Starting phenix.real_space_refine on Tue Mar 11 21:14:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy6_25518/03_2025/7sy6_25518.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy6_25518/03_2025/7sy6_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_25518/03_2025/7sy6_25518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy6_25518/03_2025/7sy6_25518.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy6_25518/03_2025/7sy6_25518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy6_25518/03_2025/7sy6_25518.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 3 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.85, per 1000 atoms: 0.74 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: 1.57 Conformation dependent library (CDL) restraints added in 888.1 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 7 sheets defined 57.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 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: 1.76 Time building geometry restraints manager: 1.89 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: 3685 17.17 - 34.34: 311 34.34 - 51.51: 45 51.51 - 68.68: 13 68.68 - 85.85: 11 Dihedral angle restraints: 4065 sinusoidal: 1726 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 4062 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: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 6736 Z= 0.354 Angle : 0.861 10.373 9155 Z= 0.470 Chirality : 0.057 0.256 978 Planarity : 0.007 0.060 1177 Dihedral : 13.403 85.851 2547 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (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 TRP 0.020 0.002 TRP E 566 HIS 0.007 0.001 HIS E 34 PHE 0.031 0.003 PHE E 369 TYR 0.046 0.002 TYR B 495 ARG 0.009 0.001 ARG E 460 *********************** 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 : 0.742 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: 1.3032 time to fit residues: 165.1712 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 : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.0020 chunk 71 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN E 154 ASN E 374 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056311 restraints weight = 16173.654| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.11 r_work: 0.2740 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6736 Z= 0.205 Angle : 0.579 8.408 9155 Z= 0.291 Chirality : 0.042 0.204 978 Planarity : 0.004 0.037 1177 Dihedral : 5.187 48.857 1013 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.29 % Allowed : 11.14 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.28), residues: 793 helix: 1.01 (0.25), residues: 390 sheet: 0.79 (0.71), residues: 43 loop : -0.49 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.019 0.001 PHE E 369 TYR 0.020 0.001 TYR B 495 ARG 0.008 0.001 ARG E 559 *********************** 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 92 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.751 Fit side-chains REVERT: B 405 ASP cc_start: 0.8846 (m-30) cc_final: 0.8417 (m-30) REVERT: B 528 LYS cc_start: 0.3500 (OUTLIER) cc_final: 0.3046 (pttt) REVERT: E 131 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8406 (ptmm) REVERT: E 142 LEU cc_start: 0.9191 (mt) cc_final: 0.8936 (tp) REVERT: E 259 ILE cc_start: 0.8458 (tp) cc_final: 0.8212 (pp) REVERT: E 462 MET cc_start: 0.9087 (mtp) cc_final: 0.8867 (mtp) REVERT: E 475 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8611 (ttpp) REVERT: E 480 MET cc_start: 0.8912 (mtp) cc_final: 0.8674 (mtm) REVERT: E 494 ASP cc_start: 0.9059 (p0) cc_final: 0.8825 (p0) outliers start: 16 outliers final: 5 residues processed: 87 average time/residue: 1.2989 time to fit residues: 119.0271 Evaluate side-chains 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 503 LEU 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 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN E 149 ASN E 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.055001 restraints weight = 16238.839| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.04 r_work: 0.2708 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6736 Z= 0.223 Angle : 0.557 9.597 9155 Z= 0.276 Chirality : 0.041 0.144 978 Planarity : 0.004 0.032 1177 Dihedral : 4.899 50.481 1013 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.86 % Allowed : 12.00 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.28), residues: 793 helix: 1.42 (0.26), residues: 391 sheet: 0.71 (0.71), residues: 43 loop : -0.19 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.019 0.001 PHE E 369 TYR 0.017 0.001 TYR B 495 ARG 0.004 0.001 ARG E 559 *********************** 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 91 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.764 Fit side-chains REVERT: B 405 ASP cc_start: 0.8882 (m-30) cc_final: 0.8451 (m-30) REVERT: B 466 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8768 (mtp85) REVERT: B 471 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: E 131 LYS cc_start: 0.8714 (ptmm) cc_final: 0.8341 (ptmm) REVERT: E 142 LEU cc_start: 0.9248 (mt) cc_final: 0.9046 (tp) REVERT: E 462 MET cc_start: 0.9097 (mtp) cc_final: 0.8887 (mtp) REVERT: E 475 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8592 (ttpp) REVERT: E 483 GLU cc_start: 0.9043 (tp30) cc_final: 0.8610 (tp30) REVERT: E 494 ASP cc_start: 0.9028 (p0) cc_final: 0.8820 (p0) REVERT: E 582 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8381 (mmm-85) outliers start: 20 outliers final: 7 residues processed: 84 average time/residue: 1.5538 time to fit residues: 136.3803 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 517 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053325 restraints weight = 16437.353| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.03 r_work: 0.2664 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6736 Z= 0.277 Angle : 0.580 10.668 9155 Z= 0.287 Chirality : 0.042 0.145 978 Planarity : 0.004 0.031 1177 Dihedral : 4.936 51.443 1013 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.57 % Allowed : 12.57 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.29), residues: 793 helix: 1.49 (0.26), residues: 393 sheet: 0.53 (0.71), residues: 43 loop : 0.01 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.020 0.001 PHE E 369 TYR 0.017 0.001 TYR B 495 ARG 0.005 0.001 ARG B 457 *********************** 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 87 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8896 (m-30) cc_final: 0.8475 (m-30) REVERT: B 466 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8722 (mtp85) REVERT: B 471 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8631 (tt0) REVERT: E 131 LYS cc_start: 0.8690 (ptmm) cc_final: 0.8201 (ptmm) REVERT: E 462 MET cc_start: 0.9111 (mtp) cc_final: 0.8909 (mtp) REVERT: E 475 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8662 (ttpp) REVERT: E 494 ASP cc_start: 0.9038 (p0) cc_final: 0.8759 (p0) REVERT: E 589 GLU cc_start: 0.9108 (tp30) cc_final: 0.8368 (tp30) outliers start: 25 outliers final: 11 residues processed: 80 average time/residue: 1.3411 time to fit residues: 112.5087 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 : 0.810 ------------------------------------------------------------------------------- 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 151 ILE 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 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 0 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN E 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053842 restraints weight = 16196.523| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.03 r_work: 0.2669 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6736 Z= 0.232 Angle : 0.557 9.856 9155 Z= 0.273 Chirality : 0.041 0.138 978 Planarity : 0.003 0.031 1177 Dihedral : 4.828 52.891 1013 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.00 % Allowed : 14.86 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 793 helix: 1.53 (0.26), residues: 393 sheet: 0.43 (0.72), residues: 43 loop : 0.11 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.018 0.001 PHE E 369 TYR 0.016 0.001 TYR B 495 ARG 0.005 0.001 ARG E 582 *********************** 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 83 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.780 Fit side-chains REVERT: B 405 ASP cc_start: 0.8910 (m-30) cc_final: 0.8465 (m-30) REVERT: B 466 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8752 (mtp85) REVERT: B 471 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: E 376 MET cc_start: 0.9159 (ttm) cc_final: 0.8939 (tpp) REVERT: E 475 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8663 (ttpp) REVERT: E 483 GLU cc_start: 0.9035 (tp30) cc_final: 0.8593 (tp30) REVERT: E 589 GLU cc_start: 0.9121 (tp30) cc_final: 0.8382 (tp30) outliers start: 21 outliers final: 11 residues processed: 80 average time/residue: 1.4196 time to fit residues: 119.2361 Evaluate side-chains 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 B residue 525 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.073961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.053556 restraints weight = 16032.555| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.99 r_work: 0.2659 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6736 Z= 0.257 Angle : 0.577 9.383 9155 Z= 0.284 Chirality : 0.041 0.138 978 Planarity : 0.003 0.031 1177 Dihedral : 4.860 53.406 1013 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.86 % Allowed : 15.57 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 793 helix: 1.61 (0.26), residues: 393 sheet: 0.38 (0.73), residues: 43 loop : 0.19 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.018 0.001 PHE E 369 TYR 0.016 0.001 TYR B 495 ARG 0.005 0.001 ARG B 346 *********************** 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 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.744 Fit side-chains REVERT: B 405 ASP cc_start: 0.8911 (m-30) cc_final: 0.8479 (m-30) REVERT: B 466 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8743 (mtp85) REVERT: B 471 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: E 376 MET cc_start: 0.9201 (ttm) cc_final: 0.8970 (tpp) REVERT: E 383 MET cc_start: 0.9259 (mtm) cc_final: 0.9052 (mtm) REVERT: E 589 GLU cc_start: 0.9130 (tp30) cc_final: 0.8411 (tp30) outliers start: 20 outliers final: 13 residues processed: 75 average time/residue: 1.2575 time to fit residues: 99.4428 Evaluate side-chains 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 474 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 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053632 restraints weight = 16158.650| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.04 r_work: 0.2676 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6736 Z= 0.243 Angle : 0.572 9.095 9155 Z= 0.281 Chirality : 0.041 0.135 978 Planarity : 0.003 0.031 1177 Dihedral : 4.836 54.161 1013 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.71 % Allowed : 16.00 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 793 helix: 1.57 (0.25), residues: 399 sheet: 0.29 (0.73), residues: 43 loop : 0.25 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.017 0.001 PHE E 369 TYR 0.015 0.001 TYR B 495 ARG 0.006 0.001 ARG B 346 *********************** 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 76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.687 Fit side-chains REVERT: B 405 ASP cc_start: 0.8898 (m-30) cc_final: 0.8447 (m-30) REVERT: B 466 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8821 (mtp85) REVERT: B 471 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8687 (tt0) REVERT: E 376 MET cc_start: 0.9189 (ttm) cc_final: 0.8960 (tpp) REVERT: E 589 GLU cc_start: 0.9139 (tp30) cc_final: 0.8435 (tp30) outliers start: 19 outliers final: 12 residues processed: 72 average time/residue: 1.3156 time to fit residues: 99.7380 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 506 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.075090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.054670 restraints weight = 16129.987| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.02 r_work: 0.2703 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6736 Z= 0.194 Angle : 0.583 12.128 9155 Z= 0.278 Chirality : 0.041 0.128 978 Planarity : 0.003 0.031 1177 Dihedral : 4.720 55.005 1013 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.29 % Allowed : 16.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 793 helix: 1.65 (0.26), residues: 397 sheet: 0.28 (0.74), residues: 43 loop : 0.26 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 PHE 0.015 0.001 PHE E 369 TYR 0.014 0.001 TYR B 495 ARG 0.007 0.000 ARG B 346 *********************** 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 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.750 Fit side-chains REVERT: B 405 ASP cc_start: 0.8910 (m-30) cc_final: 0.8473 (m-30) REVERT: B 466 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8775 (mtp85) REVERT: B 471 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: E 376 MET cc_start: 0.9194 (ttm) cc_final: 0.8968 (tpp) REVERT: E 589 GLU cc_start: 0.9130 (tp30) cc_final: 0.8446 (tp30) outliers start: 16 outliers final: 11 residues processed: 71 average time/residue: 1.3474 time to fit residues: 100.5478 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 506 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054632 restraints weight = 16248.744| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.05 r_work: 0.2699 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6736 Z= 0.197 Angle : 0.591 12.271 9155 Z= 0.281 Chirality : 0.041 0.172 978 Planarity : 0.003 0.031 1177 Dihedral : 4.688 54.985 1013 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.43 % Allowed : 17.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.29), residues: 793 helix: 1.73 (0.26), residues: 397 sheet: 0.20 (0.74), residues: 43 loop : 0.35 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.016 0.001 PHE E 369 TYR 0.017 0.001 TYR B 369 ARG 0.008 0.001 ARG E 582 *********************** 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 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.698 Fit side-chains REVERT: B 405 ASP cc_start: 0.8918 (m-30) cc_final: 0.8479 (m-30) REVERT: B 466 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8759 (mtp85) REVERT: B 471 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: E 270 MET cc_start: 0.8746 (mmm) cc_final: 0.8536 (tpt) REVERT: E 376 MET cc_start: 0.9204 (ttm) cc_final: 0.8972 (tpp) REVERT: E 589 GLU cc_start: 0.9131 (tp30) cc_final: 0.8442 (tp30) outliers start: 17 outliers final: 12 residues processed: 73 average time/residue: 1.2587 time to fit residues: 96.9550 Evaluate side-chains 71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.053918 restraints weight = 16327.326| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.05 r_work: 0.2679 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6736 Z= 0.241 Angle : 0.626 14.014 9155 Z= 0.296 Chirality : 0.042 0.165 978 Planarity : 0.004 0.031 1177 Dihedral : 4.749 54.795 1013 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.86 % Allowed : 17.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 793 helix: 1.70 (0.26), residues: 399 sheet: 0.22 (0.74), residues: 43 loop : 0.40 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.018 0.001 PHE E 369 TYR 0.014 0.001 TYR E 385 ARG 0.006 0.001 ARG B 346 ********************** 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 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.745 Fit side-chains REVERT: B 386 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8736 (pmtt) REVERT: B 405 ASP cc_start: 0.8918 (m-30) cc_final: 0.8504 (m-30) REVERT: B 466 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8819 (mtp85) REVERT: B 471 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8702 (tt0) REVERT: E 270 MET cc_start: 0.8843 (mmm) cc_final: 0.8478 (tpt) REVERT: E 376 MET cc_start: 0.9248 (ttm) cc_final: 0.9008 (tpp) REVERT: E 589 GLU cc_start: 0.9146 (tp30) cc_final: 0.8456 (tp30) outliers start: 13 outliers final: 12 residues processed: 68 average time/residue: 1.2863 time to fit residues: 92.2249 Evaluate side-chains 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 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 78 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 72 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055749 restraints weight = 16356.722| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.04 r_work: 0.2725 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6736 Z= 0.171 Angle : 0.588 13.161 9155 Z= 0.278 Chirality : 0.040 0.139 978 Planarity : 0.003 0.031 1177 Dihedral : 4.600 55.751 1013 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.86 % Allowed : 17.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 793 helix: 1.75 (0.26), residues: 398 sheet: 0.26 (0.74), residues: 43 loop : 0.41 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 PHE 0.014 0.001 PHE E 369 TYR 0.013 0.001 TYR B 495 ARG 0.006 0.001 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4780.45 seconds wall clock time: 82 minutes 31.52 seconds (4951.52 seconds total)