Starting phenix.real_space_refine on Thu Jul 2 04:37:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mjn_23879/07_2026/7mjn_23879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjn_23879/07_2026/7mjn_23879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2026/7mjn_23879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2026/7mjn_23879.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2026/7mjn_23879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2026/7mjn_23879.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2026/7mjn_23879.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mjn_23879/07_2026/7mjn_23879.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 4175 2.51 5 N 1075 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s 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: 6526 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1594 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: {'PTRANS': 27, '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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.54, per 1000 atoms: 0.24 Number of scatterers: 6526 At special positions: 0 Unit cell: (100, 72, 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 1239 8.00 N 1075 7.00 C 4175 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=2.03 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 322 " " NAG E 704 " - " ASN E 546 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 365.1 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: 38 helices and 5 sheets defined 56.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.587A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.622A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.519A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 52 removed outlier: 3.807A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.721A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) 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: 3.871A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 4.017A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.639A 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 147 through 155 Processing helix chain 'E' and resid 158 through 194 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 221 through 249 removed outlier: 3.953A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.721A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 294 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.636A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.538A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.707A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.328A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.718A 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 removed outlier: 4.122A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.564A 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 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.282A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.631A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 4.247A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 removed outlier: 3.726A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) 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: 3.757A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.932A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.070A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 891 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: 1.03 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.47: 1755 1.47 - 1.59: 2816 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 6709 Sorted by residual: bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.337 1.369 -0.033 1.06e-02 8.90e+03 9.53e+00 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 ... (remaining 6704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 8752 1.89 - 3.77: 297 3.77 - 5.66: 47 5.66 - 7.55: 16 7.55 - 9.43: 6 Bond angle restraints: 9118 Sorted by residual: angle pdb=" N GLY E 147 " pdb=" CA GLY E 147 " pdb=" C GLY E 147 " ideal model delta sigma weight residual 110.21 114.42 -4.21 9.10e-01 1.21e+00 2.14e+01 angle pdb=" C ASP E 292 " pdb=" N VAL E 293 " pdb=" CA VAL E 293 " ideal model delta sigma weight residual 121.97 130.09 -8.12 1.80e+00 3.09e-01 2.04e+01 angle pdb=" O GLY E 147 " pdb=" C GLY E 147 " pdb=" N LEU E 148 " ideal model delta sigma weight residual 121.85 124.37 -2.52 5.60e-01 3.19e+00 2.02e+01 angle pdb=" CG ARG B 346 " pdb=" CD ARG B 346 " pdb=" NE ARG B 346 " ideal model delta sigma weight residual 112.00 120.75 -8.75 2.20e+00 2.07e-01 1.58e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 117.91 -4.75 1.42e+00 4.96e-01 1.12e+01 ... (remaining 9113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3555 17.64 - 35.27: 298 35.27 - 52.91: 54 52.91 - 70.54: 7 70.54 - 88.18: 5 Dihedral angle restraints: 3919 sinusoidal: 1580 harmonic: 2339 Sorted by residual: dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TRP E 606 " pdb=" C TRP E 606 " pdb=" N SER E 607 " pdb=" CA SER E 607 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE E 233 " pdb=" C ILE E 233 " pdb=" N LYS E 234 " pdb=" CA LYS E 234 " ideal model delta harmonic sigma weight residual -180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 3916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 710 0.049 - 0.097: 176 0.097 - 0.146: 67 0.146 - 0.195: 10 0.195 - 0.243: 5 Chirality restraints: 968 Sorted by residual: 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 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL E 447 " pdb=" CA VAL E 447 " pdb=" CG1 VAL E 447 " pdb=" CG2 VAL E 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU E 520 " pdb=" CB LEU E 520 " pdb=" CD1 LEU E 520 " pdb=" CD2 LEU E 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 965 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 463 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 467 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" CG ASP B 467 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP B 467 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 467 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 134 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO E 135 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 135 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 135 " -0.026 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1922 2.82 - 3.34: 6061 3.34 - 3.86: 10993 3.86 - 4.38: 12649 4.38 - 4.90: 21926 Nonbonded interactions: 53551 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.295 3.040 nonbonded pdb=" OD1 ASP E 494 " pdb=" OG1 THR E 496 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR E 215 " pdb=" OE1 GLU E 571 " model vdw 2.352 3.040 nonbonded pdb=" OG SER B 383 " pdb=" OG1 THR B 385 " model vdw 2.354 3.040 nonbonded pdb=" O PHE E 314 " pdb=" OG SER E 317 " model vdw 2.378 3.040 ... (remaining 53546 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: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.270 Find NCS groups from input model: 0.040 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 0.053 6720 Z= 0.222 Angle : 0.858 9.434 9145 Z= 0.465 Chirality : 0.053 0.243 968 Planarity : 0.007 0.054 1175 Dihedral : 13.413 88.178 2401 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.27), residues: 793 helix: -0.80 (0.23), residues: 374 sheet: 0.98 (0.78), residues: 51 loop : -1.07 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 115 TYR 0.015 0.002 TYR E 237 PHE 0.016 0.002 PHE E 369 TRP 0.019 0.002 TRP E 165 HIS 0.006 0.002 HIS E 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 ( 6709) covalent geometry : angle 0.84420 / 0.46 ( 9118) SS BOND : bond 0.00376 / 0.22 ( 6) SS BOND : angle 1.14367 / 0.67 ( 12) hydrogen bonds : bond 0.16856 / 10.81 ( 309) hydrogen bonds : angle 6.97752 / 4.94 ( 891) link_NAG-ASN : bond 0.00610 / 0.40 ( 5) link_NAG-ASN : angle 3.76346 / 2.48 ( 15) *********************** 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.190 Fit side-chains REVERT: B 506 GLN cc_start: 0.8870 (mt0) cc_final: 0.8656 (mt0) REVERT: E 123 MET cc_start: 0.9504 (mmt) cc_final: 0.9288 (mmt) REVERT: E 190 MET cc_start: 0.9238 (tmm) cc_final: 0.9037 (tmm) REVERT: E 249 MET cc_start: 0.9160 (mmm) cc_final: 0.8745 (mmt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0742 time to fit residues: 5.9175 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 378 HIS E 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.042665 restraints weight = 28332.595| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.14 r_work: 0.2611 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6720 Z= 0.140 Angle : 0.548 8.403 9145 Z= 0.281 Chirality : 0.041 0.166 968 Planarity : 0.004 0.036 1175 Dihedral : 4.353 16.419 866 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.43 % Allowed : 4.86 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.29), residues: 793 helix: 0.58 (0.25), residues: 392 sheet: 0.81 (0.82), residues: 48 loop : -0.65 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 115 TYR 0.016 0.001 TYR B 451 PHE 0.011 0.001 PHE E 369 TRP 0.017 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 6709) covalent geometry : angle 0.53963 / 0.28 ( 9118) SS BOND : bond 0.00261 / 0.17 ( 6) SS BOND : angle 0.69327 / 0.40 ( 12) hydrogen bonds : bond 0.04598 / 3.06 ( 309) hydrogen bonds : angle 4.76712 / 3.30 ( 891) link_NAG-ASN : bond 0.00310 / 0.20 ( 5) link_NAG-ASN : angle 2.41690 / 1.68 ( 15) *********************** 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 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.256 Fit side-chains REVERT: B 386 LYS cc_start: 0.9392 (mtmm) cc_final: 0.9180 (mtmt) REVERT: E 123 MET cc_start: 0.9460 (mmt) cc_final: 0.9236 (mmt) REVERT: E 190 MET cc_start: 0.9261 (tmm) cc_final: 0.9057 (tmm) REVERT: E 249 MET cc_start: 0.9144 (mmm) cc_final: 0.8700 (mmt) REVERT: E 332 MET cc_start: 0.8092 (ppp) cc_final: 0.7857 (ppp) REVERT: E 462 MET cc_start: 0.9298 (mmm) cc_final: 0.8978 (mtm) outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.0770 time to fit residues: 5.3232 Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.042031 restraints weight = 28052.993| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 4.09 r_work: 0.2588 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6720 Z= 0.147 Angle : 0.521 8.437 9145 Z= 0.263 Chirality : 0.040 0.145 968 Planarity : 0.004 0.031 1175 Dihedral : 3.988 14.602 866 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 6.29 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.30), residues: 793 helix: 1.26 (0.26), residues: 386 sheet: 0.23 (0.79), residues: 48 loop : -0.35 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 115 TYR 0.013 0.001 TYR B 369 PHE 0.012 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 6709) covalent geometry : angle 0.51425 / 0.26 ( 9118) SS BOND : bond 0.00291 / 0.19 ( 6) SS BOND : angle 0.66757 / 0.38 ( 12) hydrogen bonds : bond 0.04193 / 2.82 ( 309) hydrogen bonds : angle 4.42729 / 3.06 ( 891) link_NAG-ASN : bond 0.00283 / 0.19 ( 5) link_NAG-ASN : angle 2.14826 / 1.55 ( 15) *********************** 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 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: E 249 MET cc_start: 0.9125 (mmm) cc_final: 0.8649 (mmt) REVERT: E 323 MET cc_start: 0.9439 (mmp) cc_final: 0.9163 (mmp) REVERT: E 332 MET cc_start: 0.8229 (ppp) cc_final: 0.8006 (ppp) REVERT: E 462 MET cc_start: 0.9347 (mmm) cc_final: 0.9077 (mtm) outliers start: 6 outliers final: 0 residues processed: 48 average time/residue: 0.0619 time to fit residues: 4.3086 Evaluate side-chains 40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.041662 restraints weight = 28826.659| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 4.06 r_work: 0.2607 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6720 Z= 0.147 Angle : 0.514 7.939 9145 Z= 0.259 Chirality : 0.041 0.143 968 Planarity : 0.003 0.036 1175 Dihedral : 3.886 14.143 866 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.57 % Allowed : 8.29 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.30), residues: 793 helix: 1.56 (0.27), residues: 386 sheet: -0.02 (0.77), residues: 48 loop : -0.22 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 115 TYR 0.015 0.001 TYR B 369 PHE 0.012 0.001 PHE E 369 TRP 0.011 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 6709) covalent geometry : angle 0.50741 / 0.26 ( 9118) SS BOND : bond 0.00310 / 0.19 ( 6) SS BOND : angle 0.69169 / 0.41 ( 12) hydrogen bonds : bond 0.04048 / 2.73 ( 309) hydrogen bonds : angle 4.30523 / 2.97 ( 891) link_NAG-ASN : bond 0.00268 / 0.18 ( 5) link_NAG-ASN : angle 2.04910 / 1.50 ( 15) *********************** 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 46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.290 Fit side-chains REVERT: B 406 GLU cc_start: 0.8859 (mp0) cc_final: 0.8272 (pm20) REVERT: E 249 MET cc_start: 0.9105 (mmm) cc_final: 0.8638 (mmt) REVERT: E 270 MET cc_start: 0.9324 (tpp) cc_final: 0.8433 (tpp) REVERT: E 323 MET cc_start: 0.9434 (mmp) cc_final: 0.9202 (mmp) REVERT: E 332 MET cc_start: 0.8303 (ppp) cc_final: 0.8097 (ppp) REVERT: E 462 MET cc_start: 0.9365 (mmm) cc_final: 0.9076 (mtm) REVERT: E 474 MET cc_start: 0.8509 (mmp) cc_final: 0.7919 (mmm) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.0704 time to fit residues: 4.5981 Evaluate side-chains 40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.042146 restraints weight = 28820.276| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 4.03 r_work: 0.2624 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6720 Z= 0.120 Angle : 0.500 7.236 9145 Z= 0.250 Chirality : 0.040 0.150 968 Planarity : 0.003 0.037 1175 Dihedral : 3.747 13.874 866 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.29 % Allowed : 8.86 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.30), residues: 793 helix: 1.68 (0.27), residues: 387 sheet: -0.07 (0.77), residues: 48 loop : -0.14 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 115 TYR 0.012 0.001 TYR B 369 PHE 0.011 0.001 PHE E 369 TRP 0.010 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6709) covalent geometry : angle 0.49364 / 0.25 ( 9118) SS BOND : bond 0.00283 / 0.17 ( 6) SS BOND : angle 0.68446 / 0.41 ( 12) hydrogen bonds : bond 0.03835 / 2.59 ( 309) hydrogen bonds : angle 4.20581 / 2.91 ( 891) link_NAG-ASN : bond 0.00303 / 0.21 ( 5) link_NAG-ASN : angle 1.98513 / 1.46 ( 15) *********************** 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 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.275 Fit side-chains REVERT: E 249 MET cc_start: 0.9110 (mmm) cc_final: 0.8637 (mmt) REVERT: E 270 MET cc_start: 0.9207 (tpp) cc_final: 0.8678 (tpp) REVERT: E 323 MET cc_start: 0.9403 (mmp) cc_final: 0.9197 (mmp) REVERT: E 462 MET cc_start: 0.9368 (mmm) cc_final: 0.9089 (mtm) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.0727 time to fit residues: 4.9129 Evaluate side-chains 40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 0.8980 chunk 67 optimal weight: 0.0170 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 39 optimal weight: 0.0470 chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.042392 restraints weight = 28542.910| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 4.05 r_work: 0.2636 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6720 Z= 0.108 Angle : 0.497 8.272 9145 Z= 0.248 Chirality : 0.040 0.155 968 Planarity : 0.003 0.038 1175 Dihedral : 3.649 13.785 866 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.86 % Allowed : 8.71 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.31), residues: 793 helix: 1.77 (0.27), residues: 388 sheet: 0.01 (0.78), residues: 48 loop : -0.08 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 115 TYR 0.011 0.001 TYR B 369 PHE 0.010 0.001 PHE E 369 TRP 0.010 0.001 TRP E 165 HIS 0.002 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 6709) covalent geometry : angle 0.49149 / 0.25 ( 9118) SS BOND : bond 0.00280 / 0.17 ( 6) SS BOND : angle 0.68210 / 0.41 ( 12) hydrogen bonds : bond 0.03699 / 2.51 ( 309) hydrogen bonds : angle 4.13646 / 2.85 ( 891) link_NAG-ASN : bond 0.00318 / 0.22 ( 5) link_NAG-ASN : angle 1.89592 / 1.41 ( 15) *********************** 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 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.270 Fit side-chains REVERT: E 249 MET cc_start: 0.9072 (mmm) cc_final: 0.8617 (mmt) REVERT: E 270 MET cc_start: 0.9110 (tpp) cc_final: 0.8463 (tpp) REVERT: E 408 MET cc_start: 0.9626 (mmm) cc_final: 0.9383 (mmm) REVERT: E 411 SER cc_start: 0.9225 (m) cc_final: 0.8704 (p) REVERT: E 462 MET cc_start: 0.9368 (mmm) cc_final: 0.9102 (mtm) outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 0.0686 time to fit residues: 4.6025 Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 0.0570 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.042913 restraints weight = 28273.571| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.05 r_work: 0.2653 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6720 Z= 0.100 Angle : 0.518 8.545 9145 Z= 0.251 Chirality : 0.040 0.160 968 Planarity : 0.003 0.037 1175 Dihedral : 3.551 13.780 866 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 9.57 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.31), residues: 793 helix: 1.75 (0.27), residues: 394 sheet: 0.02 (0.78), residues: 48 loop : -0.12 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.009 0.001 TYR B 369 PHE 0.009 0.001 PHE E 369 TRP 0.009 0.001 TRP E 165 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 6709) covalent geometry : angle 0.51281 / 0.25 ( 9118) SS BOND : bond 0.00259 / 0.15 ( 6) SS BOND : angle 0.66834 / 0.41 ( 12) hydrogen bonds : bond 0.03550 / 2.40 ( 309) hydrogen bonds : angle 4.11473 / 2.83 ( 891) link_NAG-ASN : bond 0.00343 / 0.24 ( 5) link_NAG-ASN : angle 1.85388 / 1.38 ( 15) *********************** 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 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.267 Fit side-chains REVERT: B 406 GLU cc_start: 0.8758 (pm20) cc_final: 0.8430 (pm20) REVERT: E 249 MET cc_start: 0.9049 (mmm) cc_final: 0.8612 (mmt) REVERT: E 411 SER cc_start: 0.9183 (m) cc_final: 0.8778 (p) REVERT: E 446 ILE cc_start: 0.9293 (mm) cc_final: 0.9049 (mp) REVERT: E 462 MET cc_start: 0.9353 (mmm) cc_final: 0.9101 (mtm) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.0562 time to fit residues: 4.2335 Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.041995 restraints weight = 28684.090| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.01 r_work: 0.2621 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6720 Z= 0.143 Angle : 0.543 8.580 9145 Z= 0.264 Chirality : 0.041 0.147 968 Planarity : 0.003 0.038 1175 Dihedral : 3.628 14.154 866 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.71 % Allowed : 10.00 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.31), residues: 793 helix: 1.96 (0.27), residues: 386 sheet: -0.04 (0.79), residues: 48 loop : 0.04 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.011 0.001 TYR E 515 PHE 0.010 0.001 PHE E 369 TRP 0.010 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6709) covalent geometry : angle 0.53545 / 0.26 ( 9118) SS BOND : bond 0.00244 / 0.17 ( 6) SS BOND : angle 1.57961 / 0.97 ( 12) hydrogen bonds : bond 0.03789 / 2.57 ( 309) hydrogen bonds : angle 4.14062 / 2.85 ( 891) link_NAG-ASN : bond 0.00290 / 0.19 ( 5) link_NAG-ASN : angle 1.91595 / 1.43 ( 15) *********************** 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 46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8768 (pm20) cc_final: 0.8369 (mp0) REVERT: E 249 MET cc_start: 0.9051 (mmm) cc_final: 0.8600 (mmt) REVERT: E 462 MET cc_start: 0.9368 (mmm) cc_final: 0.9093 (mtm) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.0693 time to fit residues: 4.5860 Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.041168 restraints weight = 29342.631| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 4.03 r_work: 0.2588 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6720 Z= 0.186 Angle : 0.601 11.091 9145 Z= 0.288 Chirality : 0.041 0.137 968 Planarity : 0.003 0.039 1175 Dihedral : 3.720 14.254 866 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.40 % Favored : 97.48 % Rotamer: Outliers : 0.57 % Allowed : 10.43 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.31), residues: 793 helix: 1.80 (0.27), residues: 395 sheet: -0.13 (0.79), residues: 48 loop : 0.01 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.011 0.001 TYR B 453 PHE 0.014 0.001 PHE E 523 TRP 0.010 0.001 TRP E 69 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 6709) covalent geometry : angle 0.59456 / 0.29 ( 9118) SS BOND : bond 0.00284 / 0.20 ( 6) SS BOND : angle 1.18548 / 0.72 ( 12) hydrogen bonds : bond 0.04016 / 2.72 ( 309) hydrogen bonds : angle 4.23063 / 2.91 ( 891) link_NAG-ASN : bond 0.00272 / 0.17 ( 5) link_NAG-ASN : angle 2.02065 / 1.52 ( 15) *********************** 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 46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: E 249 MET cc_start: 0.9078 (mmm) cc_final: 0.8620 (mmt) REVERT: E 270 MET cc_start: 0.8882 (tpp) cc_final: 0.8166 (tpp) REVERT: E 462 MET cc_start: 0.9392 (mmm) cc_final: 0.9080 (mtm) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.0688 time to fit residues: 4.6030 Evaluate side-chains 42 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 8 optimal weight: 0.0060 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.042269 restraints weight = 27924.448| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 4.08 r_work: 0.2606 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6720 Z= 0.112 Angle : 0.556 10.413 9145 Z= 0.265 Chirality : 0.040 0.155 968 Planarity : 0.003 0.038 1175 Dihedral : 3.617 13.543 866 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.64 % Favored : 98.23 % Rotamer: Outliers : 0.71 % Allowed : 10.86 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.31), residues: 793 helix: 1.91 (0.27), residues: 389 sheet: -0.19 (0.78), residues: 48 loop : 0.05 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 115 TYR 0.017 0.001 TYR B 369 PHE 0.009 0.001 PHE E 369 TRP 0.009 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 6709) covalent geometry : angle 0.54989 / 0.26 ( 9118) SS BOND : bond 0.00179 / 0.12 ( 6) SS BOND : angle 1.17362 / 0.72 ( 12) hydrogen bonds : bond 0.03679 / 2.50 ( 309) hydrogen bonds : angle 4.13778 / 2.84 ( 891) link_NAG-ASN : bond 0.00322 / 0.22 ( 5) link_NAG-ASN : angle 1.84742 / 1.38 ( 15) ********************** 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 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: B 378 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8996 (mmtm) REVERT: B 406 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: E 152 MET cc_start: 0.8786 (mmt) cc_final: 0.8196 (mmm) REVERT: E 249 MET cc_start: 0.9067 (mmm) cc_final: 0.8639 (mmt) REVERT: E 270 MET cc_start: 0.8831 (tpp) cc_final: 0.8064 (tpp) REVERT: E 462 MET cc_start: 0.9384 (mmm) cc_final: 0.9091 (mtm) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.0712 time to fit residues: 4.5584 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.042063 restraints weight = 28276.199| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.14 r_work: 0.2620 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6720 Z= 0.127 Angle : 0.568 11.654 9145 Z= 0.273 Chirality : 0.041 0.153 968 Planarity : 0.003 0.038 1175 Dihedral : 3.641 13.647 866 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.60 % Rotamer: Outliers : 0.43 % Allowed : 11.29 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.31), residues: 793 helix: 1.90 (0.27), residues: 390 sheet: -0.37 (0.76), residues: 50 loop : 0.02 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 115 TYR 0.018 0.001 TYR B 369 PHE 0.010 0.001 PHE E 369 TRP 0.009 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6709) covalent geometry : angle 0.56206 / 0.27 ( 9118) SS BOND : bond 0.00211 / 0.14 ( 6) SS BOND : angle 1.14568 / 0.70 ( 12) hydrogen bonds : bond 0.03696 / 2.51 ( 309) hydrogen bonds : angle 4.12012 / 2.83 ( 891) link_NAG-ASN : bond 0.00292 / 0.20 ( 5) link_NAG-ASN : angle 1.87444 / 1.39 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.40 seconds wall clock time: 30 minutes 18.64 seconds (1818.64 seconds total)