Starting phenix.real_space_refine on Thu Jul 24 19:24:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm8_27530/07_2025/8dm8_27530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm8_27530/07_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_27530/07_2025/8dm8_27530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2025/8dm8_27530.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2025/8dm8_27530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm8_27530/07_2025/8dm8_27530.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.71, per 1000 atoms: 0.88 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: 1.58 Conformation dependent library (CDL) restraints added in 995.8 milliseconds 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: 0.74 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: 1.86 Time building geometry restraints manager: 1.90 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: 2.570 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.450 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (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 TRP 0.023 0.002 TRP D 163 HIS 0.006 0.002 HIS A 505 PHE 0.024 0.003 PHE A 375 TYR 0.032 0.003 TYR D 385 ARG 0.008 0.001 ARG D 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 3) link_NAG-ASN : angle 3.10303 ( 9) hydrogen bonds : bond 0.14393 ( 309) hydrogen bonds : angle 6.53863 ( 951) SS BOND : bond 0.00698 ( 6) SS BOND : angle 2.22262 ( 12) covalent geometry : bond 0.00621 ( 6662) covalent geometry : angle 0.89375 ( 9048) *********************** 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 : 1.103 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: 1.3827 time to fit residues: 232.4558 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 : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN D 34 GLN D 137 ASN D 188 ASN D 378 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.096511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.073099 restraints weight = 11732.209| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.60 r_work: 0.2801 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6671 Z= 0.273 Angle : 0.661 8.635 9069 Z= 0.344 Chirality : 0.047 0.191 947 Planarity : 0.005 0.039 1172 Dihedral : 5.609 46.978 931 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.04 % Allowed : 10.85 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.28), residues: 790 helix: 0.50 (0.25), residues: 410 sheet: 1.28 (0.76), residues: 43 loop : -0.26 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 163 HIS 0.004 0.001 HIS D 493 PHE 0.014 0.002 PHE D 32 TYR 0.018 0.002 TYR A 396 ARG 0.009 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 3) link_NAG-ASN : angle 2.40000 ( 9) hydrogen bonds : bond 0.05477 ( 309) hydrogen bonds : angle 4.94377 ( 951) SS BOND : bond 0.00610 ( 6) SS BOND : angle 1.30499 ( 12) covalent geometry : bond 0.00634 ( 6662) covalent geometry : angle 0.65548 ( 9048) *********************** 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: 21 poor density : 103 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8577 (mtmm) REVERT: D 145 GLU cc_start: 0.8351 (tp30) cc_final: 0.7812 (tm-30) REVERT: D 190 MET cc_start: 0.9029 (tmm) cc_final: 0.8749 (tmm) REVERT: D 341 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8511 (mppt) REVERT: D 347 THR cc_start: 0.8812 (m) cc_final: 0.8455 (p) REVERT: D 383 MET cc_start: 0.9368 (mtp) cc_final: 0.9081 (mtp) REVERT: D 483 GLU cc_start: 0.9035 (tp30) cc_final: 0.8643 (tp30) outliers start: 21 outliers final: 7 residues processed: 109 average time/residue: 1.2685 time to fit residues: 145.1079 Evaluate side-chains 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 503 VAL 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 9 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.074260 restraints weight = 11804.922| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.63 r_work: 0.2842 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2741 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= 0.169 Angle : 0.571 7.863 9069 Z= 0.295 Chirality : 0.043 0.162 947 Planarity : 0.004 0.039 1172 Dihedral : 5.091 47.688 931 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 13.17 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.29), residues: 790 helix: 0.86 (0.25), residues: 410 sheet: 1.33 (0.78), residues: 43 loop : -0.03 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.013 0.001 PHE D 315 TYR 0.014 0.001 TYR D 385 ARG 0.009 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 3) link_NAG-ASN : angle 2.09235 ( 9) hydrogen bonds : bond 0.04717 ( 309) hydrogen bonds : angle 4.70251 ( 951) SS BOND : bond 0.00468 ( 6) SS BOND : angle 1.23589 ( 12) covalent geometry : bond 0.00390 ( 6662) covalent geometry : angle 0.56644 ( 9048) *********************** 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 102 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8480 (tp30) cc_final: 0.7897 (tm-30) REVERT: D 190 MET cc_start: 0.9035 (tmm) cc_final: 0.8714 (tmm) REVERT: D 383 MET cc_start: 0.9362 (mtp) cc_final: 0.9035 (mtp) REVERT: D 483 GLU cc_start: 0.8982 (tp30) cc_final: 0.8615 (tp30) REVERT: D 597 GLU cc_start: 0.8761 (tp30) cc_final: 0.8295 (tt0) outliers start: 18 outliers final: 10 residues processed: 93 average time/residue: 1.3773 time to fit residues: 134.3833 Evaluate side-chains 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 98 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 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 15 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 chunk 60 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.098239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.074798 restraints weight = 11880.561| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.64 r_work: 0.2855 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6671 Z= 0.151 Angle : 0.617 15.687 9069 Z= 0.301 Chirality : 0.043 0.225 947 Planarity : 0.004 0.041 1172 Dihedral : 6.012 57.170 931 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 12.59 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 790 helix: 1.07 (0.26), residues: 409 sheet: 1.17 (0.77), residues: 43 loop : -0.01 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.014 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.006 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 3) link_NAG-ASN : angle 6.89218 ( 9) hydrogen bonds : bond 0.04456 ( 309) hydrogen bonds : angle 4.61954 ( 951) SS BOND : bond 0.00550 ( 6) SS BOND : angle 1.13881 ( 12) covalent geometry : bond 0.00343 ( 6662) covalent geometry : angle 0.57722 ( 9048) *********************** 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 106 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8605 (mp10) REVERT: D 114 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8328 (mmmm) REVERT: D 145 GLU cc_start: 0.8455 (tp30) cc_final: 0.7884 (tm-30) REVERT: D 383 MET cc_start: 0.9348 (mtp) cc_final: 0.9079 (mtp) REVERT: D 483 GLU cc_start: 0.8970 (tp30) cc_final: 0.8547 (tp30) REVERT: D 491 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8543 (pt) REVERT: D 597 GLU cc_start: 0.8853 (tp30) cc_final: 0.8327 (tt0) REVERT: D 598 GLN cc_start: 0.8316 (mt0) cc_final: 0.8095 (mt0) outliers start: 18 outliers final: 11 residues processed: 94 average time/residue: 1.3892 time to fit residues: 137.0018 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 : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 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 114 LYS Chi-restraints excluded: chain D residue 182 GLU 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 51 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.070313 restraints weight = 11012.202| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.54 r_work: 0.2729 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3053 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= 0.170 Angle : 0.595 11.723 9069 Z= 0.295 Chirality : 0.043 0.173 947 Planarity : 0.004 0.041 1172 Dihedral : 5.765 55.721 931 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.46 % Allowed : 13.60 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.30), residues: 790 helix: 1.22 (0.26), residues: 409 sheet: 1.21 (0.76), residues: 43 loop : 0.10 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.013 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.006 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 3) link_NAG-ASN : angle 5.55580 ( 9) hydrogen bonds : bond 0.04551 ( 309) hydrogen bonds : angle 4.61764 ( 951) SS BOND : bond 0.00451 ( 6) SS BOND : angle 1.14909 ( 12) covalent geometry : bond 0.00392 ( 6662) covalent geometry : angle 0.56796 ( 9048) *********************** 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 105 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 87 GLU cc_start: 0.8049 (pm20) cc_final: 0.7813 (pm20) REVERT: D 145 GLU cc_start: 0.8441 (tp30) cc_final: 0.7859 (tm-30) REVERT: D 190 MET cc_start: 0.8985 (tmm) cc_final: 0.8708 (tmm) REVERT: D 383 MET cc_start: 0.9344 (mtp) cc_final: 0.9096 (mtp) REVERT: D 483 GLU cc_start: 0.9016 (tp30) cc_final: 0.8612 (tp30) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 1.2504 time to fit residues: 127.6983 Evaluate side-chains 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.097679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.074365 restraints weight = 11825.498| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.63 r_work: 0.2827 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3134 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= 0.150 Angle : 0.582 10.172 9069 Z= 0.290 Chirality : 0.043 0.153 947 Planarity : 0.004 0.041 1172 Dihedral : 5.641 56.965 931 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.46 % Allowed : 14.47 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.30), residues: 790 helix: 1.42 (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 TRP 0.015 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.019 0.001 PHE D 603 TYR 0.012 0.001 TYR D 385 ARG 0.010 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 3) link_NAG-ASN : angle 4.99149 ( 9) hydrogen bonds : bond 0.04378 ( 309) hydrogen bonds : angle 4.55821 ( 951) SS BOND : bond 0.00451 ( 6) SS BOND : angle 1.13964 ( 12) covalent geometry : bond 0.00343 ( 6662) covalent geometry : angle 0.55896 ( 9048) *********************** 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 99 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 87 GLU cc_start: 0.8135 (pm20) cc_final: 0.7850 (pm20) REVERT: D 114 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8320 (mmmm) REVERT: D 145 GLU cc_start: 0.8419 (tp30) cc_final: 0.7856 (tm-30) REVERT: D 151 ILE cc_start: 0.8006 (mt) cc_final: 0.7740 (mt) REVERT: D 190 MET cc_start: 0.9007 (tmm) cc_final: 0.8780 (tmm) REVERT: D 383 MET cc_start: 0.9328 (mtp) cc_final: 0.9092 (mtp) REVERT: D 483 GLU cc_start: 0.8989 (tp30) cc_final: 0.8614 (tp30) REVERT: D 597 GLU cc_start: 0.8745 (tp30) cc_final: 0.8286 (tt0) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 1.2621 time to fit residues: 120.8585 Evaluate side-chains 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 114 LYS Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 305 GLU 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 43 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.094469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.069521 restraints weight = 10965.172| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.61 r_work: 0.2716 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6671 Z= 0.192 Angle : 0.603 9.734 9069 Z= 0.302 Chirality : 0.044 0.150 947 Planarity : 0.004 0.051 1172 Dihedral : 5.615 54.515 931 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.46 % Allowed : 14.62 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.30), residues: 790 helix: 1.41 (0.26), residues: 403 sheet: 1.09 (0.77), residues: 44 loop : 0.16 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.018 0.001 PHE D 603 TYR 0.014 0.001 TYR D 385 ARG 0.013 0.001 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 3) link_NAG-ASN : angle 4.92710 ( 9) hydrogen bonds : bond 0.04656 ( 309) hydrogen bonds : angle 4.63079 ( 951) SS BOND : bond 0.00451 ( 6) SS BOND : angle 1.20565 ( 12) covalent geometry : bond 0.00447 ( 6662) covalent geometry : angle 0.58197 ( 9048) *********************** 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 96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8768 (ptm160) REVERT: D 87 GLU cc_start: 0.8199 (pm20) cc_final: 0.7948 (pm20) REVERT: D 114 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8298 (mmmm) REVERT: D 145 GLU cc_start: 0.8443 (tp30) cc_final: 0.7880 (tm-30) REVERT: D 151 ILE cc_start: 0.8108 (mt) cc_final: 0.7845 (mt) REVERT: D 383 MET cc_start: 0.9310 (mtp) cc_final: 0.9079 (mtp) REVERT: D 483 GLU cc_start: 0.9046 (tp30) cc_final: 0.8691 (tp30) REVERT: D 597 GLU cc_start: 0.8804 (tp30) cc_final: 0.8240 (tt0) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 1.3366 time to fit residues: 123.3981 Evaluate side-chains 93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 389 ASP 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 114 LYS Chi-restraints excluded: chain D residue 182 GLU 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 19 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 17 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 = 0.3369 r_free = 0.3369 target = 0.096722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073484 restraints weight = 11899.022| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.61 r_work: 0.2814 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6671 Z= 0.180 Angle : 0.601 9.373 9069 Z= 0.300 Chirality : 0.044 0.154 947 Planarity : 0.004 0.040 1172 Dihedral : 5.611 55.158 931 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.32 % Allowed : 14.76 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.30), residues: 790 helix: 1.43 (0.26), residues: 403 sheet: 1.04 (0.77), residues: 44 loop : 0.17 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.018 0.001 PHE D 603 TYR 0.014 0.001 TYR D 385 ARG 0.009 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 3) link_NAG-ASN : angle 4.77515 ( 9) hydrogen bonds : bond 0.04581 ( 309) hydrogen bonds : angle 4.61406 ( 951) SS BOND : bond 0.00433 ( 6) SS BOND : angle 1.19752 ( 12) covalent geometry : bond 0.00418 ( 6662) covalent geometry : angle 0.58127 ( 9048) *********************** 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 96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8704 (ptm160) REVERT: A 478 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8508 (mmmt) REVERT: D 87 GLU cc_start: 0.8166 (pm20) cc_final: 0.7887 (pm20) REVERT: D 114 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8346 (mmmm) REVERT: D 145 GLU cc_start: 0.8466 (tp30) cc_final: 0.7908 (tm-30) REVERT: D 151 ILE cc_start: 0.8139 (mt) cc_final: 0.7884 (mt) REVERT: D 190 MET cc_start: 0.8988 (tmm) cc_final: 0.8767 (tmm) REVERT: D 383 MET cc_start: 0.9333 (mtp) cc_final: 0.9107 (mtp) REVERT: D 483 GLU cc_start: 0.9028 (tp30) cc_final: 0.8665 (tp30) REVERT: D 597 GLU cc_start: 0.8864 (tp30) cc_final: 0.8327 (tt0) REVERT: D 598 GLN cc_start: 0.8301 (mt0) cc_final: 0.8094 (mt0) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 1.4716 time to fit residues: 139.0864 Evaluate side-chains 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 114 LYS Chi-restraints excluded: chain D residue 182 GLU 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 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.070024 restraints weight = 11205.325| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.59 r_work: 0.2742 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6671 Z= 0.148 Angle : 0.590 9.202 9069 Z= 0.293 Chirality : 0.043 0.145 947 Planarity : 0.004 0.064 1172 Dihedral : 5.523 55.208 931 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.74 % Allowed : 15.05 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.30), residues: 790 helix: 1.48 (0.26), residues: 403 sheet: 1.06 (0.77), residues: 44 loop : 0.16 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 163 HIS 0.003 0.001 HIS D 374 PHE 0.018 0.001 PHE D 603 TYR 0.012 0.001 TYR D 385 ARG 0.013 0.001 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 3) link_NAG-ASN : angle 4.64249 ( 9) hydrogen bonds : bond 0.04320 ( 309) hydrogen bonds : angle 4.54645 ( 951) SS BOND : bond 0.00457 ( 6) SS BOND : angle 1.21851 ( 12) covalent geometry : bond 0.00342 ( 6662) covalent geometry : angle 0.57059 ( 9048) *********************** 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 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8542 (mmmt) REVERT: D 87 GLU cc_start: 0.8158 (pm20) cc_final: 0.7852 (pm20) REVERT: D 114 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8308 (mmmm) REVERT: D 145 GLU cc_start: 0.8472 (tp30) cc_final: 0.7926 (tm-30) REVERT: D 190 MET cc_start: 0.8983 (tmm) cc_final: 0.8750 (tmm) REVERT: D 383 MET cc_start: 0.9293 (mtp) cc_final: 0.9077 (mtp) REVERT: D 483 GLU cc_start: 0.9041 (tp30) cc_final: 0.8730 (tp30) REVERT: D 597 GLU cc_start: 0.8775 (tp30) cc_final: 0.8282 (tt0) REVERT: D 598 GLN cc_start: 0.8256 (mt0) cc_final: 0.8033 (mt0) outliers start: 12 outliers final: 11 residues processed: 87 average time/residue: 1.8003 time to fit residues: 164.1506 Evaluate side-chains 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 320 LEU Chi-restraints excluded: chain D residue 334 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.097673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.074411 restraints weight = 11899.177| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.64 r_work: 0.2846 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6671 Z= 0.152 Angle : 0.590 9.275 9069 Z= 0.294 Chirality : 0.043 0.145 947 Planarity : 0.004 0.040 1172 Dihedral : 5.481 55.449 931 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.59 % Allowed : 15.20 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.30), residues: 790 helix: 1.47 (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 TRP 0.018 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.018 0.001 PHE D 603 TYR 0.013 0.001 TYR D 385 ARG 0.006 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 3) link_NAG-ASN : angle 4.62425 ( 9) hydrogen bonds : bond 0.04343 ( 309) hydrogen bonds : angle 4.54943 ( 951) SS BOND : bond 0.00453 ( 6) SS BOND : angle 1.19467 ( 12) covalent geometry : bond 0.00350 ( 6662) covalent geometry : angle 0.57096 ( 9048) ********************** 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 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8517 (mmmt) REVERT: D 87 GLU cc_start: 0.8136 (pm20) cc_final: 0.7871 (pm20) REVERT: D 114 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8326 (mmmm) REVERT: D 145 GLU cc_start: 0.8468 (tp30) cc_final: 0.7927 (tm-30) REVERT: D 151 ILE cc_start: 0.8070 (mt) cc_final: 0.7820 (mt) REVERT: D 190 MET cc_start: 0.9020 (tmm) cc_final: 0.8777 (tmm) REVERT: D 383 MET cc_start: 0.9319 (mtp) cc_final: 0.9101 (mtp) REVERT: D 483 GLU cc_start: 0.8997 (tp30) cc_final: 0.8677 (tp30) REVERT: D 597 GLU cc_start: 0.8874 (tp30) cc_final: 0.8329 (tt0) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 2.4781 time to fit residues: 229.0258 Evaluate side-chains 92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 114 LYS Chi-restraints excluded: chain D residue 182 GLU 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 68 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.094257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.069383 restraints weight = 11300.955| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.64 r_work: 0.2711 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6671 Z= 0.187 Angle : 0.613 9.439 9069 Z= 0.306 Chirality : 0.044 0.150 947 Planarity : 0.004 0.069 1172 Dihedral : 5.538 55.186 931 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.74 % Allowed : 15.20 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.30), residues: 790 helix: 1.41 (0.26), residues: 403 sheet: 1.05 (0.77), residues: 44 loop : 0.14 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.018 0.001 PHE D 603 TYR 0.014 0.001 TYR D 385 ARG 0.014 0.001 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 3) link_NAG-ASN : angle 4.73509 ( 9) hydrogen bonds : bond 0.04619 ( 309) hydrogen bonds : angle 4.61422 ( 951) SS BOND : bond 0.00471 ( 6) SS BOND : angle 1.19042 ( 12) covalent geometry : bond 0.00437 ( 6662) covalent geometry : angle 0.59387 ( 9048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7102.50 seconds wall clock time: 126 minutes 49.97 seconds (7609.97 seconds total)