Starting phenix.real_space_refine on Tue Feb 11 21:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy6_25518/02_2025/7sy6_25518.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy6_25518/02_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_25518/02_2025/7sy6_25518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy6_25518/02_2025/7sy6_25518.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy6_25518/02_2025/7sy6_25518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy6_25518/02_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-5592/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: 4.86, 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: 1.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.72 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: 1.96 Time building geometry restraints manager: 1.84 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: 4.240 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- 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 : 0.765 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: 1.3807 time to fit residues: 174.8443 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 : 0.739 ------------------------------------------------------------------------------- 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 = 0.076649 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 = 16173.273| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.11 r_work: 0.2739 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- 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 : 0.837 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: 0.3503 (OUTLIER) cc_final: 0.3048 (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: 0.8213 (pp) REVERT: E 462 MET cc_start: 0.9086 (mtp) cc_final: 0.8866 (mtp) REVERT: E 475 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8611 (ttpp) REVERT: E 480 MET cc_start: 0.8913 (mtp) cc_final: 0.8675 (mtm) REVERT: E 494 ASP cc_start: 0.9060 (p0) cc_final: 0.8826 (p0) outliers start: 16 outliers final: 5 residues processed: 87 average time/residue: 1.3376 time to fit residues: 122.2997 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 : 0.832 ------------------------------------------------------------------------------- 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: 0.9990 chunk 27 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 472 GLN E 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054542 restraints weight = 16269.906| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.02 r_work: 0.2693 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6736 Z= 0.243 Angle : 0.564 9.398 9155 Z= 0.281 Chirality : 0.042 0.146 978 Planarity : 0.004 0.032 1177 Dihedral : 4.923 50.573 1013 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.29 % Allowed : 11.71 % 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 (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: 0.96 (0.28), residues: 793 helix: 1.38 (0.25), residues: 393 sheet: 0.69 (0.71), residues: 43 loop : -0.13 (0.31), residues: 357 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 0.018 0.001 TYR B 495 ARG 0.005 0.001 ARG B 457 *********************** 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 93 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.782 Fit side-chains REVERT: B 405 ASP cc_start: 0.8882 (m-30) cc_final: 0.8479 (m-30) REVERT: B 466 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8769 (mtp85) REVERT: B 471 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8663 (tt0) REVERT: E 114 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8898 (mptt) REVERT: E 131 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8341 (ptmm) REVERT: E 475 LYS cc_start: 0.8871 (ttpp) cc_final: 0.8630 (ttpp) REVERT: E 494 ASP cc_start: 0.9049 (p0) cc_final: 0.8832 (p0) REVERT: E 582 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8372 (mmm-85) outliers start: 23 outliers final: 9 residues processed: 85 average time/residue: 1.4524 time to fit residues: 129.3870 Evaluate side-chains 77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 517 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 114 LYS 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: 0.9980 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.052701 restraints weight = 16429.985| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.01 r_work: 0.2638 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6736 Z= 0.321 Angle : 0.602 11.187 9155 Z= 0.298 Chirality : 0.043 0.150 978 Planarity : 0.004 0.032 1177 Dihedral : 5.027 51.369 1013 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.71 % Allowed : 13.14 % Favored : 83.14 % 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: 1.12 (0.29), residues: 793 helix: 1.50 (0.26), residues: 393 sheet: 0.41 (0.71), residues: 43 loop : 0.03 (0.32), residues: 357 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 0.020 0.002 PHE E 369 TYR 0.018 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: 26 poor density : 61 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8909 (m-30) cc_final: 0.8485 (m-30) REVERT: B 466 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8703 (mtp85) REVERT: B 471 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: E 131 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8191 (ptmm) REVERT: E 142 LEU cc_start: 0.9112 (tp) cc_final: 0.8851 (tp) REVERT: E 383 MET cc_start: 0.9309 (mtm) cc_final: 0.9066 (mtm) REVERT: E 589 GLU cc_start: 0.9136 (tp30) cc_final: 0.8398 (tp30) outliers start: 26 outliers final: 10 residues processed: 81 average time/residue: 1.4466 time to fit residues: 122.9664 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 151 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.073941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.053456 restraints weight = 16187.490| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.03 r_work: 0.2656 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2701 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= 0.245 Angle : 0.566 10.545 9155 Z= 0.279 Chirality : 0.042 0.140 978 Planarity : 0.003 0.032 1177 Dihedral : 4.879 52.735 1013 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.14 % Allowed : 14.86 % 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 (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: 1.19 (0.29), residues: 793 helix: 1.51 (0.26), residues: 393 sheet: 0.30 (0.72), residues: 43 loop : 0.15 (0.32), residues: 357 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 0.016 0.001 TYR B 495 ARG 0.005 0.001 ARG B 346 *********************** 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 84 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.793 Fit side-chains REVERT: B 340 GLU cc_start: 0.9230 (mt-10) cc_final: 0.9028 (mt-10) REVERT: B 386 LYS cc_start: 0.9355 (ptpp) cc_final: 0.9154 (ptpp) REVERT: B 405 ASP cc_start: 0.8915 (m-30) cc_final: 0.8470 (m-30) REVERT: B 466 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8748 (mtp85) REVERT: B 471 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: E 131 LYS cc_start: 0.8689 (ptmm) cc_final: 0.8227 (ptmm) REVERT: E 142 LEU cc_start: 0.9071 (tp) cc_final: 0.8786 (tp) REVERT: E 376 MET cc_start: 0.9161 (ttm) cc_final: 0.8943 (tpp) REVERT: E 483 GLU cc_start: 0.9050 (tp30) cc_final: 0.8623 (tp30) REVERT: E 589 GLU cc_start: 0.9128 (tp30) cc_final: 0.8419 (tp30) outliers start: 22 outliers final: 10 residues processed: 78 average time/residue: 1.4277 time to fit residues: 116.6984 Evaluate side-chains 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 455 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 506 VAL 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: 0.8980 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.073852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.053490 restraints weight = 16031.800| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.97 r_work: 0.2658 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6736 Z= 0.248 Angle : 0.579 10.186 9155 Z= 0.282 Chirality : 0.041 0.135 978 Planarity : 0.003 0.032 1177 Dihedral : 4.858 53.574 1013 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.00 % Allowed : 15.29 % 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 (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: 1.58 (0.26), residues: 393 sheet: 0.29 (0.72), residues: 43 loop : 0.24 (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 0.017 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 79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.749 Fit side-chains REVERT: B 405 ASP cc_start: 0.8898 (m-30) cc_final: 0.8450 (m-30) REVERT: B 466 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8734 (mtp85) REVERT: B 471 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8653 (tt0) REVERT: E 270 MET cc_start: 0.8718 (mmm) cc_final: 0.8339 (tpt) REVERT: E 376 MET cc_start: 0.9193 (ttm) cc_final: 0.8971 (tpp) REVERT: E 589 GLU cc_start: 0.9135 (tp30) cc_final: 0.8442 (tp30) outliers start: 21 outliers final: 12 residues processed: 74 average time/residue: 1.2773 time to fit residues: 99.6642 Evaluate side-chains 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.073297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.052918 restraints weight = 16231.837| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.00 r_work: 0.2640 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6736 Z= 0.284 Angle : 0.587 10.417 9155 Z= 0.288 Chirality : 0.042 0.136 978 Planarity : 0.003 0.032 1177 Dihedral : 4.914 53.911 1013 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.00 % Allowed : 15.57 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.26), residues: 399 sheet: 0.26 (0.73), residues: 43 loop : 0.31 (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 0.018 0.001 PHE E 369 TYR 0.016 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 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.795 Fit side-chains REVERT: B 405 ASP cc_start: 0.8904 (m-30) cc_final: 0.8459 (m-30) REVERT: B 466 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8809 (mtp85) REVERT: B 468 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9160 (pp) REVERT: B 471 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8655 (tt0) REVERT: E 376 MET cc_start: 0.9240 (ttm) cc_final: 0.9014 (tpp) REVERT: E 589 GLU cc_start: 0.9161 (tp30) cc_final: 0.8481 (tp30) outliers start: 21 outliers final: 12 residues processed: 70 average time/residue: 1.3395 time to fit residues: 98.7725 Evaluate side-chains 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 468 ILE 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 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 45 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.0000 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.074605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054253 restraints weight = 16107.900| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.01 r_work: 0.2691 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2936 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= 0.197 Angle : 0.575 10.632 9155 Z= 0.275 Chirality : 0.040 0.127 978 Planarity : 0.003 0.031 1177 Dihedral : 4.771 54.926 1013 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.29 % Allowed : 16.43 % 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: 1.43 (0.29), residues: 793 helix: 1.64 (0.26), residues: 399 sheet: 0.28 (0.74), residues: 43 loop : 0.36 (0.33), residues: 351 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 0.016 0.001 PHE E 369 TYR 0.014 0.001 TYR B 495 ARG 0.006 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 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.684 Fit side-chains REVERT: B 405 ASP cc_start: 0.8908 (m-30) cc_final: 0.8466 (m-30) REVERT: B 466 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8822 (mtp85) REVERT: B 471 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8651 (tt0) REVERT: E 376 MET cc_start: 0.9162 (ttm) cc_final: 0.8949 (tpp) REVERT: E 589 GLU cc_start: 0.9126 (tp30) cc_final: 0.8464 (tp30) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 1.3891 time to fit residues: 103.5796 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 : 0.779 ------------------------------------------------------------------------------- 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 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 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 20 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.074675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054379 restraints weight = 16246.939| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.03 r_work: 0.2688 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6736 Z= 0.206 Angle : 0.593 13.956 9155 Z= 0.281 Chirality : 0.041 0.128 978 Planarity : 0.003 0.031 1177 Dihedral : 4.737 54.830 1013 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.43 % Allowed : 16.86 % 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: 1.47 (0.29), residues: 793 helix: 1.67 (0.26), residues: 398 sheet: 0.26 (0.74), residues: 43 loop : 0.39 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.005 0.001 HIS E 374 PHE 0.017 0.001 PHE E 369 TYR 0.014 0.001 TYR B 495 ARG 0.007 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 72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.783 Fit side-chains REVERT: B 405 ASP cc_start: 0.8911 (m-30) cc_final: 0.8475 (m-30) REVERT: B 466 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8831 (mtp85) REVERT: B 471 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: E 376 MET cc_start: 0.9213 (ttm) cc_final: 0.8988 (tpp) REVERT: E 589 GLU cc_start: 0.9129 (tp30) cc_final: 0.8475 (tp30) outliers start: 17 outliers final: 12 residues processed: 70 average time/residue: 1.2995 time to fit residues: 96.2336 Evaluate side-chains 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.074916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054625 restraints weight = 16291.038| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.02 r_work: 0.2690 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 0.031 6736 Z= 0.203 Angle : 0.609 14.312 9155 Z= 0.284 Chirality : 0.041 0.127 978 Planarity : 0.004 0.031 1177 Dihedral : 4.708 55.168 1013 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.00 % Allowed : 17.14 % Favored : 80.86 % 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: 1.54 (0.29), residues: 793 helix: 1.73 (0.26), residues: 399 sheet: 0.20 (0.74), residues: 43 loop : 0.43 (0.33), residues: 351 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 0.016 0.001 PHE E 369 TYR 0.013 0.001 TYR B 495 ARG 0.007 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: 14 poor density : 55 time to evaluate : 0.829 Fit side-chains REVERT: B 405 ASP cc_start: 0.8911 (m-30) cc_final: 0.8473 (m-30) REVERT: B 466 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8836 (mtp85) REVERT: B 471 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: E 376 MET cc_start: 0.9221 (ttm) cc_final: 0.8994 (tpp) REVERT: E 408 MET cc_start: 0.9517 (mmt) cc_final: 0.9220 (mmt) REVERT: E 589 GLU cc_start: 0.9129 (tp30) cc_final: 0.8460 (tp30) outliers start: 14 outliers final: 13 residues processed: 67 average time/residue: 1.3205 time to fit residues: 93.3684 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 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 78 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.075108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054733 restraints weight = 16400.092| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.05 r_work: 0.2705 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3025 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= 0.191 Angle : 0.589 13.516 9155 Z= 0.279 Chirality : 0.041 0.125 978 Planarity : 0.004 0.032 1177 Dihedral : 4.649 55.315 1013 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.49 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: 1.55 (0.29), residues: 793 helix: 1.74 (0.26), residues: 399 sheet: 0.22 (0.74), residues: 43 loop : 0.44 (0.33), residues: 351 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 0.017 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: 4409.85 seconds wall clock time: 79 minutes 0.61 seconds (4740.61 seconds total)