle 1.53805 ( 14) hydrogen bonds : bond 0.05035 ( 302) hydrogen bonds : angle 4.65073 ( 846) metal coordination : bond 0.00327 ( 2) link_NAG-ASN : bond 0.00610 ( 4) link_NAG-ASN : angle 2.66446 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.202 Fit side-chains REVERT: A 269 ASP cc_start: 0.7700 (p0) cc_final: 0.7434 (p0) REVERT: B 472 ILE cc_start: 0.7954 (mp) cc_final: 0.7650 (tp) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.0653 time to fit residues: 8.6951 Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 0.0000 chunk 45 optimal weight: 0.0470 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.199149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.161376 restraints weight = 7446.191| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.24 r_work: 0.3561 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 6680 Z= 0.101 Angle : 0.490 11.359 9089 Z= 0.250 Chirality : 0.041 0.233 959 Planarity : 0.003 0.033 1170 Dihedral : 5.018 50.057 947 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 1.01 % Allowed : 10.34 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.30), residues: 787 helix: 1.58 (0.27), residues: 381 sheet: 0.41 (0.76), residues: 46 loop : -0.44 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 482 TYR 0.014 0.001 TYR A 50 PHE 0.009 0.001 PHE A 308 TRP 0.020 0.001 TRP A 478 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6667) covalent geometry : angle 0.48070 ( 9063) SS BOND : bond 0.00802 ( 7) SS BOND : angle 1.54742 ( 14) hydrogen bonds : bond 0.03997 ( 302) hydrogen bonds : angle 4.42196 ( 846) metal coordination : bond 0.00167 ( 2) link_NAG-ASN : bond 0.00478 ( 4) link_NAG-ASN : angle 2.06812 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.282 Fit side-chains REVERT: A 269 ASP cc_start: 0.7543 (p0) cc_final: 0.7104 (p0) REVERT: A 287 GLN cc_start: 0.8064 (pm20) cc_final: 0.7690 (mm-40) REVERT: A 479 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6199 (mt-10) REVERT: B 472 ILE cc_start: 0.7944 (mp) cc_final: 0.7676 (tp) outliers start: 7 outliers final: 6 residues processed: 103 average time/residue: 0.0678 time to fit residues: 10.0085 Evaluate side-chains 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 194 ASN A 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.198455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.160091 restraints weight = 7565.855| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.03 r_work: 0.3560 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6680 Z= 0.120 Angle : 0.503 11.892 9089 Z= 0.258 Chirality : 0.041 0.214 959 Planarity : 0.004 0.035 1170 Dihedral : 4.666 36.736 945 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 2.16 % Allowed : 11.35 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.30), residues: 787 helix: 1.53 (0.27), residues: 382 sheet: 0.11 (0.68), residues: 56 loop : -0.40 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 482 TYR 0.012 0.001 TYR B 501 PHE 0.011 0.001 PHE A 308 TRP 0.019 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6667) covalent geometry : angle 0.49536 ( 9063) SS BOND : bond 0.00666 ( 7) SS BOND : angle 1.61177 ( 14) hydrogen bonds : bond 0.04355 ( 302) hydrogen bonds : angle 4.38968 ( 846) metal coordination : bond 0.00289 ( 2) link_NAG-ASN : bond 0.00428 ( 4) link_NAG-ASN : angle 1.86212 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7650 (p0) cc_final: 0.7354 (p0) REVERT: A 287 GLN cc_start: 0.8001 (pm20) cc_final: 0.7653 (mm-40) REVERT: A 293 VAL cc_start: 0.6926 (OUTLIER) cc_final: 0.6721 (t) REVERT: B 472 ILE cc_start: 0.7975 (mp) cc_final: 0.7723 (tp) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.0663 time to fit residues: 9.6593 Evaluate side-chains 100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 0.0070 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.193546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.154745 restraints weight = 7647.167| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.14 r_work: 0.3518 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6680 Z= 0.148 Angle : 0.531 11.916 9089 Z= 0.272 Chirality : 0.043 0.207 959 Planarity : 0.004 0.037 1170 Dihedral : 4.652 32.571 945 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.16 % Allowed : 11.93 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.30), residues: 787 helix: 1.49 (0.27), residues: 376 sheet: 0.14 (0.68), residues: 56 loop : -0.42 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 482 TYR 0.011 0.002 TYR A 587 PHE 0.013 0.001 PHE A 308 TRP 0.015 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6667) covalent geometry : angle 0.52365 ( 9063) SS BOND : bond 0.00697 ( 7) SS BOND : angle 1.55227 ( 14) hydrogen bonds : bond 0.04747 ( 302) hydrogen bonds : angle 4.45313 ( 846) metal coordination : bond 0.00437 ( 2) link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 1.85832 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 287 GLN cc_start: 0.7997 (pm20) cc_final: 0.7763 (mm-40) REVERT: A 293 VAL cc_start: 0.7020 (OUTLIER) cc_final: 0.6806 (t) REVERT: B 472 ILE cc_start: 0.8009 (mp) cc_final: 0.7735 (tp) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.0601 time to fit residues: 8.8198 Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 194 ASN A 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.196909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.161314 restraints weight = 7493.759| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.19 r_work: 0.3539 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 6680 Z= 0.109 Angle : 0.503 11.813 9089 Z= 0.255 Chirality : 0.041 0.200 959 Planarity : 0.003 0.034 1170 Dihedral : 4.312 31.428 945 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.01 % Allowed : 12.64 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.30), residues: 787 helix: 1.65 (0.27), residues: 376 sheet: 0.25 (0.68), residues: 56 loop : -0.39 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 482 TYR 0.010 0.001 TYR A 50 PHE 0.010 0.001 PHE A 308 TRP 0.020 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6667) covalent geometry : angle 0.49554 ( 9063) SS BOND : bond 0.00827 ( 7) SS BOND : angle 1.70597 ( 14) hydrogen bonds : bond 0.04082 ( 302) hydrogen bonds : angle 4.36872 ( 846) metal coordination : bond 0.00252 ( 2) link_NAG-ASN : bond 0.00356 ( 4) link_NAG-ASN : angle 1.69372 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7562 (p0) cc_final: 0.7082 (p0) REVERT: A 287 GLN cc_start: 0.7937 (pm20) cc_final: 0.7704 (mm-40) REVERT: A 293 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6705 (t) REVERT: B 472 ILE cc_start: 0.7990 (mp) cc_final: 0.7735 (tp) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.0639 time to fit residues: 9.1638 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.196635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.159014 restraints weight = 7436.827| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.16 r_work: 0.3541 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6680 Z= 0.112 Angle : 0.519 11.728 9089 Z= 0.260 Chirality : 0.041 0.196 959 Planarity : 0.003 0.034 1170 Dihedral : 4.260 30.860 945 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 2.01 % Allowed : 13.94 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.30), residues: 787 helix: 1.63 (0.27), residues: 378 sheet: 0.34 (0.69), residues: 56 loop : -0.38 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.009 0.001 TYR B 423 PHE 0.011 0.001 PHE A 308 TRP 0.020 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6667) covalent geometry : angle 0.51274 ( 9063) SS BOND : bond 0.00783 ( 7) SS BOND : angle 1.59275 ( 14) hydrogen bonds : bond 0.04142 ( 302) hydrogen bonds : angle 4.36055 ( 846) metal coordination : bond 0.00265 ( 2) link_NAG-ASN : bond 0.00358 ( 4) link_NAG-ASN : angle 1.66621 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 287 GLN cc_start: 0.7983 (pm20) cc_final: 0.7668 (mm-40) REVERT: B 472 ILE cc_start: 0.8003 (mp) cc_final: 0.7748 (tp) outliers start: 14 outliers final: 11 residues processed: 97 average time/residue: 0.0621 time to fit residues: 8.8621 Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.197628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.160474 restraints weight = 7477.866| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.25 r_work: 0.3534 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 6680 Z= 0.106 Angle : 0.513 11.740 9089 Z= 0.258 Chirality : 0.041 0.195 959 Planarity : 0.003 0.033 1170 Dihedral : 4.160 29.889 945 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 1.58 % Allowed : 14.51 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.30), residues: 787 helix: 1.70 (0.27), residues: 378 sheet: 0.46 (0.70), residues: 56 loop : -0.36 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.013 0.001 TYR A 516 PHE 0.010 0.001 PHE A 308 TRP 0.022 0.001 TRP A 478 HIS 0.004 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6667) covalent geometry : angle 0.50634 ( 9063) SS BOND : bond 0.00756 ( 7) SS BOND : angle 1.57154 ( 14) hydrogen bonds : bond 0.03954 ( 302) hydrogen bonds : angle 4.33113 ( 846) metal coordination : bond 0.00232 ( 2) link_NAG-ASN : bond 0.00353 ( 4) link_NAG-ASN : angle 1.62611 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 287 GLN cc_start: 0.7969 (pm20) cc_final: 0.7643 (mm-40) REVERT: B 472 ILE cc_start: 0.7989 (mp) cc_final: 0.7735 (tp) outliers start: 11 outliers final: 11 residues processed: 91 average time/residue: 0.0617 time to fit residues: 8.2058 Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.190061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.150701 restraints weight = 7645.765| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.29 r_work: 0.3470 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6680 Z= 0.188 Angle : 0.604 11.824 9089 Z= 0.308 Chirality : 0.045 0.188 959 Planarity : 0.004 0.039 1170 Dihedral : 4.872 32.228 945 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 1.87 % Allowed : 14.66 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.30), residues: 787 helix: 1.30 (0.27), residues: 378 sheet: 0.23 (0.68), residues: 56 loop : -0.53 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 482 TYR 0.015 0.002 TYR A 587 PHE 0.019 0.002 PHE A 308 TRP 0.024 0.002 TRP A 478 HIS 0.005 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 6667) covalent geometry : angle 0.59639 ( 9063) SS BOND : bond 0.00778 ( 7) SS BOND : angle 1.81036 ( 14) hydrogen bonds : bond 0.05450 ( 302) hydrogen bonds : angle 4.56810 ( 846) metal coordination : bond 0.00547 ( 2) link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 1.98445 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 159 ASN cc_start: 0.6907 (m-40) cc_final: 0.6519 (m-40) REVERT: A 287 GLN cc_start: 0.7994 (pm20) cc_final: 0.7778 (mm-40) REVERT: B 472 ILE cc_start: 0.8056 (mp) cc_final: 0.7759 (tp) outliers start: 13 outliers final: 12 residues processed: 95 average time/residue: 0.0708 time to fit residues: 9.4444 Evaluate side-chains 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0000 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.196187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.158285 restraints weight = 7432.323| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.15 r_work: 0.3524 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 6680 Z= 0.107 Angle : 0.524 11.990 9089 Z= 0.263 Chirality : 0.041 0.189 959 Planarity : 0.003 0.036 1170 Dihedral : 4.385 31.302 945 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 1.72 % Allowed : 14.94 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.30), residues: 787 helix: 1.54 (0.27), residues: 378 sheet: 0.37 (0.70), residues: 56 loop : -0.42 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.016 0.001 TYR A 515 PHE 0.010 0.001 PHE A 308 TRP 0.027 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6667) covalent geometry : angle 0.51755 ( 9063) SS BOND : bond 0.00743 ( 7) SS BOND : angle 1.61127 ( 14) hydrogen bonds : bond 0.04096 ( 302) hydrogen bonds : angle 4.39433 ( 846) metal coordination : bond 0.00174 ( 2) link_NAG-ASN : bond 0.00335 ( 4) link_NAG-ASN : angle 1.69315 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.7543 (p0) cc_final: 0.7104 (p0) REVERT: A 287 GLN cc_start: 0.7883 (pm20) cc_final: 0.7657 (mm-40) REVERT: B 472 ILE cc_start: 0.8020 (mp) cc_final: 0.7747 (tp) outliers start: 12 outliers final: 12 residues processed: 92 average time/residue: 0.0643 time to fit residues: 8.6433 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.200349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.162509 restraints weight = 7445.427| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.18 r_work: 0.3553 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6680 Z= 0.097 Angle : 0.501 11.609 9089 Z= 0.250 Chirality : 0.040 0.195 959 Planarity : 0.003 0.031 1170 Dihedral : 3.939 28.476 945 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 1.58 % Allowed : 15.09 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.31), residues: 787 helix: 1.66 (0.27), residues: 384 sheet: 0.63 (0.74), residues: 56 loop : -0.29 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.013 0.001 TYR A 515 PHE 0.007 0.001 PHE A 308 TRP 0.025 0.001 TRP A 478 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 6667) covalent geometry : angle 0.49494 ( 9063) SS BOND : bond 0.00716 ( 7) SS BOND : angle 1.54855 ( 14) hydrogen bonds : bond 0.03614 ( 302) hydrogen bonds : angle 4.26829 ( 846) metal coordination : bond 0.00141 ( 2) link_NAG-ASN : bond 0.00313 ( 4) link_NAG-ASN : angle 1.60219 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.06 seconds wall clock time: 27 minutes 38.59 seconds (1658.59 seconds total)