Starting phenix.real_space_refine on Fri Aug 22 17:44:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm8_27530/08_2025/8dm8_27530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm8_27530/08_2025/8dm8_27530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm8_27530/08_2025/8dm8_27530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm8_27530/08_2025/8dm8_27530.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm8_27530/08_2025/8dm8_27530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm8_27530/08_2025/8dm8_27530.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4139 2.51 5 N 1087 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1604 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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 Time building chain proxies: 1.86, per 1000 atoms: 0.29 Number of scatterers: 6479 At special positions: 0 Unit cell: (77, 86, 121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1216 8.00 N 1087 7.00 C 4139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 400.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 56.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.909A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.409A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 21 through 52 removed outlier: 3.502A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.739A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.670A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 193 removed outlier: 5.033A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.698A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 232 removed outlier: 3.709A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.613A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.525A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.622A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.848A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.613A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.419A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.672A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.663A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.307A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.128A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.549A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.019A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.332A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2071 1.35 - 1.47: 1789 1.47 - 1.60: 2744 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6662 Sorted by residual: bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.589 -0.086 3.40e-02 8.65e+02 6.41e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.24e+00 bond pdb=" CB ASN A 439 " pdb=" CG ASN A 439 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.64e+00 bond pdb=" CB VAL D 573 " pdb=" CG2 VAL D 573 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.60e+00 ... (remaining 6657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 8688 2.10 - 4.19: 313 4.19 - 6.29: 37 6.29 - 8.38: 7 8.38 - 10.48: 3 Bond angle restraints: 9048 Sorted by residual: angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 120.01 -10.20 2.21e+00 2.05e-01 2.13e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 124.88 -10.48 2.30e+00 1.89e-01 2.07e+01 angle pdb=" N VAL D 364 " pdb=" CA VAL D 364 " pdb=" C VAL D 364 " ideal model delta sigma weight residual 106.21 110.87 -4.66 1.07e+00 8.73e-01 1.90e+01 angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 105.96 6.04 1.40e+00 5.10e-01 1.86e+01 angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 122.07 126.87 -4.80 1.43e+00 4.89e-01 1.13e+01 ... (remaining 9043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3594 17.35 - 34.71: 323 34.71 - 52.06: 46 52.06 - 69.41: 14 69.41 - 86.77: 6 Dihedral angle restraints: 3983 sinusoidal: 1650 harmonic: 2333 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 55.15 37.85 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CG ARG D 245 " pdb=" CD ARG D 245 " pdb=" NE ARG D 245 " pdb=" CZ ARG D 245 " ideal model delta sinusoidal sigma weight residual 90.00 134.53 -44.53 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 641 0.051 - 0.103: 234 0.103 - 0.154: 56 0.154 - 0.205: 13 0.205 - 0.257: 3 Chirality restraints: 947 Sorted by residual: chirality pdb=" CB ILE D 291 " pdb=" CA ILE D 291 " pdb=" CG1 ILE D 291 " pdb=" CG2 ILE D 291 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR A 333 " pdb=" CA THR A 333 " pdb=" OG1 THR A 333 " pdb=" CG2 THR A 333 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN A 360 " pdb=" N ASN A 360 " pdb=" C ASN A 360 " pdb=" CB ASN A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 944 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 36 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.60e+01 pdb=" C ALA D 36 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA D 36 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU D 37 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 31 " -0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN D 31 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN D 31 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE D 32 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.044 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO D 500 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.037 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1992 2.82 - 3.34: 5892 3.34 - 3.86: 11313 3.86 - 4.38: 13110 4.38 - 4.90: 22401 Nonbonded interactions: 54708 Sorted by model distance: nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.315 3.040 nonbonded pdb=" OH TYR D 217 " pdb=" OD2 ASP D 225 " model vdw 2.339 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.349 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.361 3.040 ... (remaining 54703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.670 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 6671 Z= 0.270 Angle : 0.902 10.477 9069 Z= 0.500 Chirality : 0.058 0.257 947 Planarity : 0.007 0.065 1172 Dihedral : 13.496 86.766 2467 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.72 % Allowed : 1.74 % Favored : 97.54 % 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 aren not related in a simple way. whole: -0.72 (0.26), residues: 790 helix: -0.44 (0.22), residues: 397 sheet: 0.63 (0.64), residues: 53 loop : -0.52 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 460 TYR 0.032 0.003 TYR D 385 PHE 0.024 0.003 PHE A 375 TRP 0.023 0.002 TRP D 163 HIS 0.006 0.002 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 6662) covalent geometry : angle 0.89375 ( 9048) SS BOND : bond 0.00698 ( 6) SS BOND : angle 2.22262 ( 12) hydrogen bonds : bond 0.14393 ( 309) hydrogen bonds : angle 6.53863 ( 951) link_NAG-ASN : bond 0.00620 ( 3) link_NAG-ASN : angle 3.10303 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.7958 (m-40) cc_final: 0.7610 (m-40) REVERT: A 414 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8665 (mm-40) REVERT: D 113 ASN cc_start: 0.8620 (t0) cc_final: 0.8359 (t0) REVERT: D 145 GLU cc_start: 0.8438 (tp30) cc_final: 0.7852 (tp30) REVERT: D 347 THR cc_start: 0.8692 (m) cc_final: 0.8432 (p) REVERT: D 383 MET cc_start: 0.9163 (mtp) cc_final: 0.8842 (mtp) REVERT: D 483 GLU cc_start: 0.8473 (tp30) cc_final: 0.8257 (tp30) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.7037 time to fit residues: 117.9026 Evaluate side-chains 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN D 137 ASN D 188 ASN D 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076382 restraints weight = 11780.939| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.61 r_work: 0.2872 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6671 Z= 0.164 Angle : 0.603 8.603 9069 Z= 0.311 Chirality : 0.043 0.186 947 Planarity : 0.005 0.038 1172 Dihedral : 5.478 48.582 931 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.46 % Allowed : 11.00 % Favored : 86.54 % 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 aren not related in a simple way. whole: 0.39 (0.28), residues: 790 helix: 0.65 (0.25), residues: 410 sheet: 1.18 (0.75), residues: 43 loop : -0.22 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 357 TYR 0.014 0.001 TYR D 385 PHE 0.013 0.001 PHE D 369 TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6662) covalent geometry : angle 0.59777 ( 9048) SS BOND : bond 0.00514 ( 6) SS BOND : angle 1.31167 ( 12) hydrogen bonds : bond 0.04773 ( 309) hydrogen bonds : angle 4.81523 ( 951) link_NAG-ASN : bond 0.00359 ( 3) link_NAG-ASN : angle 2.30374 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.9011 (ptm160) cc_final: 0.8797 (ptm-80) REVERT: A 378 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8648 (mtmm) REVERT: A 405 ASN cc_start: 0.8592 (m-40) cc_final: 0.8259 (m110) REVERT: D 145 GLU cc_start: 0.8351 (tp30) cc_final: 0.7860 (tm-30) REVERT: D 163 TRP cc_start: 0.8480 (t60) cc_final: 0.8069 (t60) REVERT: D 190 MET cc_start: 0.9004 (tmm) cc_final: 0.8738 (tmm) REVERT: D 341 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8408 (mppt) REVERT: D 347 THR cc_start: 0.8745 (m) cc_final: 0.8403 (p) REVERT: D 383 MET cc_start: 0.9273 (mtp) cc_final: 0.9034 (mtp) REVERT: D 483 GLU cc_start: 0.8975 (tp30) cc_final: 0.8608 (tp30) REVERT: D 597 GLU cc_start: 0.8759 (tp30) cc_final: 0.8335 (tt0) outliers start: 17 outliers final: 6 residues processed: 112 average time/residue: 0.6568 time to fit residues: 77.0290 Evaluate side-chains 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN D 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.071562 restraints weight = 11912.514| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.58 r_work: 0.2770 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 6671 Z= 0.292 Angle : 0.698 14.118 9069 Z= 0.348 Chirality : 0.048 0.274 947 Planarity : 0.005 0.040 1172 Dihedral : 6.648 59.839 931 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.75 % Allowed : 13.17 % Favored : 84.08 % 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 aren not related in a simple way. whole: 0.59 (0.29), residues: 790 helix: 0.84 (0.26), residues: 403 sheet: 0.95 (0.78), residues: 44 loop : -0.08 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.018 0.002 TYR D 385 PHE 0.014 0.002 PHE D 308 TRP 0.012 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 6662) covalent geometry : angle 0.66309 ( 9048) SS BOND : bond 0.00521 ( 6) SS BOND : angle 1.29425 ( 12) hydrogen bonds : bond 0.05533 ( 309) hydrogen bonds : angle 4.89543 ( 951) link_NAG-ASN : bond 0.00607 ( 3) link_NAG-ASN : angle 6.84603 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8644 (mp10) REVERT: D 145 GLU cc_start: 0.8483 (tp30) cc_final: 0.7885 (tm-30) REVERT: D 298 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8466 (mtt) REVERT: D 341 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8556 (mppt) REVERT: D 383 MET cc_start: 0.9366 (mtp) cc_final: 0.9131 (mtp) REVERT: D 483 GLU cc_start: 0.9037 (tp30) cc_final: 0.8663 (tp30) REVERT: D 597 GLU cc_start: 0.8848 (tp30) cc_final: 0.8625 (tp30) outliers start: 19 outliers final: 9 residues processed: 97 average time/residue: 0.5732 time to fit residues: 58.1779 Evaluate side-chains 98 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073762 restraints weight = 11870.443| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.61 r_work: 0.2812 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6671 Z= 0.157 Angle : 0.592 11.129 9069 Z= 0.295 Chirality : 0.043 0.184 947 Planarity : 0.004 0.039 1172 Dihedral : 6.915 80.088 931 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.60 % Allowed : 13.02 % Favored : 84.37 % 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 aren not related in a simple way. whole: 0.81 (0.29), residues: 790 helix: 1.02 (0.25), residues: 409 sheet: 1.16 (0.78), residues: 43 loop : -0.02 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.013 0.001 TYR D 385 PHE 0.014 0.001 PHE D 315 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6662) covalent geometry : angle 0.57472 ( 9048) SS BOND : bond 0.00458 ( 6) SS BOND : angle 1.10282 ( 12) hydrogen bonds : bond 0.04594 ( 309) hydrogen bonds : angle 4.69824 ( 951) link_NAG-ASN : bond 0.00482 ( 3) link_NAG-ASN : angle 4.39019 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8421 (tp30) cc_final: 0.7860 (tm-30) REVERT: D 190 MET cc_start: 0.8975 (tmm) cc_final: 0.8689 (tmm) REVERT: D 298 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8434 (mtt) REVERT: D 360 MET cc_start: 0.9026 (ttm) cc_final: 0.8791 (ptm) REVERT: D 383 MET cc_start: 0.9349 (mtp) cc_final: 0.9063 (mtp) REVERT: D 483 GLU cc_start: 0.9011 (tp30) cc_final: 0.8608 (tp30) REVERT: D 491 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8523 (pt) REVERT: D 597 GLU cc_start: 0.8839 (tp30) cc_final: 0.8611 (tp30) outliers start: 18 outliers final: 9 residues processed: 91 average time/residue: 0.5553 time to fit residues: 53.0616 Evaluate side-chains 93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN D 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074087 restraints weight = 11930.039| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.62 r_work: 0.2849 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6671 Z= 0.147 Angle : 0.564 8.283 9069 Z= 0.286 Chirality : 0.043 0.172 947 Planarity : 0.004 0.040 1172 Dihedral : 7.639 103.732 931 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.89 % Allowed : 14.62 % Favored : 82.49 % 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 aren not related in a simple way. whole: 1.05 (0.30), residues: 790 helix: 1.23 (0.26), residues: 409 sheet: 1.26 (0.77), residues: 43 loop : 0.07 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.013 0.001 TYR D 385 PHE 0.014 0.001 PHE D 315 TRP 0.009 0.001 TRP D 594 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6662) covalent geometry : angle 0.55361 ( 9048) SS BOND : bond 0.00438 ( 6) SS BOND : angle 1.16514 ( 12) hydrogen bonds : bond 0.04437 ( 309) hydrogen bonds : angle 4.59443 ( 951) link_NAG-ASN : bond 0.00522 ( 3) link_NAG-ASN : angle 3.21044 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 87 GLU cc_start: 0.8077 (pm20) cc_final: 0.7826 (pm20) REVERT: D 145 GLU cc_start: 0.8458 (tp30) cc_final: 0.7904 (tm-30) REVERT: D 298 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8483 (mtt) REVERT: D 376 MET cc_start: 0.9187 (ttm) cc_final: 0.8750 (ttm) REVERT: D 383 MET cc_start: 0.9334 (mtp) cc_final: 0.9079 (mtp) REVERT: D 483 GLU cc_start: 0.8989 (tp30) cc_final: 0.8632 (tp30) REVERT: D 491 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8573 (pt) REVERT: D 597 GLU cc_start: 0.8751 (tp30) cc_final: 0.8445 (tp30) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.5754 time to fit residues: 58.0424 Evaluate side-chains 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.073805 restraints weight = 11901.610| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.62 r_work: 0.2835 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6671 Z= 0.155 Angle : 0.565 7.820 9069 Z= 0.287 Chirality : 0.043 0.153 947 Planarity : 0.004 0.039 1172 Dihedral : 7.699 106.225 931 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.17 % Allowed : 15.20 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.30), residues: 790 helix: 1.41 (0.26), residues: 403 sheet: 1.05 (0.78), residues: 44 loop : 0.13 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.013 0.001 TYR D 385 PHE 0.019 0.001 PHE D 603 TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6662) covalent geometry : angle 0.55629 ( 9048) SS BOND : bond 0.00460 ( 6) SS BOND : angle 1.14727 ( 12) hydrogen bonds : bond 0.04437 ( 309) hydrogen bonds : angle 4.57797 ( 951) link_NAG-ASN : bond 0.00490 ( 3) link_NAG-ASN : angle 3.01718 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: D 87 GLU cc_start: 0.8125 (pm20) cc_final: 0.7830 (pm20) REVERT: D 145 GLU cc_start: 0.8423 (tp30) cc_final: 0.7881 (tm-30) REVERT: D 190 MET cc_start: 0.8929 (tmm) cc_final: 0.8705 (tmm) REVERT: D 298 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8470 (mtt) REVERT: D 383 MET cc_start: 0.9337 (mtp) cc_final: 0.9101 (mtp) REVERT: D 483 GLU cc_start: 0.9023 (tp30) cc_final: 0.8671 (tp30) REVERT: D 597 GLU cc_start: 0.8823 (tp30) cc_final: 0.8521 (tp30) outliers start: 15 outliers final: 11 residues processed: 88 average time/residue: 0.5590 time to fit residues: 51.7946 Evaluate side-chains 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 33 optimal weight: 0.0470 chunk 44 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.070870 restraints weight = 11031.072| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.58 r_work: 0.2736 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6671 Z= 0.145 Angle : 0.564 8.215 9069 Z= 0.286 Chirality : 0.043 0.146 947 Planarity : 0.004 0.054 1172 Dihedral : 7.747 107.988 931 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.32 % Allowed : 15.20 % Favored : 82.49 % 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 aren not related in a simple way. whole: 1.26 (0.30), residues: 790 helix: 1.45 (0.26), residues: 403 sheet: 1.05 (0.77), residues: 44 loop : 0.17 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 600 TYR 0.013 0.001 TYR D 385 PHE 0.018 0.001 PHE D 603 TRP 0.015 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6662) covalent geometry : angle 0.55552 ( 9048) SS BOND : bond 0.00455 ( 6) SS BOND : angle 1.18013 ( 12) hydrogen bonds : bond 0.04351 ( 309) hydrogen bonds : angle 4.54975 ( 951) link_NAG-ASN : bond 0.00467 ( 3) link_NAG-ASN : angle 2.91580 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: D 87 GLU cc_start: 0.8178 (pm20) cc_final: 0.7920 (pm20) REVERT: D 145 GLU cc_start: 0.8457 (tp30) cc_final: 0.7900 (tm-30) REVERT: D 163 TRP cc_start: 0.8166 (t60) cc_final: 0.7958 (t60) REVERT: D 190 MET cc_start: 0.8949 (tmm) cc_final: 0.8688 (tmm) REVERT: D 298 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8507 (mtt) REVERT: D 383 MET cc_start: 0.9329 (mtp) cc_final: 0.9096 (mtp) REVERT: D 483 GLU cc_start: 0.9056 (tp30) cc_final: 0.8716 (tp30) REVERT: D 597 GLU cc_start: 0.8760 (tp30) cc_final: 0.8489 (tp30) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 0.6301 time to fit residues: 57.0077 Evaluate side-chains 90 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 0.0040 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.073876 restraints weight = 11878.617| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.62 r_work: 0.2819 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6671 Z= 0.164 Angle : 0.575 8.561 9069 Z= 0.291 Chirality : 0.043 0.147 947 Planarity : 0.004 0.039 1172 Dihedral : 7.795 109.083 931 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.46 % Allowed : 15.05 % Favored : 82.49 % 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 aren not related in a simple way. whole: 1.23 (0.30), residues: 790 helix: 1.42 (0.26), residues: 403 sheet: 1.06 (0.77), residues: 44 loop : 0.15 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 357 TYR 0.013 0.001 TYR D 385 PHE 0.018 0.001 PHE D 603 TRP 0.013 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6662) covalent geometry : angle 0.56713 ( 9048) SS BOND : bond 0.00422 ( 6) SS BOND : angle 1.18534 ( 12) hydrogen bonds : bond 0.04466 ( 309) hydrogen bonds : angle 4.58665 ( 951) link_NAG-ASN : bond 0.00479 ( 3) link_NAG-ASN : angle 2.91028 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8555 (ptm160) REVERT: D 87 GLU cc_start: 0.8147 (pm20) cc_final: 0.7866 (pm20) REVERT: D 145 GLU cc_start: 0.8462 (tp30) cc_final: 0.7912 (tm-30) REVERT: D 298 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8504 (mtt) REVERT: D 383 MET cc_start: 0.9337 (mtp) cc_final: 0.9113 (mtp) REVERT: D 483 GLU cc_start: 0.9016 (tp30) cc_final: 0.8665 (tp30) REVERT: D 597 GLU cc_start: 0.8876 (tp30) cc_final: 0.8606 (tp30) REVERT: D 600 ARG cc_start: 0.8330 (ptp90) cc_final: 0.8112 (ptp-110) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.6031 time to fit residues: 54.3949 Evaluate side-chains 89 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074216 restraints weight = 11931.511| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.61 r_work: 0.2824 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6671 Z= 0.154 Angle : 0.581 8.965 9069 Z= 0.293 Chirality : 0.043 0.144 947 Planarity : 0.004 0.038 1172 Dihedral : 7.813 109.705 931 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.03 % Allowed : 15.20 % Favored : 82.78 % 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 aren not related in a simple way. whole: 1.23 (0.30), residues: 790 helix: 1.44 (0.26), residues: 403 sheet: 1.04 (0.78), residues: 44 loop : 0.14 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 357 TYR 0.013 0.001 TYR D 385 PHE 0.018 0.001 PHE D 603 TRP 0.018 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6662) covalent geometry : angle 0.57285 ( 9048) SS BOND : bond 0.00465 ( 6) SS BOND : angle 1.20249 ( 12) hydrogen bonds : bond 0.04400 ( 309) hydrogen bonds : angle 4.55400 ( 951) link_NAG-ASN : bond 0.00464 ( 3) link_NAG-ASN : angle 2.81890 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8512 (ptm160) REVERT: D 87 GLU cc_start: 0.8153 (pm20) cc_final: 0.7888 (pm20) REVERT: D 114 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8279 (mmmm) REVERT: D 145 GLU cc_start: 0.8479 (tp30) cc_final: 0.7919 (tm-30) REVERT: D 190 MET cc_start: 0.8891 (tmm) cc_final: 0.8636 (tmm) REVERT: D 298 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8503 (mtt) REVERT: D 383 MET cc_start: 0.9300 (mtp) cc_final: 0.9077 (mtp) REVERT: D 483 GLU cc_start: 0.9007 (tp30) cc_final: 0.8653 (tp30) REVERT: D 597 GLU cc_start: 0.8847 (tp30) cc_final: 0.8575 (tp30) REVERT: D 600 ARG cc_start: 0.8396 (ptp90) cc_final: 0.8192 (ptp-110) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.6032 time to fit residues: 53.8432 Evaluate side-chains 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073522 restraints weight = 11849.998| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.60 r_work: 0.2812 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6671 Z= 0.181 Angle : 0.597 9.220 9069 Z= 0.302 Chirality : 0.044 0.148 947 Planarity : 0.004 0.038 1172 Dihedral : 7.837 109.851 931 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.74 % Allowed : 15.48 % Favored : 82.78 % 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 aren not related in a simple way. whole: 1.18 (0.30), residues: 790 helix: 1.39 (0.26), residues: 403 sheet: 1.09 (0.77), residues: 44 loop : 0.12 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.014 0.001 TYR D 385 PHE 0.018 0.001 PHE D 603 TRP 0.020 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 6662) covalent geometry : angle 0.58858 ( 9048) SS BOND : bond 0.00480 ( 6) SS BOND : angle 1.19139 ( 12) hydrogen bonds : bond 0.04566 ( 309) hydrogen bonds : angle 4.59936 ( 951) link_NAG-ASN : bond 0.00514 ( 3) link_NAG-ASN : angle 2.89688 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8617 (ptm160) REVERT: D 87 GLU cc_start: 0.8132 (pm20) cc_final: 0.7830 (pm20) REVERT: D 145 GLU cc_start: 0.8481 (tp30) cc_final: 0.7925 (tm-30) REVERT: D 298 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8509 (mtt) REVERT: D 325 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8282 (tp40) REVERT: D 383 MET cc_start: 0.9327 (mtp) cc_final: 0.9102 (mtp) REVERT: D 483 GLU cc_start: 0.9033 (tp30) cc_final: 0.8693 (tp30) REVERT: D 597 GLU cc_start: 0.8862 (tp30) cc_final: 0.8572 (tp30) outliers start: 12 outliers final: 11 residues processed: 86 average time/residue: 0.5617 time to fit residues: 50.7381 Evaluate side-chains 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.070514 restraints weight = 11067.652| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.56 r_work: 0.2731 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6671 Z= 0.158 Angle : 0.594 9.246 9069 Z= 0.298 Chirality : 0.043 0.143 947 Planarity : 0.004 0.067 1172 Dihedral : 7.837 109.772 931 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.74 % Allowed : 15.63 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.30), residues: 790 helix: 1.37 (0.26), residues: 403 sheet: 1.10 (0.77), residues: 44 loop : 0.12 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 600 TYR 0.013 0.001 TYR D 385 PHE 0.018 0.001 PHE D 603 TRP 0.018 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6662) covalent geometry : angle 0.58621 ( 9048) SS BOND : bond 0.00465 ( 6) SS BOND : angle 1.21355 ( 12) hydrogen bonds : bond 0.04437 ( 309) hydrogen bonds : angle 4.56885 ( 951) link_NAG-ASN : bond 0.00470 ( 3) link_NAG-ASN : angle 2.84336 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2748.63 seconds wall clock time: 47 minutes 28.66 seconds (2848.66 seconds total)