Starting phenix.real_space_refine on Tue Aug 4 19:56:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yss_73429/08_2026/9yss_73429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yss_73429/08_2026/9yss_73429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yss_73429/08_2026/9yss_73429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yss_73429/08_2026/9yss_73429.map" model { file = "/net/cci-nas-00/data/ceres_data/9yss_73429/08_2026/9yss_73429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yss_73429/08_2026/9yss_73429.cif" } resolution = 3.67 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4043 2.51 5 N 1037 2.21 5 O 1199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6312 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4752 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 25, 'TRANS': 556} Chain breaks: 1 Chain: "B" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1448 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} 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: "D" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.14, per 1000 atoms: 0.18 Number of scatterers: 6312 At special positions: 0 Unit cell: (99.84, 69.888, 110.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1199 8.00 N 1037 7.00 C 4043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 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 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 D 1 " - " NAG D 2 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 432 " " NAG A 703 " - " ASN A 90 " " NAG B1301 " - " ASN B 355 " " NAG C 1 " - " ASN A 546 " " NAG D 1 " - " ASN A 103 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 254.1 milliseconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 58.3% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 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 92 through 102 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.695A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.820A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 Proline residue: A 178 - end of helix removed outlier: 3.758A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) 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 218 through 251 removed outlier: 3.888A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.702A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) 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 279 removed outlier: 3.751A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.859A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.870A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.836A 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: 3.889A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.202A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) 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 483 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.129A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.713A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.712A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.692A pdb=" N ALA B 373 " --> pdb=" O TYR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.534A pdb=" N LEU B 391 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.658A pdb=" N ALA B 412 " --> pdb=" O SER B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.620A pdb=" N ASP B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.245A 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: 6.093A 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 359 removed outlier: 3.859A pdb=" N VAL B 396 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 395 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 453 through 455 Processing sheet with id=AA5, first strand: chain 'B' and resid 474 through 475 305 hydrogen bonds defined for protein. 879 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: 0.69 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1964 1.34 - 1.46: 1303 1.46 - 1.58: 3171 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6492 Sorted by residual: bond pdb=" N ILE A 54 " pdb=" CA ILE A 54 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.98e+00 bond pdb=" N GLU A 589 " pdb=" CA GLU A 589 " ideal model delta sigma weight residual 1.462 1.488 -0.026 8.50e-03 1.38e+04 9.48e+00 bond pdb=" N VAL B 434 " pdb=" CA VAL B 434 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.37e+00 bond pdb=" N TYR A 83 " pdb=" CA TYR A 83 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.78e+00 bond pdb=" N ILE A 21 " pdb=" CA ILE A 21 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.24e+00 ... (remaining 6487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 8515 1.93 - 3.85: 277 3.85 - 5.78: 21 5.78 - 7.71: 1 7.71 - 9.63: 2 Bond angle restraints: 8816 Sorted by residual: angle pdb=" N LYS A 481 " pdb=" CA LYS A 481 " pdb=" C LYS A 481 " ideal model delta sigma weight residual 112.45 107.11 5.34 1.39e+00 5.18e-01 1.48e+01 angle pdb=" N PHE A 588 " pdb=" CA PHE A 588 " pdb=" C PHE A 588 " ideal model delta sigma weight residual 112.72 108.87 3.85 1.14e+00 7.69e-01 1.14e+01 angle pdb=" C ARG B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 123.00 -3.44 1.02e+00 9.61e-01 1.14e+01 angle pdb=" CA VAL B 383 " pdb=" C VAL B 383 " pdb=" O VAL B 383 " ideal model delta sigma weight residual 120.96 118.16 2.80 8.40e-01 1.42e+00 1.11e+01 angle pdb=" N THR A 52 " pdb=" CA THR A 52 " pdb=" C THR A 52 " ideal model delta sigma weight residual 113.72 109.47 4.25 1.30e+00 5.92e-01 1.07e+01 ... (remaining 8811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 3410 15.95 - 31.90: 343 31.90 - 47.84: 107 47.84 - 63.79: 47 63.79 - 79.74: 5 Dihedral angle restraints: 3912 sinusoidal: 1678 harmonic: 2234 Sorted by residual: 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 -130.46 44.46 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA ASN A 508 " pdb=" C ASN A 508 " pdb=" N ASP A 509 " pdb=" CA ASP A 509 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP A 543 " pdb=" CB ASP A 543 " pdb=" CG ASP A 543 " pdb=" OD1 ASP A 543 " ideal model delta sinusoidal sigma weight residual -30.00 -85.01 55.01 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 3909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 677 0.046 - 0.092: 168 0.092 - 0.138: 73 0.138 - 0.184: 13 0.184 - 0.229: 6 Chirality restraints: 937 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.82e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.28 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 934 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 480 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C MET A 480 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A 480 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 481 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 41 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C TYR A 41 " 0.042 2.00e-02 2.50e+03 pdb=" O TYR A 41 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN A 42 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 491 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO A 492 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 492 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 492 " -0.032 5.00e-02 4.00e+02 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 3158 2.97 - 3.46: 6446 3.46 - 3.94: 10631 3.94 - 4.42: 11887 4.42 - 4.90: 19180 Nonbonded interactions: 51302 Sorted by model distance: nonbonded pdb=" O VAL A 212 " pdb=" OD1 ASP A 216 " model vdw 2.493 3.040 nonbonded pdb=" NE2 GLN A 81 " pdb=" O GLN A 101 " model vdw 2.501 3.120 nonbonded pdb=" O LYS A 74 " pdb=" OG SER A 77 " model vdw 2.549 3.040 nonbonded pdb=" O SER B 447 " pdb=" NH1 ARG B 498 " model vdw 2.560 3.120 nonbonded pdb=" O ALA A 80 " pdb=" NE2 GLN A 101 " model vdw 2.574 3.120 ... (remaining 51297 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 9.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 0.045 6502 Z= 0.311 Angle : 0.727 9.632 8844 Z= 0.463 Chirality : 0.051 0.229 937 Planarity : 0.005 0.063 1127 Dihedral : 15.347 79.741 2472 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.75 % Allowed : 18.68 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.30), residues: 755 helix: 0.95 (0.26), residues: 389 sheet: -0.92 (0.91), residues: 31 loop : -0.69 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 115 TYR 0.014 0.001 TYR A 385 PHE 0.012 0.001 PHE A 452 TRP 0.014 0.001 TRP A 69 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.31 ( 6492) covalent geometry : angle 0.71677 / 0.46 ( 8816) SS BOND : bond 0.00180 / 0.09 ( 2) SS BOND : angle 0.54198 / 0.27 ( 4) hydrogen bonds : bond 0.14654 / 9.67 ( 305) hydrogen bonds : angle 5.98062 / 4.26 ( 879) link_BETA1-4 : bond 0.03242 / 1.55 ( 2) link_BETA1-4 : angle 4.09201 / 2.14 ( 6) link_NAG-ASN : bond 0.00384 / 0.20 ( 6) link_NAG-ASN : angle 1.52548 / 1.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.7393 (tttt) cc_final: 0.7055 (mtpp) REVERT: A 152 MET cc_start: 0.7504 (mmm) cc_final: 0.6754 (mmm) REVERT: A 168 TRP cc_start: 0.7113 (t-100) cc_final: 0.6537 (t-100) REVERT: A 201 ASP cc_start: 0.7148 (t0) cc_final: 0.5909 (t0) REVERT: A 206 ASP cc_start: 0.6746 (t0) cc_final: 0.6531 (t0) REVERT: A 219 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6509 (mtp85) REVERT: A 232 GLU cc_start: 0.7152 (tp30) cc_final: 0.6793 (tp30) REVERT: A 234 LYS cc_start: 0.8258 (mttt) cc_final: 0.7880 (ttmm) REVERT: A 247 LYS cc_start: 0.7833 (mmmm) cc_final: 0.7181 (mmmm) REVERT: A 357 ARG cc_start: 0.8400 (mtt-85) cc_final: 0.8170 (mtt180) REVERT: A 437 ASN cc_start: 0.7846 (m-40) cc_final: 0.7574 (m-40) REVERT: A 485 VAL cc_start: 0.8664 (t) cc_final: 0.8418 (p) REVERT: A 488 VAL cc_start: 0.7873 (p) cc_final: 0.7507 (m) REVERT: B 400 SER cc_start: 0.8536 (m) cc_final: 0.7919 (p) REVERT: B 455 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.7921 (ttm110) REVERT: B 494 SER cc_start: 0.8766 (t) cc_final: 0.8368 (m) outliers start: 5 outliers final: 4 residues processed: 191 average time/residue: 0.0628 time to fit residues: 15.6721 Evaluate side-chains 184 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 34 HIS A 154 ASN A 340 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110867 restraints weight = 10049.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114065 restraints weight = 5130.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116212 restraints weight = 3164.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117456 restraints weight = 2222.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118203 restraints weight = 1752.060| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6502 Z= 0.165 Angle : 0.629 19.172 8844 Z= 0.299 Chirality : 0.048 0.666 937 Planarity : 0.004 0.048 1127 Dihedral : 6.848 55.593 1006 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.93 % Allowed : 16.59 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.30), residues: 755 helix: 1.24 (0.26), residues: 390 sheet: -0.73 (0.81), residues: 31 loop : -0.66 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 482 TYR 0.018 0.001 TYR A 385 PHE 0.018 0.001 PHE A 369 TRP 0.012 0.001 TRP A 48 HIS 0.009 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6492) covalent geometry : angle 0.57697 / 0.29 ( 8816) SS BOND : bond 0.00312 / 0.15 ( 2) SS BOND : angle 0.77888 / 0.39 ( 4) hydrogen bonds : bond 0.05123 / 3.49 ( 305) hydrogen bonds : angle 4.84082 / 3.57 ( 879) link_BETA1-4 : bond 0.00679 / 0.35 ( 2) link_BETA1-4 : angle 2.20427 / 1.04 ( 6) link_NAG-ASN : bond 0.00934 / 0.50 ( 6) link_NAG-ASN : angle 5.42215 / 4.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7413 (mmm) cc_final: 0.6992 (mmm) REVERT: A 168 TRP cc_start: 0.7176 (t-100) cc_final: 0.6601 (t-100) REVERT: A 201 ASP cc_start: 0.7111 (t0) cc_final: 0.6048 (t0) REVERT: A 206 ASP cc_start: 0.6791 (t0) cc_final: 0.6545 (t0) REVERT: A 219 ARG cc_start: 0.7840 (mpp80) cc_final: 0.6720 (mtp85) REVERT: A 234 LYS cc_start: 0.8257 (mttt) cc_final: 0.7908 (ttmm) REVERT: A 247 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7302 (mmmm) REVERT: A 349 TRP cc_start: 0.8381 (m100) cc_final: 0.7901 (m-10) REVERT: A 435 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6914 (pt0) REVERT: A 437 ASN cc_start: 0.7663 (m-40) cc_final: 0.7401 (m-40) REVERT: A 459 TRP cc_start: 0.8015 (t60) cc_final: 0.7720 (t60) REVERT: A 476 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6987 (mmtt) REVERT: A 488 VAL cc_start: 0.7839 (p) cc_final: 0.7582 (t) REVERT: B 400 SER cc_start: 0.8626 (m) cc_final: 0.8021 (p) REVERT: B 424 TYR cc_start: 0.7881 (t80) cc_final: 0.7598 (t80) REVERT: B 455 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.8015 (ttm110) REVERT: B 494 SER cc_start: 0.8706 (t) cc_final: 0.8309 (m) outliers start: 33 outliers final: 24 residues processed: 196 average time/residue: 0.0599 time to fit residues: 15.5707 Evaluate side-chains 206 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109139 restraints weight = 10037.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112219 restraints weight = 5137.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114289 restraints weight = 3193.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115761 restraints weight = 2259.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116713 restraints weight = 1731.334| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6502 Z= 0.215 Angle : 0.620 15.051 8844 Z= 0.305 Chirality : 0.046 0.450 937 Planarity : 0.004 0.050 1127 Dihedral : 6.974 58.381 1000 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.33 % Allowed : 18.39 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 755 helix: 1.03 (0.26), residues: 394 sheet: -0.49 (0.82), residues: 31 loop : -0.68 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 509 TYR 0.021 0.002 TYR B 501 PHE 0.020 0.002 PHE A 369 TRP 0.014 0.002 TRP B 437 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 ( 6492) covalent geometry : angle 0.58302 / 0.30 ( 8816) SS BOND : bond 0.00377 / 0.19 ( 2) SS BOND : angle 0.91422 / 0.46 ( 4) hydrogen bonds : bond 0.05358 / 3.67 ( 305) hydrogen bonds : angle 4.70528 / 3.51 ( 879) link_BETA1-4 : bond 0.00586 / 0.29 ( 2) link_BETA1-4 : angle 2.31614 / 1.14 ( 6) link_NAG-ASN : bond 0.00585 / 0.31 ( 6) link_NAG-ASN : angle 4.53186 / 3.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8538 (mm110) cc_final: 0.8271 (mm-40) REVERT: A 83 TYR cc_start: 0.7972 (m-80) cc_final: 0.7644 (m-80) REVERT: A 152 MET cc_start: 0.7437 (mmm) cc_final: 0.6923 (mmm) REVERT: A 168 TRP cc_start: 0.7221 (t-100) cc_final: 0.6913 (t-100) REVERT: A 219 ARG cc_start: 0.7810 (mpp80) cc_final: 0.6697 (mtp85) REVERT: A 234 LYS cc_start: 0.8249 (mttt) cc_final: 0.7906 (ttmm) REVERT: A 247 LYS cc_start: 0.7884 (mmmm) cc_final: 0.7344 (mmmm) REVERT: A 297 MET cc_start: 0.7928 (mmm) cc_final: 0.7673 (mmm) REVERT: A 349 TRP cc_start: 0.8415 (m100) cc_final: 0.7924 (m-10) REVERT: A 437 ASN cc_start: 0.7707 (m-40) cc_final: 0.7423 (m-40) REVERT: A 485 VAL cc_start: 0.8605 (t) cc_final: 0.8368 (p) REVERT: B 400 SER cc_start: 0.8621 (m) cc_final: 0.8039 (p) REVERT: B 455 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7962 (ttm110) REVERT: B 494 SER cc_start: 0.8685 (t) cc_final: 0.8244 (m) outliers start: 29 outliers final: 25 residues processed: 192 average time/residue: 0.0610 time to fit residues: 15.4301 Evaluate side-chains 205 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 0.0770 chunk 51 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 65 optimal weight: 0.1980 chunk 69 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 0.0570 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.126326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110522 restraints weight = 9900.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113745 restraints weight = 5066.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115877 restraints weight = 3105.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117288 restraints weight = 2163.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118233 restraints weight = 1661.328| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6502 Z= 0.136 Angle : 0.579 15.270 8844 Z= 0.281 Chirality : 0.044 0.424 937 Planarity : 0.004 0.045 1127 Dihedral : 6.859 57.995 1000 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.48 % Allowed : 20.18 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.30), residues: 755 helix: 1.10 (0.26), residues: 393 sheet: -0.31 (0.80), residues: 31 loop : -0.75 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 115 TYR 0.019 0.001 TYR B 501 PHE 0.015 0.001 PHE A 369 TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 6492) covalent geometry : angle 0.54165 / 0.27 ( 8816) SS BOND : bond 0.00242 / 0.12 ( 2) SS BOND : angle 0.75835 / 0.35 ( 4) hydrogen bonds : bond 0.04800 / 3.30 ( 305) hydrogen bonds : angle 4.57492 / 3.42 ( 879) link_BETA1-4 : bond 0.00620 / 0.32 ( 2) link_BETA1-4 : angle 2.12941 / 1.03 ( 6) link_NAG-ASN : bond 0.00625 / 0.34 ( 6) link_NAG-ASN : angle 4.39896 / 3.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7415 (mmm) cc_final: 0.6871 (mmm) REVERT: A 168 TRP cc_start: 0.7174 (t-100) cc_final: 0.6847 (t-100) REVERT: A 201 ASP cc_start: 0.6947 (t0) cc_final: 0.5607 (t0) REVERT: A 219 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6679 (mtp85) REVERT: A 234 LYS cc_start: 0.8272 (mttt) cc_final: 0.7911 (ttmm) REVERT: A 247 LYS cc_start: 0.7890 (mmmm) cc_final: 0.7352 (mmmm) REVERT: A 297 MET cc_start: 0.7907 (mmm) cc_final: 0.7689 (mmm) REVERT: A 335 ASP cc_start: 0.7396 (t0) cc_final: 0.7195 (t0) REVERT: A 349 TRP cc_start: 0.8367 (m100) cc_final: 0.7878 (m-10) REVERT: A 437 ASN cc_start: 0.7676 (m-40) cc_final: 0.7290 (m110) REVERT: A 459 TRP cc_start: 0.7987 (t60) cc_final: 0.7690 (t60) REVERT: A 474 MET cc_start: 0.7046 (mmp) cc_final: 0.6285 (mmt) REVERT: B 400 SER cc_start: 0.8616 (m) cc_final: 0.8022 (p) REVERT: B 424 TYR cc_start: 0.7945 (t80) cc_final: 0.7438 (t80) REVERT: B 455 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7948 (ttm110) REVERT: B 494 SER cc_start: 0.8681 (t) cc_final: 0.8240 (m) outliers start: 30 outliers final: 23 residues processed: 193 average time/residue: 0.0635 time to fit residues: 16.0440 Evaluate side-chains 207 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110039 restraints weight = 10114.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113133 restraints weight = 5038.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115168 restraints weight = 3035.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116597 restraints weight = 2080.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117211 restraints weight = 1559.582| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 0.030 6502 Z= 0.200 Angle : 0.616 15.013 8844 Z= 0.301 Chirality : 0.046 0.458 937 Planarity : 0.004 0.049 1127 Dihedral : 6.889 56.652 1000 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.08 % Allowed : 19.58 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.30), residues: 755 helix: 1.00 (0.26), residues: 390 sheet: -0.07 (0.83), residues: 31 loop : -0.85 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 467 TYR 0.018 0.002 TYR A 385 PHE 0.018 0.002 PHE A 369 TRP 0.015 0.001 TRP B 437 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 6492) covalent geometry : angle 0.58018 / 0.29 ( 8816) SS BOND : bond 0.00264 / 0.13 ( 2) SS BOND : angle 0.72385 / 0.35 ( 4) hydrogen bonds : bond 0.05150 / 3.54 ( 305) hydrogen bonds : angle 4.58413 / 3.44 ( 879) link_BETA1-4 : bond 0.00479 / 0.24 ( 2) link_BETA1-4 : angle 2.15507 / 1.06 ( 6) link_NAG-ASN : bond 0.00628 / 0.34 ( 6) link_NAG-ASN : angle 4.43625 / 3.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8054 (m-80) cc_final: 0.7782 (m-80) REVERT: A 152 MET cc_start: 0.7424 (mmm) cc_final: 0.6925 (mmm) REVERT: A 168 TRP cc_start: 0.7205 (t-100) cc_final: 0.6894 (t-100) REVERT: A 201 ASP cc_start: 0.6916 (t0) cc_final: 0.5617 (t0) REVERT: A 219 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6669 (mtp85) REVERT: A 234 LYS cc_start: 0.8255 (mttt) cc_final: 0.7902 (ttmm) REVERT: A 247 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7355 (mmmm) REVERT: A 335 ASP cc_start: 0.7483 (t0) cc_final: 0.7271 (t0) REVERT: A 349 TRP cc_start: 0.8407 (m100) cc_final: 0.7943 (m-10) REVERT: A 437 ASN cc_start: 0.7713 (m-40) cc_final: 0.7386 (m-40) REVERT: A 459 TRP cc_start: 0.8021 (t60) cc_final: 0.7685 (t60) REVERT: A 474 MET cc_start: 0.7099 (mmp) cc_final: 0.6256 (mmt) REVERT: A 598 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7515 (mm-40) REVERT: B 400 SER cc_start: 0.8622 (m) cc_final: 0.8039 (p) REVERT: B 494 SER cc_start: 0.8685 (t) cc_final: 0.8170 (m) outliers start: 34 outliers final: 27 residues processed: 193 average time/residue: 0.0665 time to fit residues: 16.8924 Evaluate side-chains 209 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 26 optimal weight: 0.0980 chunk 44 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 154 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111970 restraints weight = 10014.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115073 restraints weight = 5016.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117119 restraints weight = 3029.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118539 restraints weight = 2086.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119341 restraints weight = 1572.656| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6502 Z= 0.128 Angle : 0.573 14.508 8844 Z= 0.278 Chirality : 0.044 0.428 937 Planarity : 0.004 0.048 1127 Dihedral : 6.534 54.677 1000 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.29 % Allowed : 21.23 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.30), residues: 755 helix: 1.15 (0.26), residues: 390 sheet: 0.18 (0.83), residues: 30 loop : -0.85 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.016 0.001 TYR B 501 PHE 0.014 0.001 PHE A 369 TRP 0.015 0.001 TRP A 69 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 6492) covalent geometry : angle 0.54048 / 0.27 ( 8816) SS BOND : bond 0.00115 / 0.06 ( 2) SS BOND : angle 0.57963 / 0.29 ( 4) hydrogen bonds : bond 0.04436 / 3.06 ( 305) hydrogen bonds : angle 4.44388 / 3.34 ( 879) link_BETA1-4 : bond 0.00645 / 0.33 ( 2) link_BETA1-4 : angle 1.96896 / 0.97 ( 6) link_NAG-ASN : bond 0.00585 / 0.32 ( 6) link_NAG-ASN : angle 4.12610 / 3.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8088 (m-80) cc_final: 0.7866 (m-80) REVERT: A 152 MET cc_start: 0.7427 (mmm) cc_final: 0.6891 (mmm) REVERT: A 168 TRP cc_start: 0.7146 (t-100) cc_final: 0.6590 (t-100) REVERT: A 201 ASP cc_start: 0.6876 (t0) cc_final: 0.6631 (t0) REVERT: A 234 LYS cc_start: 0.8266 (mttt) cc_final: 0.7912 (ttmm) REVERT: A 247 LYS cc_start: 0.7908 (mmmm) cc_final: 0.7368 (mmmm) REVERT: A 335 ASP cc_start: 0.7494 (t0) cc_final: 0.7257 (t0) REVERT: A 349 TRP cc_start: 0.8337 (m100) cc_final: 0.7923 (m-10) REVERT: A 435 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6800 (pt0) REVERT: A 437 ASN cc_start: 0.7683 (m-40) cc_final: 0.7338 (m-40) REVERT: A 459 TRP cc_start: 0.7946 (t60) cc_final: 0.7651 (t60) REVERT: A 474 MET cc_start: 0.7037 (mmp) cc_final: 0.6317 (mmt) REVERT: A 514 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7425 (mtp85) REVERT: A 559 ARG cc_start: 0.7584 (ttp-110) cc_final: 0.7324 (ptm-80) REVERT: A 598 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7434 (mm-40) REVERT: B 400 SER cc_start: 0.8557 (m) cc_final: 0.8009 (p) REVERT: B 424 TYR cc_start: 0.7898 (t80) cc_final: 0.7503 (t80) REVERT: B 453 TRP cc_start: 0.8589 (m100) cc_final: 0.8351 (m100) REVERT: B 455 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8056 (ttm110) outliers start: 22 outliers final: 17 residues processed: 194 average time/residue: 0.0647 time to fit residues: 16.4801 Evaluate side-chains 201 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109241 restraints weight = 10049.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112277 restraints weight = 5028.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114267 restraints weight = 3025.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115425 restraints weight = 2088.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116427 restraints weight = 1628.015| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6502 Z= 0.266 Angle : 0.677 14.808 8844 Z= 0.335 Chirality : 0.049 0.499 937 Planarity : 0.004 0.052 1127 Dihedral : 6.691 56.056 1000 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.04 % Allowed : 20.93 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.30), residues: 755 helix: 0.86 (0.25), residues: 396 sheet: 0.21 (0.85), residues: 31 loop : -0.93 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 482 TYR 0.020 0.002 TYR A 385 PHE 0.032 0.002 PHE B 515 TRP 0.015 0.002 TRP B 437 HIS 0.006 0.002 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.27 ( 6492) covalent geometry : angle 0.64433 / 0.33 ( 8816) SS BOND : bond 0.00402 / 0.20 ( 2) SS BOND : angle 0.99385 / 0.49 ( 4) hydrogen bonds : bond 0.05457 / 3.73 ( 305) hydrogen bonds : angle 4.67112 / 3.51 ( 879) link_BETA1-4 : bond 0.00358 / 0.18 ( 2) link_BETA1-4 : angle 2.17934 / 1.10 ( 6) link_NAG-ASN : bond 0.00664 / 0.35 ( 6) link_NAG-ASN : angle 4.49210 / 3.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7406 (mmm) cc_final: 0.7018 (mmm) REVERT: A 168 TRP cc_start: 0.7244 (t-100) cc_final: 0.6910 (t-100) REVERT: A 219 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6787 (mtp85) REVERT: A 234 LYS cc_start: 0.8200 (mttt) cc_final: 0.7878 (ttmm) REVERT: A 247 LYS cc_start: 0.7895 (mmmm) cc_final: 0.7374 (mmmm) REVERT: A 330 ASN cc_start: 0.7376 (p0) cc_final: 0.7119 (p0) REVERT: A 335 ASP cc_start: 0.7538 (t0) cc_final: 0.7297 (t0) REVERT: A 349 TRP cc_start: 0.8437 (m100) cc_final: 0.7997 (m-10) REVERT: A 350 ASP cc_start: 0.7779 (t70) cc_final: 0.7067 (p0) REVERT: A 437 ASN cc_start: 0.7732 (m-40) cc_final: 0.7386 (m-40) REVERT: A 474 MET cc_start: 0.7080 (mmp) cc_final: 0.6419 (mmt) REVERT: A 514 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7542 (mtp85) REVERT: A 598 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7559 (mm-40) REVERT: B 400 SER cc_start: 0.8623 (m) cc_final: 0.8055 (p) REVERT: B 494 SER cc_start: 0.8643 (t) cc_final: 0.8157 (m) outliers start: 27 outliers final: 25 residues processed: 190 average time/residue: 0.0632 time to fit residues: 15.6506 Evaluate side-chains 206 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 73 optimal weight: 0.1980 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 0.0040 chunk 31 optimal weight: 0.0060 chunk 13 optimal weight: 0.6980 chunk 36 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.4737 > 50:) chunk 69 optimal weight: 0.9990 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 154 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111889 restraints weight = 9989.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114970 restraints weight = 5023.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117008 restraints weight = 3029.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118188 restraints weight = 2076.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119221 restraints weight = 1617.350| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6502 Z= 0.133 Angle : 0.618 14.341 8844 Z= 0.302 Chirality : 0.045 0.441 937 Planarity : 0.004 0.050 1127 Dihedral : 6.342 55.326 1000 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.14 % Allowed : 22.57 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.30), residues: 755 helix: 1.04 (0.26), residues: 390 sheet: 0.16 (0.84), residues: 31 loop : -0.88 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 115 TYR 0.017 0.001 TYR B 424 PHE 0.014 0.001 PHE A 369 TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6492) covalent geometry : angle 0.58795 / 0.30 ( 8816) SS BOND : bond 0.00222 / 0.11 ( 2) SS BOND : angle 0.81654 / 0.40 ( 4) hydrogen bonds : bond 0.04614 / 3.18 ( 305) hydrogen bonds : angle 4.53414 / 3.42 ( 879) link_BETA1-4 : bond 0.00558 / 0.29 ( 2) link_BETA1-4 : angle 1.87897 / 0.94 ( 6) link_NAG-ASN : bond 0.00603 / 0.33 ( 6) link_NAG-ASN : angle 4.12525 / 3.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7394 (mmm) cc_final: 0.6900 (mmm) REVERT: A 168 TRP cc_start: 0.7160 (t-100) cc_final: 0.6865 (t-100) REVERT: A 201 ASP cc_start: 0.6854 (t0) cc_final: 0.6632 (t0) REVERT: A 234 LYS cc_start: 0.8255 (mttt) cc_final: 0.7901 (ttmm) REVERT: A 247 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7356 (mmmm) REVERT: A 330 ASN cc_start: 0.7312 (p0) cc_final: 0.7092 (p0) REVERT: A 335 ASP cc_start: 0.7533 (t0) cc_final: 0.7271 (t0) REVERT: A 349 TRP cc_start: 0.8316 (m100) cc_final: 0.7940 (m-10) REVERT: A 437 ASN cc_start: 0.7707 (m-40) cc_final: 0.7308 (m110) REVERT: A 474 MET cc_start: 0.7026 (mmp) cc_final: 0.6239 (mmt) REVERT: A 495 GLU cc_start: 0.6786 (mp0) cc_final: 0.6447 (mm-30) REVERT: A 509 ASP cc_start: 0.7167 (t0) cc_final: 0.6911 (t0) REVERT: A 514 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7395 (mtp85) REVERT: A 527 GLU cc_start: 0.7028 (tp30) cc_final: 0.6691 (mm-30) REVERT: A 598 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7492 (mm-40) REVERT: A 606 TRP cc_start: 0.7246 (p90) cc_final: 0.6895 (p90) REVERT: B 400 SER cc_start: 0.8560 (m) cc_final: 0.7994 (p) REVERT: B 424 TYR cc_start: 0.7895 (t80) cc_final: 0.7516 (t80) REVERT: B 453 TRP cc_start: 0.8628 (m100) cc_final: 0.8368 (m100) outliers start: 21 outliers final: 19 residues processed: 198 average time/residue: 0.0665 time to fit residues: 17.2831 Evaluate side-chains 206 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 0.0980 chunk 52 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 41 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 74 optimal weight: 0.0170 chunk 6 optimal weight: 0.6980 overall best weight: 0.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 154 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112880 restraints weight = 10030.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116150 restraints weight = 4979.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118305 restraints weight = 2999.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119685 restraints weight = 2048.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120702 restraints weight = 1558.488| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6502 Z= 0.115 Angle : 0.594 14.026 8844 Z= 0.291 Chirality : 0.043 0.407 937 Planarity : 0.004 0.051 1127 Dihedral : 6.015 54.915 1000 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.54 % Allowed : 23.32 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.30), residues: 755 helix: 1.21 (0.26), residues: 391 sheet: 0.37 (0.81), residues: 30 loop : -0.83 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.017 0.001 TYR B 424 PHE 0.011 0.001 PHE A 369 TRP 0.015 0.001 TRP A 69 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6492) covalent geometry : angle 0.56522 / 0.28 ( 8816) SS BOND : bond 0.00195 / 0.10 ( 2) SS BOND : angle 0.64740 / 0.32 ( 4) hydrogen bonds : bond 0.04249 / 2.90 ( 305) hydrogen bonds : angle 4.45129 / 3.37 ( 879) link_BETA1-4 : bond 0.00656 / 0.34 ( 2) link_BETA1-4 : angle 1.78218 / 0.89 ( 6) link_NAG-ASN : bond 0.00521 / 0.28 ( 6) link_NAG-ASN : angle 3.97165 / 3.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7414 (mmm) cc_final: 0.6893 (mmm) REVERT: A 168 TRP cc_start: 0.7109 (t-100) cc_final: 0.6638 (t-100) REVERT: A 201 ASP cc_start: 0.6892 (t0) cc_final: 0.5578 (t0) REVERT: A 219 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6707 (mtp85) REVERT: A 234 LYS cc_start: 0.8256 (mttt) cc_final: 0.7895 (ttmm) REVERT: A 247 LYS cc_start: 0.7883 (mmmm) cc_final: 0.7317 (mmmm) REVERT: A 335 ASP cc_start: 0.7530 (t0) cc_final: 0.7242 (t0) REVERT: A 349 TRP cc_start: 0.8259 (m100) cc_final: 0.7882 (m-10) REVERT: A 437 ASN cc_start: 0.7733 (m-40) cc_final: 0.7391 (m-40) REVERT: A 459 TRP cc_start: 0.7882 (t60) cc_final: 0.7583 (t60) REVERT: A 474 MET cc_start: 0.6994 (mmp) cc_final: 0.6196 (mmt) REVERT: A 495 GLU cc_start: 0.6646 (mp0) cc_final: 0.6407 (mm-30) REVERT: A 509 ASP cc_start: 0.7189 (t0) cc_final: 0.6954 (t0) REVERT: A 514 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7361 (mtp85) REVERT: A 559 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.7325 (ptm-80) REVERT: A 598 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7452 (mm-40) REVERT: A 606 TRP cc_start: 0.7208 (p90) cc_final: 0.6858 (p90) REVERT: B 400 SER cc_start: 0.8509 (m) cc_final: 0.7957 (p) REVERT: B 424 TYR cc_start: 0.7878 (t80) cc_final: 0.7652 (t80) REVERT: B 453 TRP cc_start: 0.8593 (m100) cc_final: 0.8372 (m100) outliers start: 17 outliers final: 14 residues processed: 197 average time/residue: 0.0874 time to fit residues: 22.5508 Evaluate side-chains 204 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 19 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 154 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112130 restraints weight = 10018.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115254 restraints weight = 5112.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117306 restraints weight = 3098.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118618 restraints weight = 2135.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119234 restraints weight = 1630.278| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6502 Z= 0.140 Angle : 0.623 14.160 8844 Z= 0.306 Chirality : 0.044 0.416 937 Planarity : 0.004 0.052 1127 Dihedral : 6.041 55.405 1000 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.39 % Allowed : 23.62 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.30), residues: 755 helix: 1.24 (0.26), residues: 391 sheet: 0.73 (0.85), residues: 30 loop : -0.84 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 115 TYR 0.034 0.002 TYR B 508 PHE 0.015 0.001 PHE A 369 TRP 0.012 0.001 TRP A 69 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 6492) covalent geometry : angle 0.59388 / 0.30 ( 8816) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 0.66928 / 0.33 ( 4) hydrogen bonds : bond 0.04440 / 3.03 ( 305) hydrogen bonds : angle 4.45625 / 3.36 ( 879) link_BETA1-4 : bond 0.00490 / 0.25 ( 2) link_BETA1-4 : angle 1.87140 / 0.94 ( 6) link_NAG-ASN : bond 0.00519 / 0.28 ( 6) link_NAG-ASN : angle 4.06504 / 3.17 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7415 (mmm) cc_final: 0.6862 (mmm) REVERT: A 168 TRP cc_start: 0.7142 (t-100) cc_final: 0.6601 (t-100) REVERT: A 201 ASP cc_start: 0.6910 (t0) cc_final: 0.6675 (t0) REVERT: A 234 LYS cc_start: 0.8261 (mttt) cc_final: 0.7903 (ttmm) REVERT: A 247 LYS cc_start: 0.7887 (mmmm) cc_final: 0.7338 (mmmm) REVERT: A 335 ASP cc_start: 0.7521 (t0) cc_final: 0.7230 (t0) REVERT: A 349 TRP cc_start: 0.8285 (m100) cc_final: 0.7911 (m-10) REVERT: A 437 ASN cc_start: 0.7730 (m-40) cc_final: 0.7400 (m-40) REVERT: A 474 MET cc_start: 0.7012 (mmp) cc_final: 0.6195 (mmt) REVERT: A 495 GLU cc_start: 0.6704 (mp0) cc_final: 0.6438 (mm-30) REVERT: A 509 ASP cc_start: 0.7212 (t0) cc_final: 0.6949 (t0) REVERT: A 514 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7391 (mtp85) REVERT: A 598 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7483 (mm-40) REVERT: A 606 TRP cc_start: 0.7225 (p90) cc_final: 0.6869 (p90) REVERT: B 400 SER cc_start: 0.8533 (m) cc_final: 0.7959 (p) outliers start: 16 outliers final: 15 residues processed: 196 average time/residue: 0.0817 time to fit residues: 21.0792 Evaluate side-chains 204 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 53 optimal weight: 0.0770 chunk 60 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 49 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 87 ASN A 154 ASN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112421 restraints weight = 10047.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115551 restraints weight = 5072.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117624 restraints weight = 3056.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118962 restraints weight = 2097.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119552 restraints weight = 1597.053| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6502 Z= 0.142 Angle : 0.622 14.108 8844 Z= 0.308 Chirality : 0.045 0.426 937 Planarity : 0.004 0.052 1127 Dihedral : 5.973 55.477 998 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.39 % Allowed : 23.77 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.30), residues: 755 helix: 1.23 (0.26), residues: 390 sheet: 0.83 (0.85), residues: 30 loop : -0.80 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 498 TYR 0.028 0.002 TYR A 50 PHE 0.015 0.001 PHE A 369 TRP 0.023 0.001 TRP B 453 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6492) covalent geometry : angle 0.59308 / 0.30 ( 8816) SS BOND : bond 0.00253 / 0.12 ( 2) SS BOND : angle 0.86499 / 0.45 ( 4) hydrogen bonds : bond 0.04489 / 3.06 ( 305) hydrogen bonds : angle 4.50322 / 3.40 ( 879) link_BETA1-4 : bond 0.00443 / 0.23 ( 2) link_BETA1-4 : angle 1.86963 / 0.94 ( 6) link_NAG-ASN : bond 0.00539 / 0.29 ( 6) link_NAG-ASN : angle 4.04913 / 3.16 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1183.77 seconds wall clock time: 21 minutes 7.25 seconds (1267.25 seconds total)