Starting phenix.real_space_refine on Tue Feb 11 22:16:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy2_25514/02_2025/7sy2_25514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy2_25514/02_2025/7sy2_25514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sy2_25514/02_2025/7sy2_25514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy2_25514/02_2025/7sy2_25514.map" model { file = "/net/cci-nas-00/data/ceres_data/7sy2_25514/02_2025/7sy2_25514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy2_25514/02_2025/7sy2_25514.cif" } resolution = 3.11 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= -0.001 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 4191 2.51 5 N 1077 2.21 5 O 1249 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: 6554 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1594 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'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: 5.03, per 1000 atoms: 0.77 Number of scatterers: 6554 At special positions: 0 Unit cell: (80, 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 1249 8.00 N 1077 7.00 C 4191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 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: 1.51 Conformation dependent library (CDL) restraints added in 881.7 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 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 removed outlier: 3.502A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.745A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.792A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.751A 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: 3.994A 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: 3.967A 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: 3.710A 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: 3.659A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.754A 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: 3.801A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.583A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.685A 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: 4.279A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.519A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.358A 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: 3.734A 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: 4.434A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.902A 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: 3.981A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.835A 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: 3.690A 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: 6.005A 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: 6.335A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 321 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: 1.84 Time building geometry restraints manager: 1.79 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: 1794 1.47 - 1.60: 2802 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6737 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.98e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 6732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 8815 2.03 - 4.05: 295 4.05 - 6.08: 35 6.08 - 8.10: 7 8.10 - 10.13: 4 Bond angle restraints: 9156 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 128.95 -6.13 1.42e+00 4.96e-01 1.86e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.57 -9.17 2.30e+00 1.89e-01 1.59e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CB MET E 323 " pdb=" CG MET E 323 " pdb=" SD MET E 323 " ideal model delta sigma weight residual 112.70 122.83 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" C TYR B 495 " ideal model delta sigma weight residual 110.52 105.59 4.93 1.48e+00 4.57e-01 1.11e+01 ... (remaining 9151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3687 17.13 - 34.25: 306 34.25 - 51.38: 48 51.38 - 68.51: 13 68.51 - 85.63: 12 Dihedral angle restraints: 4066 sinusoidal: 1727 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 -43.43 -42.57 1 1.00e+01 1.00e-02 2.53e+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 16.60 62.40 1 2.00e+01 2.50e-03 1.29e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.73 8.13 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 4063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 713 0.053 - 0.107: 200 0.107 - 0.160: 55 0.160 - 0.213: 8 0.213 - 0.267: 2 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 2.24 0.27 2.00e-01 2.50e+01 1.78e+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 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN E 437 " pdb=" N ASN E 437 " pdb=" C ASN E 437 " pdb=" CB ASN E 437 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 975 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ARG E 169 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.022 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 168 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C TRP E 168 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP E 168 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG E 169 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 41 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C TYR E 41 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR E 41 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN E 42 " -0.015 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1934 2.83 - 3.34: 5949 3.34 - 3.86: 11371 3.86 - 4.38: 12856 4.38 - 4.90: 22341 Nonbonded interactions: 54451 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.307 3.040 nonbonded pdb=" O ASN E 117 " pdb=" ND2 ASN E 121 " model vdw 2.349 3.120 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.354 3.040 nonbonded pdb=" O MET E 152 " pdb=" NH1 ARG E 161 " model vdw 2.355 3.120 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.356 3.040 ... (remaining 54446 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.370 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.059 6737 Z= 0.322 Angle : 0.844 10.130 9156 Z= 0.460 Chirality : 0.055 0.267 978 Planarity : 0.007 0.065 1177 Dihedral : 13.461 85.634 2548 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.14 % Allowed : 1.86 % Favored : 98.00 % 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: -0.46 (0.26), residues: 793 helix: -0.05 (0.23), residues: 385 sheet: 0.55 (0.66), residues: 53 loop : -0.59 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 566 HIS 0.004 0.001 HIS E 34 PHE 0.031 0.002 PHE E 369 TYR 0.029 0.002 TYR E 385 ARG 0.007 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 96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8467 (m-30) cc_final: 0.8200 (m-30) REVERT: E 290 ASN cc_start: 0.8480 (t0) cc_final: 0.7701 (t0) REVERT: E 408 MET cc_start: 0.9425 (mmt) cc_final: 0.9219 (mmt) REVERT: E 474 MET cc_start: 0.8855 (mmt) cc_final: 0.8342 (mmm) REVERT: E 498 CYS cc_start: 0.7597 (t) cc_final: 0.6794 (t) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.3094 time to fit residues: 35.9112 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 4.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN E 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.049441 restraints weight = 21252.482| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.57 r_work: 0.2734 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6737 Z= 0.225 Angle : 0.553 9.455 9156 Z= 0.288 Chirality : 0.041 0.146 978 Planarity : 0.004 0.040 1177 Dihedral : 5.667 51.293 1013 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.71 % Allowed : 6.43 % Favored : 92.86 % 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: 0.80 (0.28), residues: 793 helix: 1.18 (0.25), residues: 396 sheet: 0.39 (0.68), residues: 52 loop : -0.11 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 165 HIS 0.005 0.001 HIS E 34 PHE 0.019 0.001 PHE E 369 TYR 0.013 0.001 TYR E 385 ARG 0.005 0.001 ARG E 306 *********************** 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8966 (m-30) cc_final: 0.8682 (m-30) REVERT: B 406 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8892 (mt-10) REVERT: B 498 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.9033 (mt0) REVERT: E 270 MET cc_start: 0.9047 (tpp) cc_final: 0.8828 (tpp) REVERT: E 498 CYS cc_start: 0.8110 (t) cc_final: 0.7513 (t) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.2281 time to fit residues: 16.6976 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 0.0270 chunk 46 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050262 restraints weight = 21370.918| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.51 r_work: 0.2754 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6737 Z= 0.170 Angle : 0.508 7.953 9156 Z= 0.260 Chirality : 0.040 0.141 978 Planarity : 0.004 0.034 1177 Dihedral : 5.183 52.884 1013 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.29 % Allowed : 7.00 % Favored : 91.71 % 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: 1.18 (0.29), residues: 793 helix: 1.48 (0.25), residues: 404 sheet: 0.78 (0.75), residues: 42 loop : 0.04 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE E 369 TYR 0.011 0.001 TYR E 385 ARG 0.004 0.000 ARG E 306 *********************** 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 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8925 (m-30) cc_final: 0.8660 (m-30) REVERT: B 406 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8940 (mt-10) REVERT: E 55 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8086 (p) REVERT: E 325 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8260 (tp-100) REVERT: E 498 CYS cc_start: 0.8062 (t) cc_final: 0.7410 (t) outliers start: 9 outliers final: 2 residues processed: 61 average time/residue: 0.2040 time to fit residues: 17.1271 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.049530 restraints weight = 21618.490| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.56 r_work: 0.2738 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6737 Z= 0.173 Angle : 0.478 5.637 9156 Z= 0.247 Chirality : 0.039 0.136 978 Planarity : 0.003 0.035 1177 Dihedral : 4.881 54.278 1013 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.29 % Allowed : 9.43 % Favored : 89.29 % 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: 401 sheet: 0.65 (0.74), residues: 42 loop : 0.29 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE E 369 TYR 0.011 0.001 TYR E 385 ARG 0.003 0.000 ARG E 306 *********************** 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 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8958 (m-30) cc_final: 0.8662 (m-30) REVERT: B 406 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8899 (mt-10) REVERT: E 55 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8061 (p) REVERT: E 249 MET cc_start: 0.8798 (ttp) cc_final: 0.8481 (ttp) REVERT: E 325 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8199 (tp-100) REVERT: E 498 CYS cc_start: 0.7960 (t) cc_final: 0.7180 (t) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.1866 time to fit residues: 14.5212 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 360 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.049174 restraints weight = 21340.756| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.53 r_work: 0.2726 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6737 Z= 0.180 Angle : 0.479 6.167 9156 Z= 0.247 Chirality : 0.040 0.145 978 Planarity : 0.003 0.039 1177 Dihedral : 4.709 55.028 1013 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.57 % Allowed : 9.86 % Favored : 88.57 % 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: 1.67 (0.25), residues: 401 sheet: 0.54 (0.72), residues: 42 loop : 0.38 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.016 0.001 PHE E 523 TYR 0.010 0.001 TYR E 385 ARG 0.003 0.000 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 60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8959 (m-30) cc_final: 0.8668 (m-30) REVERT: B 406 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8904 (mt-10) REVERT: E 55 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8082 (p) REVERT: E 131 LYS cc_start: 0.8972 (ptmm) cc_final: 0.8697 (ttpp) REVERT: E 249 MET cc_start: 0.8840 (ttp) cc_final: 0.8495 (ttp) REVERT: E 325 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8375 (tp40) REVERT: E 376 MET cc_start: 0.9135 (tpp) cc_final: 0.8916 (tpp) REVERT: E 498 CYS cc_start: 0.8139 (t) cc_final: 0.7316 (t) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.1981 time to fit residues: 15.5936 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0060 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.049032 restraints weight = 21385.974| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.51 r_work: 0.2730 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6737 Z= 0.168 Angle : 0.467 5.547 9156 Z= 0.243 Chirality : 0.040 0.132 978 Planarity : 0.003 0.040 1177 Dihedral : 4.583 55.780 1013 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.43 % Allowed : 10.71 % Favored : 87.86 % 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: 1.56 (0.29), residues: 793 helix: 1.69 (0.25), residues: 406 sheet: 0.49 (0.73), residues: 42 loop : 0.43 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE E 523 TYR 0.009 0.001 TYR E 516 ARG 0.003 0.000 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 58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8971 (m-30) cc_final: 0.8671 (m-30) REVERT: B 406 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8914 (mt-10) REVERT: E 55 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8042 (p) REVERT: E 325 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8353 (tp40) REVERT: E 498 CYS cc_start: 0.8183 (t) cc_final: 0.7196 (t) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.2095 time to fit residues: 15.6078 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 62 optimal weight: 0.3980 chunk 67 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.048978 restraints weight = 21304.454| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.53 r_work: 0.2736 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6737 Z= 0.167 Angle : 0.470 5.644 9156 Z= 0.246 Chirality : 0.040 0.129 978 Planarity : 0.003 0.043 1177 Dihedral : 4.511 56.055 1013 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.43 % Allowed : 12.00 % 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: 1.64 (0.29), residues: 793 helix: 1.74 (0.26), residues: 406 sheet: 0.42 (0.72), residues: 42 loop : 0.52 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE E 523 TYR 0.010 0.001 TYR E 385 ARG 0.003 0.000 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 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8953 (m-30) cc_final: 0.8658 (m-30) REVERT: B 406 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8894 (mt-10) REVERT: E 55 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8066 (p) REVERT: E 325 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8341 (tp40) REVERT: E 498 CYS cc_start: 0.8252 (t) cc_final: 0.7298 (t) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1918 time to fit residues: 13.8671 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.048488 restraints weight = 21465.065| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.55 r_work: 0.2719 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6737 Z= 0.189 Angle : 0.474 6.949 9156 Z= 0.248 Chirality : 0.040 0.129 978 Planarity : 0.003 0.043 1177 Dihedral : 4.509 56.199 1013 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.43 % Allowed : 12.29 % Favored : 86.29 % 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: 1.69 (0.30), residues: 793 helix: 1.77 (0.26), residues: 406 sheet: 0.39 (0.73), residues: 42 loop : 0.58 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.015 0.001 PHE E 523 TYR 0.011 0.001 TYR E 385 ARG 0.003 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 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8964 (m-30) cc_final: 0.8714 (m-30) REVERT: B 406 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8896 (mt-10) REVERT: E 55 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8050 (p) REVERT: E 325 GLN cc_start: 0.8842 (tp-100) cc_final: 0.8322 (tp40) REVERT: E 498 CYS cc_start: 0.8212 (t) cc_final: 0.7272 (t) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.2003 time to fit residues: 14.7838 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 0.0970 chunk 41 optimal weight: 0.3980 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049844 restraints weight = 21280.035| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.51 r_work: 0.2752 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6737 Z= 0.152 Angle : 0.477 6.564 9156 Z= 0.250 Chirality : 0.039 0.125 978 Planarity : 0.003 0.042 1177 Dihedral : 4.425 56.375 1013 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.14 % Allowed : 13.00 % Favored : 85.86 % 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: 1.68 (0.30), residues: 793 helix: 1.72 (0.25), residues: 407 sheet: 0.37 (0.73), residues: 42 loop : 0.62 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 PHE 0.014 0.001 PHE E 523 TYR 0.013 0.001 TYR E 50 ARG 0.003 0.000 ARG B 346 *********************** 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 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8952 (m-30) cc_final: 0.8698 (m-30) REVERT: B 518 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7557 (tt) REVERT: E 55 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (p) REVERT: E 325 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8304 (tp40) REVERT: E 498 CYS cc_start: 0.8020 (t) cc_final: 0.7044 (t) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.1802 time to fit residues: 13.3598 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.062002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.047297 restraints weight = 21659.874| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.55 r_work: 0.2682 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6737 Z= 0.258 Angle : 0.527 7.104 9156 Z= 0.276 Chirality : 0.041 0.140 978 Planarity : 0.004 0.044 1177 Dihedral : 4.616 56.202 1013 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.29 % Allowed : 13.29 % Favored : 85.43 % 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: 1.72 (0.30), residues: 793 helix: 1.73 (0.26), residues: 401 sheet: 0.38 (0.73), residues: 42 loop : 0.70 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.017 0.001 PHE E 369 TYR 0.014 0.001 TYR E 385 ARG 0.004 0.000 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 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8960 (m-30) cc_final: 0.8650 (m-30) REVERT: B 518 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7537 (tt) REVERT: E 55 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8042 (p) REVERT: E 325 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8331 (tp40) REVERT: E 498 CYS cc_start: 0.8390 (t) cc_final: 0.7446 (t) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.1792 time to fit residues: 12.5375 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.062758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.048570 restraints weight = 21442.207| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.45 r_work: 0.2725 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6737 Z= 0.179 Angle : 0.492 6.369 9156 Z= 0.257 Chirality : 0.040 0.146 978 Planarity : 0.003 0.045 1177 Dihedral : 4.512 56.559 1013 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.14 % Allowed : 13.43 % Favored : 85.43 % 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: 1.68 (0.30), residues: 793 helix: 1.68 (0.25), residues: 407 sheet: 0.32 (0.73), residues: 42 loop : 0.69 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 PHE 0.014 0.001 PHE E 523 TYR 0.014 0.001 TYR E 50 ARG 0.003 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.50 seconds wall clock time: 56 minutes 22.76 seconds (3382.76 seconds total)