Starting phenix.real_space_refine on Thu Jul 24 19:33:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dma_27532/07_2025/8dma_27532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dma_27532/07_2025/8dma_27532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2025/8dma_27532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2025/8dma_27532.map" model { file = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2025/8dma_27532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dma_27532/07_2025/8dma_27532.cif" } resolution = 2.79 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 4142 2.51 5 N 1089 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6487 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 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: 5.13, per 1000 atoms: 0.79 Number of scatterers: 6487 At special positions: 0 Unit cell: (77, 87, 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 1219 8.00 N 1089 7.00 C 4142 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=2.03 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=2.04 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=2.02 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: 1.49 Conformation dependent library (CDL) restraints added in 961.5 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: 1502 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.781A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.564A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.301A pdb=" N ARG A 408 " --> pdb=" O ASP 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: 4.051A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.547A pdb=" N THR D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) 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: 3.749A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.512A 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: 3.700A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.819A 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: 5.092A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.706A 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 218 through 252 removed outlier: 3.658A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.622A 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: 3.557A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.709A 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: 3.868A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.615A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.449A 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: 3.605A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.743A 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: 4.242A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.687A 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: 4.159A 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 removed outlier: 3.539A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.993A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.273A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 882 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: 1.82 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2077 1.34 - 1.47: 1743 1.47 - 1.59: 2791 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6669 Sorted by residual: 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 5.20e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+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 3.70e+00 bond pdb=" CG LEU D 558 " pdb=" CD1 LEU D 558 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8675 1.82 - 3.63: 315 3.63 - 5.45: 42 5.45 - 7.27: 19 7.27 - 9.08: 7 Bond angle restraints: 9058 Sorted by residual: angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C VAL D 364 " pdb=" CA VAL D 364 " pdb=" CB VAL D 364 " ideal model delta sigma weight residual 113.22 116.94 -3.72 1.12e+00 7.97e-01 1.10e+01 angle pdb=" CA VAL D 364 " pdb=" CB VAL D 364 " pdb=" CG1 VAL D 364 " ideal model delta sigma weight residual 110.40 115.87 -5.47 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 116.76 -6.95 2.21e+00 2.05e-01 9.89e+00 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 121.44 -7.04 2.30e+00 1.89e-01 9.38e+00 ... (remaining 9053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3592 17.14 - 34.28: 334 34.28 - 51.42: 51 51.42 - 68.56: 9 68.56 - 85.70: 8 Dihedral angle restraints: 3994 sinusoidal: 1657 harmonic: 2337 Sorted by residual: 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 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ALA D 396 " pdb=" C ALA D 396 " pdb=" N ASN D 397 " pdb=" CA ASN D 397 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA THR D 445 " pdb=" C THR D 445 " pdb=" N ILE D 446 " pdb=" CA ILE D 446 " ideal model delta harmonic sigma weight residual 180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 3991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 619 0.046 - 0.092: 234 0.092 - 0.138: 81 0.138 - 0.184: 14 0.184 - 0.230: 3 Chirality restraints: 951 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 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA GLU D 182 " pdb=" N GLU D 182 " pdb=" C GLU D 182 " pdb=" CB GLU D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU D 558 " pdb=" CB LEU D 558 " pdb=" CD1 LEU D 558 " pdb=" CD2 LEU D 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 948 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.17e+00 pdb=" N PRO A 373 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 224 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLU D 224 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU D 224 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 225 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 468 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO D 469 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " 0.034 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1333 2.78 - 3.31: 5871 3.31 - 3.84: 11379 3.84 - 4.37: 13370 4.37 - 4.90: 22664 Nonbonded interactions: 54617 Sorted by model distance: nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.244 3.040 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.340 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.350 3.120 ... (remaining 54612 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.990 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.005 0.064 6678 Z= 0.236 Angle : 0.841 9.082 9079 Z= 0.442 Chirality : 0.055 0.230 951 Planarity : 0.007 0.067 1172 Dihedral : 13.455 85.700 2474 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.53 (0.26), residues: 790 helix: -1.27 (0.22), residues: 399 sheet: 0.24 (0.64), residues: 60 loop : -0.69 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 163 HIS 0.005 0.002 HIS D 241 PHE 0.021 0.002 PHE D 369 TYR 0.029 0.002 TYR D 385 ARG 0.005 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 3) link_NAG-ASN : angle 3.32018 ( 9) hydrogen bonds : bond 0.13661 ( 307) hydrogen bonds : angle 6.78139 ( 882) SS BOND : bond 0.00608 ( 6) SS BOND : angle 1.57620 ( 12) covalent geometry : bond 0.00543 ( 6669) covalent geometry : angle 0.83298 ( 9058) *********************** 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 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.658 Fit side-chains REVERT: A 386 LYS cc_start: 0.9051 (mttt) cc_final: 0.8823 (mptt) REVERT: A 420 ASP cc_start: 0.8793 (m-30) cc_final: 0.8478 (m-30) REVERT: D 564 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8453 (mm-30) REVERT: D 597 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 607 ASN cc_start: 0.8700 (t0) cc_final: 0.8418 (t0) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 1.4626 time to fit residues: 166.6076 Evaluate side-chains 68 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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: 0.6980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 188 ASN D 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070102 restraints weight = 13192.194| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.86 r_work: 0.2825 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6678 Z= 0.176 Angle : 0.586 6.324 9079 Z= 0.300 Chirality : 0.043 0.179 951 Planarity : 0.005 0.046 1172 Dihedral : 5.882 57.060 932 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.44 % Allowed : 8.65 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 790 helix: 0.23 (0.25), residues: 395 sheet: 0.13 (0.65), residues: 59 loop : -0.22 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.018 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.006 0.001 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 3) link_NAG-ASN : angle 2.49560 ( 9) hydrogen bonds : bond 0.04389 ( 307) hydrogen bonds : angle 4.90997 ( 882) SS BOND : bond 0.00502 ( 6) SS BOND : angle 1.16664 ( 12) covalent geometry : bond 0.00406 ( 6669) covalent geometry : angle 0.57939 ( 9058) *********************** 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 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.737 Fit side-chains REVERT: D 23 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8260 (mp0) REVERT: D 149 ASP cc_start: 0.8539 (m-30) cc_final: 0.8335 (p0) REVERT: D 163 TRP cc_start: 0.8471 (t60) cc_final: 0.8137 (t60) REVERT: D 564 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8945 (mm-30) REVERT: D 597 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8302 (tm-30) REVERT: D 607 ASN cc_start: 0.8860 (t0) cc_final: 0.8416 (t0) outliers start: 10 outliers final: 4 residues processed: 77 average time/residue: 1.2225 time to fit residues: 99.3208 Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain D residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 0.0010 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3313 r_free = 0.3313 target = 0.091015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.070673 restraints weight = 13300.285| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.87 r_work: 0.2833 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6678 Z= 0.138 Angle : 0.542 6.635 9079 Z= 0.276 Chirality : 0.042 0.177 951 Planarity : 0.004 0.038 1172 Dihedral : 5.370 56.411 932 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.87 % Allowed : 10.81 % Favored : 87.32 % 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: 0.51 (0.30), residues: 790 helix: 0.73 (0.26), residues: 396 sheet: 0.14 (0.66), residues: 59 loop : 0.07 (0.35), residues: 335 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 0.017 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.007 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 3) link_NAG-ASN : angle 2.31027 ( 9) hydrogen bonds : bond 0.04051 ( 307) hydrogen bonds : angle 4.65290 ( 882) SS BOND : bond 0.00390 ( 6) SS BOND : angle 1.04618 ( 12) covalent geometry : bond 0.00318 ( 6669) covalent geometry : angle 0.53605 ( 9058) *********************** 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 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.701 Fit side-chains REVERT: A 385 THR cc_start: 0.9424 (p) cc_final: 0.9207 (p) REVERT: A 386 LYS cc_start: 0.9304 (mttt) cc_final: 0.8874 (mptt) REVERT: A 496 SER cc_start: 0.8332 (p) cc_final: 0.8041 (m) REVERT: D 149 ASP cc_start: 0.8554 (m-30) cc_final: 0.8326 (p0) REVERT: D 471 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: D 597 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8406 (tm-30) REVERT: D 607 ASN cc_start: 0.8893 (t0) cc_final: 0.8446 (t0) outliers start: 13 outliers final: 4 residues processed: 83 average time/residue: 1.3231 time to fit residues: 115.4155 Evaluate side-chains 71 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 0.0170 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN D 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.091940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071714 restraints weight = 13321.886| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.87 r_work: 0.2872 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6678 Z= 0.115 Angle : 0.539 7.739 9079 Z= 0.269 Chirality : 0.041 0.179 951 Planarity : 0.004 0.036 1172 Dihedral : 4.998 55.302 932 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.30 % Allowed : 12.25 % Favored : 86.46 % 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: 0.90 (0.30), residues: 790 helix: 1.14 (0.26), residues: 389 sheet: 0.13 (0.66), residues: 59 loop : 0.20 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.003 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.007 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 3) link_NAG-ASN : angle 2.05468 ( 9) hydrogen bonds : bond 0.03708 ( 307) hydrogen bonds : angle 4.49602 ( 882) SS BOND : bond 0.00476 ( 6) SS BOND : angle 0.99636 ( 12) covalent geometry : bond 0.00261 ( 6669) covalent geometry : angle 0.53404 ( 9058) *********************** 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 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.784 Fit side-chains REVERT: A 385 THR cc_start: 0.9406 (p) cc_final: 0.9197 (p) REVERT: A 386 LYS cc_start: 0.9331 (mttt) cc_final: 0.8886 (mptt) REVERT: A 440 LYS cc_start: 0.9253 (mppt) cc_final: 0.8996 (mppt) REVERT: A 496 SER cc_start: 0.8268 (p) cc_final: 0.8029 (m) REVERT: D 149 ASP cc_start: 0.8571 (m-30) cc_final: 0.8346 (p0) REVERT: D 471 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: D 597 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8472 (tm-30) REVERT: D 607 ASN cc_start: 0.8855 (t0) cc_final: 0.8454 (t0) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.4940 time to fit residues: 130.3547 Evaluate side-chains 73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain D residue 471 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3318 r_free = 0.3318 target = 0.091047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.070978 restraints weight = 13275.925| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.85 r_work: 0.2839 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6678 Z= 0.139 Angle : 0.551 7.593 9079 Z= 0.277 Chirality : 0.042 0.184 951 Planarity : 0.004 0.043 1172 Dihedral : 4.961 55.164 932 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.87 % Allowed : 13.83 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.30), residues: 790 helix: 1.19 (0.26), residues: 396 sheet: 0.13 (0.65), residues: 59 loop : 0.26 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.009 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 3) link_NAG-ASN : angle 2.06965 ( 9) hydrogen bonds : bond 0.03817 ( 307) hydrogen bonds : angle 4.45639 ( 882) SS BOND : bond 0.00410 ( 6) SS BOND : angle 0.91068 ( 12) covalent geometry : bond 0.00322 ( 6669) covalent geometry : angle 0.54704 ( 9058) *********************** 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 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9325 (mttt) cc_final: 0.9038 (mmmm) REVERT: A 440 LYS cc_start: 0.9266 (mppt) cc_final: 0.9015 (mppt) REVERT: D 149 ASP cc_start: 0.8627 (m-30) cc_final: 0.8383 (p0) REVERT: D 171 GLU cc_start: 0.7809 (mp0) cc_final: 0.7466 (mp0) REVERT: D 471 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: D 472 GLN cc_start: 0.8380 (mp10) cc_final: 0.8097 (mp-120) REVERT: D 479 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8488 (mt-10) REVERT: D 579 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8774 (ttp) REVERT: D 597 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8511 (tm-30) REVERT: D 607 ASN cc_start: 0.8807 (t0) cc_final: 0.8390 (t0) outliers start: 13 outliers final: 5 residues processed: 78 average time/residue: 1.3744 time to fit residues: 112.4298 Evaluate side-chains 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.0040 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.090659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.070456 restraints weight = 13180.676| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.86 r_work: 0.2832 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6678 Z= 0.146 Angle : 0.554 7.908 9079 Z= 0.277 Chirality : 0.042 0.191 951 Planarity : 0.004 0.047 1172 Dihedral : 4.938 55.222 932 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.44 % Allowed : 13.54 % Favored : 85.01 % 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: 1.07 (0.30), residues: 790 helix: 1.27 (0.26), residues: 396 sheet: 0.11 (0.64), residues: 59 loop : 0.29 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.011 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 3) link_NAG-ASN : angle 2.12208 ( 9) hydrogen bonds : bond 0.03859 ( 307) hydrogen bonds : angle 4.43688 ( 882) SS BOND : bond 0.00411 ( 6) SS BOND : angle 0.80038 ( 12) covalent geometry : bond 0.00341 ( 6669) covalent geometry : angle 0.54990 ( 9058) *********************** 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 81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.685 Fit side-chains REVERT: A 378 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8172 (mtpm) REVERT: A 386 LYS cc_start: 0.9318 (mttt) cc_final: 0.8860 (mptt) REVERT: A 440 LYS cc_start: 0.9282 (mppt) cc_final: 0.9035 (mppt) REVERT: D 131 LYS cc_start: 0.8410 (tppt) cc_final: 0.8205 (tptt) REVERT: D 149 ASP cc_start: 0.8643 (m-30) cc_final: 0.8402 (p0) REVERT: D 171 GLU cc_start: 0.7860 (mp0) cc_final: 0.7584 (mp0) REVERT: D 471 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: D 472 GLN cc_start: 0.8390 (mp10) cc_final: 0.8083 (mp10) REVERT: D 479 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8519 (mt-10) REVERT: D 597 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 607 ASN cc_start: 0.8796 (t0) cc_final: 0.8351 (t0) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 1.4283 time to fit residues: 116.6475 Evaluate side-chains 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3290 r_free = 0.3290 target = 0.089422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.069358 restraints weight = 13157.130| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.82 r_work: 0.2810 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6678 Z= 0.173 Angle : 0.582 8.355 9079 Z= 0.292 Chirality : 0.043 0.202 951 Planarity : 0.004 0.049 1172 Dihedral : 5.015 55.701 932 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.59 % Allowed : 12.97 % Favored : 84.44 % 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: 1.10 (0.30), residues: 790 helix: 1.32 (0.26), residues: 390 sheet: 0.02 (0.64), residues: 59 loop : 0.32 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.017 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.011 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 3) link_NAG-ASN : angle 2.24871 ( 9) hydrogen bonds : bond 0.04117 ( 307) hydrogen bonds : angle 4.47792 ( 882) SS BOND : bond 0.00478 ( 6) SS BOND : angle 0.85283 ( 12) covalent geometry : bond 0.00405 ( 6669) covalent geometry : angle 0.57706 ( 9058) *********************** 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 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8241 (mtpm) REVERT: A 386 LYS cc_start: 0.9347 (mttt) cc_final: 0.8896 (mptt) REVERT: A 440 LYS cc_start: 0.9311 (mppt) cc_final: 0.9073 (mppt) REVERT: D 171 GLU cc_start: 0.7994 (mp0) cc_final: 0.7677 (mp0) REVERT: D 471 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: D 472 GLN cc_start: 0.8355 (mp10) cc_final: 0.8060 (mp-120) REVERT: D 597 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8468 (tm-30) REVERT: D 607 ASN cc_start: 0.8790 (t0) cc_final: 0.8347 (t0) outliers start: 18 outliers final: 9 residues processed: 78 average time/residue: 1.3947 time to fit residues: 114.1550 Evaluate side-chains 73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS 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 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3302 r_free = 0.3302 target = 0.090076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.069824 restraints weight = 13307.269| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.86 r_work: 0.2822 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6678 Z= 0.150 Angle : 0.583 8.635 9079 Z= 0.291 Chirality : 0.043 0.210 951 Planarity : 0.004 0.056 1172 Dihedral : 4.984 55.434 932 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.45 % Allowed : 13.98 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.30), residues: 790 helix: 1.34 (0.26), residues: 390 sheet: -0.03 (0.64), residues: 59 loop : 0.38 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.015 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.012 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 3) link_NAG-ASN : angle 2.21346 ( 9) hydrogen bonds : bond 0.03942 ( 307) hydrogen bonds : angle 4.49528 ( 882) SS BOND : bond 0.00436 ( 6) SS BOND : angle 1.16080 ( 12) covalent geometry : bond 0.00352 ( 6669) covalent geometry : angle 0.57758 ( 9058) *********************** 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 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8177 (mtpm) REVERT: A 386 LYS cc_start: 0.9337 (mttt) cc_final: 0.8856 (mptt) REVERT: A 440 LYS cc_start: 0.9306 (mppt) cc_final: 0.9052 (mppt) REVERT: D 171 GLU cc_start: 0.7925 (mp0) cc_final: 0.7479 (mp0) REVERT: D 471 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: D 472 GLN cc_start: 0.8348 (mp10) cc_final: 0.7988 (mp10) REVERT: D 597 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8444 (tm-30) REVERT: D 607 ASN cc_start: 0.8741 (t0) cc_final: 0.8271 (t0) outliers start: 17 outliers final: 9 residues processed: 78 average time/residue: 1.4240 time to fit residues: 116.3104 Evaluate side-chains 73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS 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 69 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3304 r_free = 0.3304 target = 0.090090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069840 restraints weight = 13349.988| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.87 r_work: 0.2825 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6678 Z= 0.150 Angle : 0.585 8.835 9079 Z= 0.292 Chirality : 0.043 0.212 951 Planarity : 0.004 0.061 1172 Dihedral : 4.913 55.197 932 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.44 % Allowed : 15.56 % Favored : 83.00 % 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: 1.18 (0.31), residues: 790 helix: 1.37 (0.26), residues: 391 sheet: -0.06 (0.63), residues: 59 loop : 0.41 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.015 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.014 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 3) link_NAG-ASN : angle 2.20910 ( 9) hydrogen bonds : bond 0.03910 ( 307) hydrogen bonds : angle 4.43922 ( 882) SS BOND : bond 0.00464 ( 6) SS BOND : angle 1.12355 ( 12) covalent geometry : bond 0.00351 ( 6669) covalent geometry : angle 0.58017 ( 9058) *********************** 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 76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8168 (mtpm) REVERT: A 386 LYS cc_start: 0.9398 (mttt) cc_final: 0.8910 (mptt) REVERT: A 440 LYS cc_start: 0.9313 (mppt) cc_final: 0.9054 (mppt) REVERT: D 171 GLU cc_start: 0.7917 (mp0) cc_final: 0.7480 (mp0) REVERT: D 471 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: D 472 GLN cc_start: 0.8306 (mp10) cc_final: 0.7919 (mp10) REVERT: D 597 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8530 (tm-30) REVERT: D 607 ASN cc_start: 0.8702 (t0) cc_final: 0.8242 (t0) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 1.6755 time to fit residues: 128.4264 Evaluate side-chains 75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3331 r_free = 0.3331 target = 0.091645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.071505 restraints weight = 13408.709| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.87 r_work: 0.2857 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6678 Z= 0.118 Angle : 0.580 9.203 9079 Z= 0.286 Chirality : 0.042 0.205 951 Planarity : 0.004 0.061 1172 Dihedral : 4.740 54.669 932 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.44 % Allowed : 15.42 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.31), residues: 790 helix: 1.43 (0.26), residues: 397 sheet: 0.00 (0.64), residues: 59 loop : 0.40 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.003 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.011 0.001 TYR D 385 ARG 0.014 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 3) link_NAG-ASN : angle 2.08668 ( 9) hydrogen bonds : bond 0.03577 ( 307) hydrogen bonds : angle 4.36240 ( 882) SS BOND : bond 0.00397 ( 6) SS BOND : angle 1.02116 ( 12) covalent geometry : bond 0.00277 ( 6669) covalent geometry : angle 0.57585 ( 9058) ********************** 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 74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.557 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8506 (pt0) REVERT: A 440 LYS cc_start: 0.9302 (mppt) cc_final: 0.9049 (mppt) REVERT: D 171 GLU cc_start: 0.7891 (mp0) cc_final: 0.7466 (mp0) REVERT: D 471 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: D 472 GLN cc_start: 0.8182 (mp10) cc_final: 0.7771 (mp10) REVERT: D 479 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8522 (mt-10) REVERT: D 597 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8553 (tm-30) REVERT: D 607 ASN cc_start: 0.8699 (t0) cc_final: 0.8235 (t0) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 1.7610 time to fit residues: 134.1201 Evaluate side-chains 69 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** 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 = 0.3307 r_free = 0.3307 target = 0.090254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.070162 restraints weight = 13501.315| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.86 r_work: 0.2826 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6678 Z= 0.152 Angle : 0.583 8.866 9079 Z= 0.290 Chirality : 0.043 0.209 951 Planarity : 0.004 0.063 1172 Dihedral : 4.842 55.112 932 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.30 % Allowed : 15.42 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.31), residues: 790 helix: 1.41 (0.26), residues: 397 sheet: -0.02 (0.64), residues: 59 loop : 0.37 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.014 0.000 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 3) link_NAG-ASN : angle 2.21229 ( 9) hydrogen bonds : bond 0.03910 ( 307) hydrogen bonds : angle 4.38825 ( 882) SS BOND : bond 0.00448 ( 6) SS BOND : angle 1.05209 ( 12) covalent geometry : bond 0.00357 ( 6669) covalent geometry : angle 0.57799 ( 9058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5334.98 seconds wall clock time: 94 minutes 55.26 seconds (5695.26 seconds total)