Starting phenix.real_space_refine on Thu Jul 2 04:36:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sy6_25518/07_2026/7sy6_25518.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy6_25518/07_2026/7sy6_25518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy6_25518/07_2026/7sy6_25518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy6_25518/07_2026/7sy6_25518.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy6_25518/07_2026/7sy6_25518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy6_25518/07_2026/7sy6_25518.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sy6_25518/07_2026/7sy6_25518.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sy6_25518/07_2026/7sy6_25518.cif" } resolution = 2.81 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= 0.032 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 4190 2.51 5 N 1078 2.21 5 O 1248 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: 1.56, per 1000 atoms: 0.24 Number of scatterers: 6553 At special positions: 0 Unit cell: (81, 83, 122, 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 1248 8.00 N 1078 7.00 C 4190 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=2.04 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 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: 0.50 Conformation dependent library (CDL) restraints added in 359.2 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 7 sheets defined 57.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 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: 3.746A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.706A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.577A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.748A 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: 4.011A 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: 3.921A 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: 3.737A 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: 3.704A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.750A 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: 3.799A 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: 3.589A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.715A 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: 4.262A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.936A 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: 3.524A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.336A 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: 3.725A 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: 4.403A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.663A 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: 3.919A 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: 3.969A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.705A 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: 6.054A 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: 6.354A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 915 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: 0.90 Time building geometry restraints manager: 0.65 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: 2083 1.35 - 1.47: 1790 1.47 - 1.60: 2805 1.60 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6736 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.62e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C SER E 611 " pdb=" N PRO E 612 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 3.99e+00 ... (remaining 6731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8819 2.07 - 4.15: 288 4.15 - 6.22: 39 6.22 - 8.30: 5 8.30 - 10.37: 4 Bond angle restraints: 9155 Sorted by residual: angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 124.27 -10.37 1.80e+00 3.09e-01 3.32e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 128.92 -6.10 1.42e+00 4.96e-01 1.84e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.31 -8.91 2.30e+00 1.89e-01 1.50e+01 angle pdb=" C PHE E 32 " pdb=" N ASN E 33 " pdb=" CA ASN E 33 " ideal model delta sigma weight residual 121.19 126.70 -5.51 1.59e+00 3.96e-01 1.20e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 115.93 -3.33 1.00e+00 1.00e+00 1.11e+01 ... (remaining 9150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 3558 17.17 - 34.34: 297 34.34 - 51.51: 40 51.51 - 68.68: 12 68.68 - 85.85: 11 Dihedral angle restraints: 3918 sinusoidal: 1579 harmonic: 2339 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 -44.82 -41.18 1 1.00e+01 1.00e-02 2.38e+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 15.54 63.46 1 2.00e+01 2.50e-03 1.33e+01 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 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 686 0.051 - 0.103: 213 0.103 - 0.154: 63 0.154 - 0.205: 11 0.205 - 0.256: 5 Chirality restraints: 978 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 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL B 350 " pdb=" CA VAL B 350 " pdb=" CG1 VAL B 350 " pdb=" CG2 VAL B 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.37e+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 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 975 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C ARG E 169 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 32 " 0.014 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C PHE E 32 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE E 32 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN E 33 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ALA E 36 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA E 36 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 37 " -0.017 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1853 2.82 - 3.34: 5981 3.34 - 3.86: 11402 3.86 - 4.38: 13066 4.38 - 4.90: 22509 Nonbonded interactions: 54811 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.296 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.365 3.120 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.368 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.382 3.120 nonbonded pdb=" OH TYR E 237 " pdb=" O VAL E 485 " model vdw 2.394 3.040 ... (remaining 54806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.740 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.330 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:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 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 0.060 6749 Z= 0.249 Angle : 0.890 12.647 9188 Z= 0.477 Chirality : 0.057 0.256 978 Planarity : 0.007 0.060 1177 Dihedral : 13.461 85.851 2400 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % 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: -0.71 (0.26), residues: 793 helix: -0.21 (0.22), residues: 389 sheet: 1.02 (0.73), residues: 43 loop : -0.84 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 460 TYR 0.046 0.002 TYR B 495 PHE 0.031 0.003 PHE E 369 TRP 0.020 0.002 TRP E 566 HIS 0.007 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 ( 6736) covalent geometry : angle 0.86133 / 0.47 ( 9155) SS BOND : bond 0.00549 / 0.34 ( 6) SS BOND : angle 2.72299 / 1.58 ( 12) hydrogen bonds : bond 0.13563 / 9.37 ( 322) hydrogen bonds : angle 6.20226 / 4.30 ( 915) link_NAG-ASN : bond 0.00829 / 0.48 ( 7) link_NAG-ASN : angle 4.36957 / 3.57 ( 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 121 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.262 Fit side-chains REVERT: B 405 ASP cc_start: 0.8361 (m-30) cc_final: 0.8003 (m-30) REVERT: B 468 ILE cc_start: 0.9409 (pt) cc_final: 0.9167 (pp) REVERT: E 256 ILE cc_start: 0.8954 (mp) cc_final: 0.8426 (mt) REVERT: E 259 ILE cc_start: 0.8587 (tp) cc_final: 0.8232 (pp) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.5902 time to fit residues: 74.5478 Evaluate side-chains 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN E 374 HIS E 522 GLN E 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053342 restraints weight = 16375.468| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.04 r_work: 0.2663 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6749 Z= 0.235 Angle : 0.656 10.058 9188 Z= 0.327 Chirality : 0.044 0.201 978 Planarity : 0.005 0.035 1177 Dihedral : 4.467 16.146 866 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.29 % Allowed : 10.71 % 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: 0.60 (0.28), residues: 793 helix: 1.06 (0.25), residues: 387 sheet: 0.82 (0.70), residues: 43 loop : -0.30 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 559 TYR 0.021 0.001 TYR B 495 PHE 0.021 0.002 PHE E 400 TRP 0.020 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 ( 6736) covalent geometry : angle 0.63587 / 0.32 ( 9155) SS BOND : bond 0.00504 / 0.31 ( 6) SS BOND : angle 2.07368 / 1.16 ( 12) hydrogen bonds : bond 0.04923 / 3.21 ( 322) hydrogen bonds : angle 4.78985 / 3.33 ( 915) link_NAG-ASN : bond 0.00481 / 0.30 ( 7) link_NAG-ASN : angle 3.11912 / 2.55 ( 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 94 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.237 Fit side-chains REVERT: B 405 ASP cc_start: 0.8846 (m-30) cc_final: 0.8443 (m-30) REVERT: B 466 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8785 (mtp85) REVERT: B 468 ILE cc_start: 0.9370 (pt) cc_final: 0.9158 (pp) REVERT: B 528 LYS cc_start: 0.3399 (OUTLIER) cc_final: 0.3147 (pttt) REVERT: E 131 LYS cc_start: 0.8677 (ptmm) cc_final: 0.8413 (ptmm) REVERT: E 142 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8992 (tp) REVERT: E 259 ILE cc_start: 0.8521 (tp) cc_final: 0.8224 (pp) REVERT: E 383 MET cc_start: 0.9312 (mtm) cc_final: 0.9046 (mtm) REVERT: E 462 MET cc_start: 0.9101 (mtp) cc_final: 0.8897 (mtp) REVERT: E 475 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8589 (ttpp) REVERT: E 589 GLU cc_start: 0.9036 (tp30) cc_final: 0.8244 (tp30) outliers start: 23 outliers final: 8 residues processed: 87 average time/residue: 0.5643 time to fit residues: 51.6487 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 548 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.0020 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN E 149 ASN E 154 ASN E 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054575 restraints weight = 16160.836| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.03 r_work: 0.2695 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6749 Z= 0.146 Angle : 0.582 9.814 9188 Z= 0.284 Chirality : 0.041 0.146 978 Planarity : 0.004 0.032 1177 Dihedral : 4.164 15.350 866 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.86 % Allowed : 12.14 % Favored : 85.00 % 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: 0.90 (0.28), residues: 793 helix: 1.30 (0.25), residues: 393 sheet: 0.67 (0.70), residues: 43 loop : -0.11 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 559 TYR 0.018 0.001 TYR B 495 PHE 0.018 0.001 PHE E 369 TRP 0.016 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 6736) covalent geometry : angle 0.56389 / 0.28 ( 9155) SS BOND : bond 0.00436 / 0.24 ( 6) SS BOND : angle 1.87978 / 1.05 ( 12) hydrogen bonds : bond 0.04327 / 2.82 ( 322) hydrogen bonds : angle 4.57123 / 3.20 ( 915) link_NAG-ASN : bond 0.00431 / 0.25 ( 7) link_NAG-ASN : angle 2.77371 / 2.26 ( 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 88 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.255 Fit side-chains REVERT: B 405 ASP cc_start: 0.8888 (m-30) cc_final: 0.8467 (m-30) REVERT: B 471 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: E 131 LYS cc_start: 0.8705 (ptmm) cc_final: 0.8339 (ptmm) REVERT: E 142 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9015 (tp) REVERT: E 462 MET cc_start: 0.9089 (mtp) cc_final: 0.8880 (mtp) REVERT: E 475 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8628 (ttpp) REVERT: E 589 GLU cc_start: 0.9038 (tp30) cc_final: 0.8280 (tp30) outliers start: 20 outliers final: 9 residues processed: 81 average time/residue: 0.5401 time to fit residues: 46.0489 Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 522 GLN E 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.053646 restraints weight = 16315.274| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.06 r_work: 0.2670 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6749 Z= 0.169 Angle : 0.582 11.049 9188 Z= 0.283 Chirality : 0.042 0.143 978 Planarity : 0.004 0.030 1177 Dihedral : 4.103 15.750 866 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.43 % Allowed : 14.00 % Favored : 82.57 % 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: 1.14 (0.29), residues: 793 helix: 1.51 (0.26), residues: 393 sheet: 0.43 (0.70), residues: 43 loop : 0.04 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 457 TYR 0.017 0.001 TYR B 495 PHE 0.019 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 6736) covalent geometry : angle 0.56946 / 0.28 ( 9155) SS BOND : bond 0.00325 / 0.20 ( 6) SS BOND : angle 1.19445 / 0.68 ( 12) hydrogen bonds : bond 0.04346 / 2.83 ( 322) hydrogen bonds : angle 4.48103 / 3.14 ( 915) link_NAG-ASN : bond 0.00368 / 0.22 ( 7) link_NAG-ASN : angle 2.47829 / 2.01 ( 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 86 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.215 Fit side-chains REVERT: B 405 ASP cc_start: 0.8930 (m-30) cc_final: 0.8491 (m-30) REVERT: B 466 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8733 (mtp85) REVERT: B 471 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: E 131 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8187 (ptmm) REVERT: E 142 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8999 (tp) REVERT: E 270 MET cc_start: 0.8743 (mmm) cc_final: 0.8422 (tpt) REVERT: E 383 MET cc_start: 0.9285 (mtm) cc_final: 0.9040 (mtm) REVERT: E 462 MET cc_start: 0.9086 (mtp) cc_final: 0.8878 (mtp) REVERT: E 480 MET cc_start: 0.8919 (mtp) cc_final: 0.8650 (mtm) REVERT: E 582 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8432 (mmm-85) REVERT: E 589 GLU cc_start: 0.9107 (tp30) cc_final: 0.8346 (tp30) outliers start: 24 outliers final: 10 residues processed: 79 average time/residue: 0.6518 time to fit residues: 53.8158 Evaluate side-chains 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 65 optimal weight: 0.0270 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054253 restraints weight = 16480.840| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.04 r_work: 0.2687 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6749 Z= 0.142 Angle : 0.561 10.998 9188 Z= 0.271 Chirality : 0.041 0.136 978 Planarity : 0.003 0.029 1177 Dihedral : 4.006 15.406 866 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.00 % Allowed : 15.00 % Favored : 82.00 % 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: 1.29 (0.29), residues: 793 helix: 1.63 (0.26), residues: 393 sheet: 0.30 (0.72), residues: 43 loop : 0.15 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 346 TYR 0.016 0.001 TYR B 495 PHE 0.017 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6736) covalent geometry : angle 0.55081 / 0.27 ( 9155) SS BOND : bond 0.00274 / 0.17 ( 6) SS BOND : angle 0.85725 / 0.50 ( 12) hydrogen bonds : bond 0.04108 / 2.67 ( 322) hydrogen bonds : angle 4.38383 / 3.07 ( 915) link_NAG-ASN : bond 0.00345 / 0.20 ( 7) link_NAG-ASN : angle 2.24964 / 1.81 ( 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 85 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.261 Fit side-chains REVERT: B 405 ASP cc_start: 0.8920 (m-30) cc_final: 0.8486 (m-30) REVERT: B 466 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8771 (mtp85) REVERT: B 471 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: B 528 LYS cc_start: 0.2823 (pttt) cc_final: 0.2400 (tttm) REVERT: E 376 MET cc_start: 0.9146 (ttm) cc_final: 0.8924 (tpp) REVERT: E 462 MET cc_start: 0.9078 (mtp) cc_final: 0.8873 (mtp) REVERT: E 480 MET cc_start: 0.8913 (mtp) cc_final: 0.8677 (mtm) REVERT: E 589 GLU cc_start: 0.9104 (tp30) cc_final: 0.8367 (tp30) outliers start: 21 outliers final: 12 residues processed: 79 average time/residue: 0.6567 time to fit residues: 54.2716 Evaluate side-chains 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.073318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.052797 restraints weight = 16484.989| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.03 r_work: 0.2647 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6749 Z= 0.201 Angle : 0.605 12.086 9188 Z= 0.294 Chirality : 0.042 0.141 978 Planarity : 0.004 0.031 1177 Dihedral : 4.138 15.661 866 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.43 % Allowed : 14.86 % Favored : 81.71 % 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: 1.35 (0.29), residues: 793 helix: 1.63 (0.26), residues: 393 sheet: 0.22 (0.73), residues: 43 loop : 0.26 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 346 TYR 0.017 0.001 TYR B 495 PHE 0.018 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 6736) covalent geometry : angle 0.59668 / 0.29 ( 9155) SS BOND : bond 0.00333 / 0.22 ( 6) SS BOND : angle 0.82773 / 0.52 ( 12) hydrogen bonds : bond 0.04412 / 2.88 ( 322) hydrogen bonds : angle 4.42639 / 3.10 ( 915) link_NAG-ASN : bond 0.00308 / 0.19 ( 7) link_NAG-ASN : angle 2.12346 / 1.71 ( 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 84 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.262 Fit side-chains REVERT: B 405 ASP cc_start: 0.8905 (m-30) cc_final: 0.8467 (m-30) REVERT: B 466 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8826 (mtp85) REVERT: B 471 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8655 (tt0) REVERT: E 114 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8913 (mttt) REVERT: E 376 MET cc_start: 0.9239 (ttm) cc_final: 0.9011 (tpp) REVERT: E 462 MET cc_start: 0.9097 (mtp) cc_final: 0.8871 (mtp) REVERT: E 589 GLU cc_start: 0.9139 (tp30) cc_final: 0.8414 (tp30) outliers start: 24 outliers final: 16 residues processed: 77 average time/residue: 0.6614 time to fit residues: 53.4761 Evaluate side-chains 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 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: 1.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.074102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.053688 restraints weight = 16378.863| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.05 r_work: 0.2670 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6749 Z= 0.153 Angle : 0.581 11.179 9188 Z= 0.279 Chirality : 0.041 0.132 978 Planarity : 0.003 0.030 1177 Dihedral : 4.037 15.409 866 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.86 % Allowed : 16.00 % Favored : 81.14 % 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: 1.39 (0.29), residues: 793 helix: 1.67 (0.26), residues: 397 sheet: 0.26 (0.74), residues: 43 loop : 0.26 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.016 0.001 TYR B 495 PHE 0.017 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6736) covalent geometry : angle 0.57292 / 0.28 ( 9155) SS BOND : bond 0.00292 / 0.18 ( 6) SS BOND : angle 0.74878 / 0.47 ( 12) hydrogen bonds : bond 0.04126 / 2.69 ( 322) hydrogen bonds : angle 4.38290 / 3.07 ( 915) link_NAG-ASN : bond 0.00301 / 0.18 ( 7) link_NAG-ASN : angle 2.03360 / 1.63 ( 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 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.186 Fit side-chains REVERT: B 405 ASP cc_start: 0.8919 (m-30) cc_final: 0.8493 (m-30) REVERT: B 466 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8841 (mtp85) REVERT: B 471 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: E 270 MET cc_start: 0.8705 (mmm) cc_final: 0.8502 (tpt) REVERT: E 376 MET cc_start: 0.9201 (ttm) cc_final: 0.8990 (tpp) REVERT: E 462 MET cc_start: 0.9080 (mtp) cc_final: 0.8859 (mtp) REVERT: E 589 GLU cc_start: 0.9123 (tp30) cc_final: 0.8422 (tp30) outliers start: 20 outliers final: 14 residues processed: 75 average time/residue: 0.5742 time to fit residues: 45.1651 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 601 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.072603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.052157 restraints weight = 16377.960| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.02 r_work: 0.2632 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6749 Z= 0.234 Angle : 0.641 11.136 9188 Z= 0.310 Chirality : 0.043 0.142 978 Planarity : 0.004 0.031 1177 Dihedral : 4.219 15.833 866 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.86 % Allowed : 16.14 % Favored : 81.00 % 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: 1.42 (0.29), residues: 793 helix: 1.64 (0.26), residues: 397 sheet: 0.23 (0.75), residues: 43 loop : 0.36 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.016 0.001 TYR B 495 PHE 0.019 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 6736) covalent geometry : angle 0.63399 / 0.31 ( 9155) SS BOND : bond 0.00337 / 0.23 ( 6) SS BOND : angle 0.91445 / 0.58 ( 12) hydrogen bonds : bond 0.04565 / 2.98 ( 322) hydrogen bonds : angle 4.47187 / 3.13 ( 915) link_NAG-ASN : bond 0.00298 / 0.18 ( 7) link_NAG-ASN : angle 1.99671 / 1.59 ( 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 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.209 Fit side-chains REVERT: B 405 ASP cc_start: 0.8912 (m-30) cc_final: 0.8459 (m-30) REVERT: B 466 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8797 (mtp85) REVERT: B 471 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: E 270 MET cc_start: 0.8821 (mmm) cc_final: 0.8418 (tpt) REVERT: E 480 MET cc_start: 0.8916 (mtp) cc_final: 0.8662 (mtm) REVERT: E 589 GLU cc_start: 0.9157 (tp30) cc_final: 0.8441 (tp30) outliers start: 20 outliers final: 12 residues processed: 71 average time/residue: 0.5951 time to fit residues: 44.3720 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 : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 601 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.0000 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 0.0670 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4122 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.075304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.054908 restraints weight = 16401.899| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.06 r_work: 0.2706 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6749 Z= 0.117 Angle : 0.583 11.981 9188 Z= 0.276 Chirality : 0.040 0.167 978 Planarity : 0.003 0.030 1177 Dihedral : 3.943 15.091 866 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.14 % Allowed : 17.29 % Favored : 80.57 % 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: 1.48 (0.29), residues: 793 helix: 1.70 (0.26), residues: 397 sheet: 0.26 (0.74), residues: 43 loop : 0.36 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.013 0.001 TYR B 495 PHE 0.015 0.001 PHE E 369 TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6736) covalent geometry : angle 0.57605 / 0.27 ( 9155) SS BOND : bond 0.00264 / 0.16 ( 6) SS BOND : angle 0.72178 / 0.46 ( 12) hydrogen bonds : bond 0.03879 / 2.53 ( 322) hydrogen bonds : angle 4.34925 / 3.05 ( 915) link_NAG-ASN : bond 0.00302 / 0.17 ( 7) link_NAG-ASN : angle 1.98290 / 1.59 ( 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 76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.154 Fit side-chains REVERT: B 405 ASP cc_start: 0.8921 (m-30) cc_final: 0.8480 (m-30) REVERT: B 466 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8793 (mtp85) REVERT: B 471 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: E 376 MET cc_start: 0.9161 (ttm) cc_final: 0.8886 (tpp) REVERT: E 408 MET cc_start: 0.9506 (mmt) cc_final: 0.9191 (mmt) REVERT: E 582 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8526 (mmm-85) REVERT: E 589 GLU cc_start: 0.9103 (tp30) cc_final: 0.8412 (tp30) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.5870 time to fit residues: 44.8719 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 548 THR 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: 2.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 0.0040 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.074837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054515 restraints weight = 16104.013| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.02 r_work: 0.2692 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6749 Z= 0.133 Angle : 0.607 12.493 9188 Z= 0.284 Chirality : 0.041 0.127 978 Planarity : 0.004 0.034 1177 Dihedral : 3.946 15.495 866 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.00 % Allowed : 17.29 % Favored : 80.71 % 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: 1.58 (0.29), residues: 793 helix: 1.78 (0.26), residues: 397 sheet: 0.23 (0.74), residues: 43 loop : 0.44 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.014 0.001 TYR B 495 PHE 0.017 0.001 PHE E 369 TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6736) covalent geometry : angle 0.60111 / 0.28 ( 9155) SS BOND : bond 0.00250 / 0.16 ( 6) SS BOND : angle 0.73718 / 0.47 ( 12) hydrogen bonds : bond 0.03962 / 2.58 ( 322) hydrogen bonds : angle 4.29671 / 3.03 ( 915) link_NAG-ASN : bond 0.00282 / 0.16 ( 7) link_NAG-ASN : angle 1.88912 / 1.50 ( 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 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.295 Fit side-chains REVERT: B 357 ARG cc_start: 0.9080 (ttp-170) cc_final: 0.8721 (ttp-170) REVERT: B 405 ASP cc_start: 0.8898 (m-30) cc_final: 0.8444 (m-30) REVERT: B 466 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8762 (mtp85) REVERT: B 471 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: E 582 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8510 (mmm-85) REVERT: E 589 GLU cc_start: 0.9100 (tp30) cc_final: 0.8412 (tp30) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.6819 time to fit residues: 51.4484 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 601 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3240 r_free = 0.3240 target = 0.073612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.053334 restraints weight = 16326.666| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.04 r_work: 0.2654 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6749 Z= 0.174 Angle : 0.623 12.285 9188 Z= 0.297 Chirality : 0.042 0.133 978 Planarity : 0.004 0.034 1177 Dihedral : 4.038 17.320 866 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.00 % Allowed : 17.71 % Favored : 80.29 % 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: 1.54 (0.29), residues: 793 helix: 1.67 (0.26), residues: 400 sheet: 0.23 (0.74), residues: 43 loop : 0.50 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.014 0.001 TYR B 495 PHE 0.019 0.001 PHE E 369 TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 6736) covalent geometry : angle 0.61703 / 0.30 ( 9155) SS BOND : bond 0.00288 / 0.19 ( 6) SS BOND : angle 0.80929 / 0.50 ( 12) hydrogen bonds : bond 0.04203 / 2.75 ( 322) hydrogen bonds : angle 4.36849 / 3.06 ( 915) link_NAG-ASN : bond 0.00269 / 0.16 ( 7) link_NAG-ASN : angle 1.83966 / 1.47 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2259.58 seconds wall clock time: 39 minutes 24.68 seconds (2364.68 seconds total)