Starting phenix.real_space_refine on Thu Jul 2 04:42:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sy0_25512/07_2026/7sy0_25512.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy0_25512/07_2026/7sy0_25512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2026/7sy0_25512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2026/7sy0_25512.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2026/7sy0_25512.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2026/7sy0_25512.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2026/7sy0_25512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy0_25512/07_2026/7sy0_25512.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 4186 2.51 5 N 1081 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6553 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 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 chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.29, per 1000 atoms: 0.20 Number of scatterers: 6553 At special positions: 0 Unit cell: (79, 84, 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 1249 8.00 N 1081 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 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 B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 346.6 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.708A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.162A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.781A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.028A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.933A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.725A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.669A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.784A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.541A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.701A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.235A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.310A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.726A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.458A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.931A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.911A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.620A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.966A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.313A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.68 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: 2086 1.35 - 1.47: 1795 1.47 - 1.60: 2796 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " 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 E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C SER E 611 " pdb=" N PRO E 612 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.73e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 8817 2.05 - 4.10: 289 4.10 - 6.15: 36 6.15 - 8.20: 6 8.20 - 10.24: 4 Bond angle restraints: 9152 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 128.96 -6.14 1.42e+00 4.96e-01 1.87e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.65 -9.25 2.30e+00 1.89e-01 1.62e+01 angle pdb=" CB MET E 323 " pdb=" CG MET E 323 " pdb=" SD MET E 323 " ideal model delta sigma weight residual 112.70 122.94 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 115.96 -3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 117.68 -4.52 1.42e+00 4.96e-01 1.01e+01 ... (remaining 9147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 3557 17.12 - 34.25: 302 34.25 - 51.37: 41 51.37 - 68.50: 9 68.50 - 85.62: 12 Dihedral angle restraints: 3921 sinusoidal: 1583 harmonic: 2338 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -42.93 -43.07 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 17.52 61.48 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.76 8.16 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 3918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 724 0.055 - 0.109: 197 0.109 - 0.164: 46 0.164 - 0.218: 7 0.218 - 0.273: 3 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL E 318 " pdb=" CA VAL E 318 " pdb=" CG1 VAL E 318 " pdb=" CG2 VAL E 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 974 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ALA E 36 " -0.086 2.00e-02 2.50e+03 pdb=" O ALA E 36 " 0.032 2.00e-02 2.50e+03 pdb=" N GLU E 37 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ARG E 169 " -0.060 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.022 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 32 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C PHE E 32 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE E 32 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN E 33 " 0.018 2.00e-02 2.50e+03 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1834 2.82 - 3.34: 5957 3.34 - 3.86: 11435 3.86 - 4.38: 12999 4.38 - 4.90: 22431 Nonbonded interactions: 54656 Sorted by model distance: nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR E 41 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.322 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.335 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.335 3.040 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.338 3.040 ... (remaining 54651 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.830 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 0.057 6748 Z= 0.237 Angle : 0.875 12.746 9185 Z= 0.467 Chirality : 0.055 0.273 977 Planarity : 0.007 0.065 1178 Dihedral : 13.431 85.622 2403 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.26), residues: 793 helix: -0.06 (0.23), residues: 387 sheet: 0.55 (0.66), residues: 52 loop : -0.63 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 460 TYR 0.032 0.002 TYR E 385 PHE 0.030 0.003 PHE E 369 TRP 0.022 0.002 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 ( 6735) covalent geometry : angle 0.84349 / 0.46 ( 9152) SS BOND : bond 0.00598 / 0.36 ( 6) SS BOND : angle 2.68049 / 1.53 ( 12) hydrogen bonds : bond 0.14199 / 9.67 ( 323) hydrogen bonds : angle 6.30716 / 4.28 ( 918) link_NAG-ASN : bond 0.00898 / 0.50 ( 7) link_NAG-ASN : angle 4.58467 / 3.47 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: E 142 LEU cc_start: 0.9130 (mt) cc_final: 0.8923 (mt) REVERT: E 149 ASN cc_start: 0.9200 (m-40) cc_final: 0.8949 (m-40) REVERT: E 249 MET cc_start: 0.9324 (ttm) cc_final: 0.9031 (ttp) REVERT: E 290 ASN cc_start: 0.8984 (t0) cc_final: 0.8685 (t0) REVERT: E 347 THR cc_start: 0.8821 (m) cc_final: 0.8354 (p) REVERT: E 371 THR cc_start: 0.9207 (m) cc_final: 0.8930 (p) REVERT: E 441 LYS cc_start: 0.8993 (tttp) cc_final: 0.8594 (ttmm) REVERT: E 455 MET cc_start: 0.8781 (tmm) cc_final: 0.8460 (tmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.5571 time to fit residues: 74.0383 Evaluate side-chains 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 154 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.077516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059644 restraints weight = 18237.287| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.48 r_work: 0.2843 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6748 Z= 0.138 Angle : 0.588 9.386 9185 Z= 0.299 Chirality : 0.041 0.142 977 Planarity : 0.005 0.038 1178 Dihedral : 4.246 15.234 866 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.43 % Allowed : 9.86 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.28), residues: 793 helix: 1.00 (0.25), residues: 402 sheet: 0.84 (0.75), residues: 43 loop : -0.14 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 466 TYR 0.012 0.001 TYR E 385 PHE 0.015 0.001 PHE E 369 TRP 0.017 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 6735) covalent geometry : angle 0.56446 / 0.29 ( 9152) SS BOND : bond 0.00444 / 0.24 ( 6) SS BOND : angle 2.07774 / 1.14 ( 12) hydrogen bonds : bond 0.04205 / 2.76 ( 323) hydrogen bonds : angle 4.64302 / 3.24 ( 918) link_NAG-ASN : bond 0.00535 / 0.32 ( 7) link_NAG-ASN : angle 3.13370 / 2.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.201 Fit side-chains REVERT: B 484 GLU cc_start: 0.8775 (tt0) cc_final: 0.8525 (tp30) REVERT: E 149 ASN cc_start: 0.9210 (m-40) cc_final: 0.8889 (m110) REVERT: E 224 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8211 (pp20) REVERT: E 249 MET cc_start: 0.9314 (ttm) cc_final: 0.9027 (ttp) REVERT: E 347 THR cc_start: 0.8782 (m) cc_final: 0.8307 (p) REVERT: E 360 MET cc_start: 0.9131 (ttp) cc_final: 0.8850 (ttm) REVERT: E 366 MET cc_start: 0.8575 (ttp) cc_final: 0.8315 (ttm) REVERT: E 371 THR cc_start: 0.9148 (m) cc_final: 0.8937 (p) REVERT: E 441 LYS cc_start: 0.8979 (tttp) cc_final: 0.8598 (ttmm) REVERT: E 455 MET cc_start: 0.9093 (tmm) cc_final: 0.8819 (tmm) REVERT: E 474 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7349 (mmt) REVERT: E 578 ASN cc_start: 0.8542 (t0) cc_final: 0.8301 (p0) outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 0.5318 time to fit residues: 35.3290 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.058328 restraints weight = 17942.164| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.42 r_work: 0.2817 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6748 Z= 0.143 Angle : 0.539 7.257 9185 Z= 0.273 Chirality : 0.041 0.144 977 Planarity : 0.004 0.041 1178 Dihedral : 4.032 14.628 866 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.29 % Allowed : 10.29 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.29), residues: 793 helix: 1.43 (0.26), residues: 402 sheet: 0.89 (0.78), residues: 42 loop : 0.15 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.012 0.001 TYR E 385 PHE 0.014 0.001 PHE E 369 TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6735) covalent geometry : angle 0.52057 / 0.27 ( 9152) SS BOND : bond 0.00355 / 0.19 ( 6) SS BOND : angle 1.41315 / 0.78 ( 12) hydrogen bonds : bond 0.04057 / 2.66 ( 323) hydrogen bonds : angle 4.36059 / 3.07 ( 918) link_NAG-ASN : bond 0.00466 / 0.27 ( 7) link_NAG-ASN : angle 2.76762 / 2.09 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 523 THR cc_start: 0.8577 (p) cc_final: 0.8313 (t) REVERT: E 55 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8763 (p) REVERT: E 149 ASN cc_start: 0.9245 (m-40) cc_final: 0.8841 (m110) REVERT: E 224 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8244 (pp20) REVERT: E 249 MET cc_start: 0.9279 (ttm) cc_final: 0.8918 (ttp) REVERT: E 347 THR cc_start: 0.8862 (m) cc_final: 0.8407 (p) REVERT: E 366 MET cc_start: 0.8707 (ttp) cc_final: 0.8452 (ttm) REVERT: E 441 LYS cc_start: 0.9078 (tttp) cc_final: 0.8594 (ttmm) REVERT: E 455 MET cc_start: 0.9145 (tmm) cc_final: 0.8929 (tmm) REVERT: E 578 ASN cc_start: 0.8576 (t0) cc_final: 0.8234 (p0) outliers start: 16 outliers final: 6 residues processed: 70 average time/residue: 0.5099 time to fit residues: 37.8998 Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** 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 = 0.075103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.057015 restraints weight = 18278.259| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.44 r_work: 0.2785 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6748 Z= 0.162 Angle : 0.542 8.895 9185 Z= 0.275 Chirality : 0.042 0.168 977 Planarity : 0.004 0.040 1178 Dihedral : 4.013 14.874 866 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.29 % Allowed : 10.43 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.30), residues: 793 helix: 1.59 (0.26), residues: 397 sheet: 0.55 (0.77), residues: 44 loop : 0.35 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.012 0.001 TYR E 385 PHE 0.015 0.001 PHE E 369 TRP 0.015 0.001 TRP E 606 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6735) covalent geometry : angle 0.52853 / 0.27 ( 9152) SS BOND : bond 0.00287 / 0.16 ( 6) SS BOND : angle 0.73586 / 0.45 ( 12) hydrogen bonds : bond 0.04033 / 2.64 ( 323) hydrogen bonds : angle 4.30219 / 3.02 ( 918) link_NAG-ASN : bond 0.00434 / 0.26 ( 7) link_NAG-ASN : angle 2.52559 / 1.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 55 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8794 (p) REVERT: E 149 ASN cc_start: 0.9264 (m-40) cc_final: 0.8894 (m110) REVERT: E 224 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8250 (pp20) REVERT: E 249 MET cc_start: 0.9299 (ttm) cc_final: 0.8961 (ttp) REVERT: E 347 THR cc_start: 0.8917 (m) cc_final: 0.8449 (p) REVERT: E 441 LYS cc_start: 0.9098 (tttp) cc_final: 0.8669 (ttmm) REVERT: E 455 MET cc_start: 0.9191 (tmm) cc_final: 0.8965 (tmm) outliers start: 16 outliers final: 6 residues processed: 68 average time/residue: 0.5434 time to fit residues: 39.2109 Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 501 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.056280 restraints weight = 18567.325| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.46 r_work: 0.2771 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6748 Z= 0.166 Angle : 0.530 6.810 9185 Z= 0.271 Chirality : 0.041 0.146 977 Planarity : 0.004 0.039 1178 Dihedral : 4.007 14.653 866 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.00 % Allowed : 12.00 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.30), residues: 793 helix: 1.77 (0.26), residues: 388 sheet: 0.85 (0.78), residues: 42 loop : 0.55 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.012 0.001 TYR E 515 PHE 0.015 0.001 PHE E 369 TRP 0.017 0.001 TRP E 606 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 6735) covalent geometry : angle 0.51858 / 0.27 ( 9152) SS BOND : bond 0.00274 / 0.15 ( 6) SS BOND : angle 0.72363 / 0.45 ( 12) hydrogen bonds : bond 0.04042 / 2.65 ( 323) hydrogen bonds : angle 4.28728 / 3.00 ( 918) link_NAG-ASN : bond 0.00408 / 0.25 ( 7) link_NAG-ASN : angle 2.33544 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8794 (p) REVERT: E 75 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: E 149 ASN cc_start: 0.9302 (m-40) cc_final: 0.8978 (m110) REVERT: E 224 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8265 (pp20) REVERT: E 249 MET cc_start: 0.9364 (ttm) cc_final: 0.9035 (ttp) REVERT: E 347 THR cc_start: 0.8952 (m) cc_final: 0.8544 (p) REVERT: E 441 LYS cc_start: 0.9098 (tttp) cc_final: 0.8651 (tppp) outliers start: 14 outliers final: 5 residues processed: 65 average time/residue: 0.5331 time to fit residues: 36.5818 Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** 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 = 0.074891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056877 restraints weight = 18533.444| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.46 r_work: 0.2781 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.137 Angle : 0.526 7.720 9185 Z= 0.267 Chirality : 0.041 0.142 977 Planarity : 0.004 0.039 1178 Dihedral : 3.917 14.033 866 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.14 % Allowed : 12.57 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.30), residues: 793 helix: 1.82 (0.26), residues: 387 sheet: 0.85 (0.79), residues: 42 loop : 0.58 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 204 TYR 0.010 0.001 TYR E 515 PHE 0.013 0.001 PHE E 369 TRP 0.018 0.001 TRP E 606 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6735) covalent geometry : angle 0.51573 / 0.26 ( 9152) SS BOND : bond 0.00264 / 0.15 ( 6) SS BOND : angle 0.63940 / 0.40 ( 12) hydrogen bonds : bond 0.03889 / 2.56 ( 323) hydrogen bonds : angle 4.24021 / 2.95 ( 918) link_NAG-ASN : bond 0.00372 / 0.22 ( 7) link_NAG-ASN : angle 2.18872 / 1.59 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8788 (p) REVERT: E 75 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: E 149 ASN cc_start: 0.9297 (m-40) cc_final: 0.8994 (m110) REVERT: E 224 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8306 (pp20) REVERT: E 249 MET cc_start: 0.9311 (ttm) cc_final: 0.8986 (ttp) REVERT: E 323 MET cc_start: 0.9423 (mmm) cc_final: 0.9096 (mmm) REVERT: E 347 THR cc_start: 0.8952 (m) cc_final: 0.8599 (p) REVERT: E 366 MET cc_start: 0.8891 (ttp) cc_final: 0.8525 (ttt) REVERT: E 411 SER cc_start: 0.9048 (m) cc_final: 0.8834 (p) REVERT: E 441 LYS cc_start: 0.9075 (tttp) cc_final: 0.8629 (tppp) REVERT: E 455 MET cc_start: 0.9208 (tmm) cc_final: 0.8995 (tmm) REVERT: E 552 GLN cc_start: 0.9002 (tp40) cc_final: 0.8601 (tm-30) outliers start: 15 outliers final: 6 residues processed: 68 average time/residue: 0.4673 time to fit residues: 33.5721 Evaluate side-chains 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 28 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** 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 = 0.3324 r_free = 0.3324 target = 0.075356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.057244 restraints weight = 18396.233| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.45 r_work: 0.2792 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6748 Z= 0.121 Angle : 0.520 8.370 9185 Z= 0.263 Chirality : 0.040 0.135 977 Planarity : 0.004 0.038 1178 Dihedral : 3.792 13.791 866 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.57 % Allowed : 14.00 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.30), residues: 793 helix: 1.89 (0.27), residues: 387 sheet: 0.88 (0.79), residues: 42 loop : 0.65 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 192 TYR 0.010 0.001 TYR E 385 PHE 0.013 0.001 PHE E 369 TRP 0.021 0.001 TRP E 606 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6735) covalent geometry : angle 0.51133 / 0.26 ( 9152) SS BOND : bond 0.00245 / 0.14 ( 6) SS BOND : angle 0.67375 / 0.41 ( 12) hydrogen bonds : bond 0.03706 / 2.43 ( 323) hydrogen bonds : angle 4.18404 / 2.91 ( 918) link_NAG-ASN : bond 0.00352 / 0.20 ( 7) link_NAG-ASN : angle 2.06520 / 1.48 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 55 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8795 (p) REVERT: E 149 ASN cc_start: 0.9272 (m-40) cc_final: 0.9008 (m110) REVERT: E 224 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8326 (pp20) REVERT: E 249 MET cc_start: 0.9308 (ttm) cc_final: 0.8977 (ttp) REVERT: E 329 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8580 (mp0) REVERT: E 347 THR cc_start: 0.8945 (m) cc_final: 0.8647 (p) REVERT: E 411 SER cc_start: 0.9002 (m) cc_final: 0.8797 (p) REVERT: E 441 LYS cc_start: 0.9057 (tttp) cc_final: 0.8604 (tppp) REVERT: E 455 MET cc_start: 0.9204 (tmm) cc_final: 0.8949 (tmm) REVERT: E 552 GLN cc_start: 0.8987 (tp40) cc_final: 0.8587 (tm-30) REVERT: E 578 ASN cc_start: 0.8574 (t0) cc_final: 0.8235 (p0) outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 0.5130 time to fit residues: 35.2305 Evaluate side-chains 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** 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 = 0.3309 r_free = 0.3309 target = 0.074560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056571 restraints weight = 18383.296| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.44 r_work: 0.2778 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6748 Z= 0.148 Angle : 0.527 8.641 9185 Z= 0.267 Chirality : 0.041 0.140 977 Planarity : 0.004 0.038 1178 Dihedral : 3.845 14.592 866 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.14 % Allowed : 14.14 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.30), residues: 793 helix: 1.86 (0.26), residues: 387 sheet: 0.70 (0.78), residues: 44 loop : 0.71 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 192 TYR 0.011 0.001 TYR E 515 PHE 0.013 0.001 PHE E 369 TRP 0.022 0.001 TRP E 606 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6735) covalent geometry : angle 0.51834 / 0.26 ( 9152) SS BOND : bond 0.00247 / 0.14 ( 6) SS BOND : angle 0.68163 / 0.41 ( 12) hydrogen bonds : bond 0.03864 / 2.54 ( 323) hydrogen bonds : angle 4.21483 / 2.93 ( 918) link_NAG-ASN : bond 0.00340 / 0.20 ( 7) link_NAG-ASN : angle 2.00693 / 1.43 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 55 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8787 (p) REVERT: E 149 ASN cc_start: 0.9251 (m-40) cc_final: 0.8968 (m110) REVERT: E 224 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8308 (pp20) REVERT: E 249 MET cc_start: 0.9370 (ttm) cc_final: 0.9027 (ttp) REVERT: E 323 MET cc_start: 0.9381 (mmm) cc_final: 0.9152 (mmm) REVERT: E 329 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8578 (mt-10) REVERT: E 347 THR cc_start: 0.8936 (m) cc_final: 0.8642 (p) REVERT: E 411 SER cc_start: 0.9050 (m) cc_final: 0.8832 (p) REVERT: E 441 LYS cc_start: 0.9080 (tttp) cc_final: 0.8631 (tppp) REVERT: E 552 GLN cc_start: 0.8992 (tp40) cc_final: 0.8588 (tm-30) REVERT: E 578 ASN cc_start: 0.8577 (t0) cc_final: 0.8215 (p0) outliers start: 15 outliers final: 7 residues processed: 68 average time/residue: 0.4502 time to fit residues: 32.3671 Evaluate side-chains 59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** 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 = 0.3308 r_free = 0.3308 target = 0.074424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.056310 restraints weight = 18586.203| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.46 r_work: 0.2771 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6748 Z= 0.157 Angle : 0.562 9.138 9185 Z= 0.285 Chirality : 0.041 0.143 977 Planarity : 0.004 0.039 1178 Dihedral : 3.880 14.386 866 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.43 % Allowed : 14.71 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.30), residues: 793 helix: 1.82 (0.26), residues: 387 sheet: 0.65 (0.78), residues: 44 loop : 0.73 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 403 TYR 0.010 0.001 TYR E 515 PHE 0.013 0.001 PHE E 369 TRP 0.023 0.001 TRP E 606 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 6735) covalent geometry : angle 0.55388 / 0.28 ( 9152) SS BOND : bond 0.00279 / 0.15 ( 6) SS BOND : angle 0.74051 / 0.44 ( 12) hydrogen bonds : bond 0.03879 / 2.55 ( 323) hydrogen bonds : angle 4.23942 / 2.94 ( 918) link_NAG-ASN : bond 0.00334 / 0.20 ( 7) link_NAG-ASN : angle 2.05357 / 1.43 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 55 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8769 (p) REVERT: E 149 ASN cc_start: 0.9246 (m-40) cc_final: 0.8964 (m110) REVERT: E 224 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8334 (pp20) REVERT: E 249 MET cc_start: 0.9377 (ttm) cc_final: 0.9049 (ttp) REVERT: E 323 MET cc_start: 0.9372 (mmm) cc_final: 0.9155 (mmm) REVERT: E 329 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8597 (mp0) REVERT: E 347 THR cc_start: 0.8948 (m) cc_final: 0.8655 (p) REVERT: E 411 SER cc_start: 0.9065 (m) cc_final: 0.8852 (p) REVERT: E 441 LYS cc_start: 0.9089 (tttp) cc_final: 0.8629 (tppp) REVERT: E 455 MET cc_start: 0.9112 (tmm) cc_final: 0.8598 (tpt) REVERT: E 552 GLN cc_start: 0.8991 (tp40) cc_final: 0.8585 (tm-30) REVERT: E 578 ASN cc_start: 0.8612 (t0) cc_final: 0.8200 (p0) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.4406 time to fit residues: 29.4431 Evaluate side-chains 61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** 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 = 0.3309 r_free = 0.3309 target = 0.074472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056499 restraints weight = 18327.432| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.44 r_work: 0.2782 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6748 Z= 0.141 Angle : 0.545 9.428 9185 Z= 0.275 Chirality : 0.041 0.144 977 Planarity : 0.004 0.038 1178 Dihedral : 3.858 14.165 866 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.57 % Allowed : 15.00 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.30), residues: 793 helix: 1.71 (0.26), residues: 395 sheet: 0.90 (0.80), residues: 42 loop : 0.77 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.010 0.001 TYR E 516 PHE 0.013 0.001 PHE E 369 TRP 0.025 0.001 TRP E 606 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6735) covalent geometry : angle 0.53640 / 0.27 ( 9152) SS BOND : bond 0.00246 / 0.14 ( 6) SS BOND : angle 0.66775 / 0.40 ( 12) hydrogen bonds : bond 0.03815 / 2.51 ( 323) hydrogen bonds : angle 4.23354 / 2.93 ( 918) link_NAG-ASN : bond 0.00317 / 0.18 ( 7) link_NAG-ASN : angle 2.02138 / 1.42 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8833 (m-30) cc_final: 0.8558 (p0) REVERT: E 55 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8768 (p) REVERT: E 149 ASN cc_start: 0.9225 (m-40) cc_final: 0.8937 (m110) REVERT: E 224 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8334 (pp20) REVERT: E 249 MET cc_start: 0.9396 (ttm) cc_final: 0.9069 (ttp) REVERT: E 347 THR cc_start: 0.8944 (m) cc_final: 0.8661 (p) REVERT: E 411 SER cc_start: 0.9049 (m) cc_final: 0.8828 (p) REVERT: E 441 LYS cc_start: 0.9062 (tttp) cc_final: 0.8584 (tppp) REVERT: E 455 MET cc_start: 0.9096 (tmm) cc_final: 0.8633 (tpt) REVERT: E 552 GLN cc_start: 0.8986 (tp40) cc_final: 0.8578 (tm-30) REVERT: E 578 ASN cc_start: 0.8598 (t0) cc_final: 0.8216 (p0) outliers start: 11 outliers final: 6 residues processed: 62 average time/residue: 0.4080 time to fit residues: 26.8154 Evaluate side-chains 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 43 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 34 HIS ** 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 = 0.3323 r_free = 0.3323 target = 0.075024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057170 restraints weight = 18488.185| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.45 r_work: 0.2796 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6748 Z= 0.124 Angle : 0.543 9.471 9185 Z= 0.274 Chirality : 0.041 0.164 977 Planarity : 0.004 0.042 1178 Dihedral : 3.879 22.191 866 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.29 % Allowed : 15.29 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.30), residues: 793 helix: 1.72 (0.26), residues: 395 sheet: 0.91 (0.80), residues: 42 loop : 0.74 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.010 0.001 TYR E 516 PHE 0.013 0.001 PHE E 369 TRP 0.025 0.001 TRP E 606 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6735) covalent geometry : angle 0.53324 / 0.27 ( 9152) SS BOND : bond 0.00208 / 0.12 ( 6) SS BOND : angle 1.44690 / 0.80 ( 12) hydrogen bonds : bond 0.03706 / 2.44 ( 323) hydrogen bonds : angle 4.20338 / 2.91 ( 918) link_NAG-ASN : bond 0.00313 / 0.18 ( 7) link_NAG-ASN : angle 1.97988 / 1.40 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.61 seconds wall clock time: 31 minutes 37.64 seconds (1897.64 seconds total)