Starting phenix.real_space_refine on Wed Sep 17 20:01:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzd_38793/09_2025/8xzd_38793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzd_38793/09_2025/8xzd_38793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xzd_38793/09_2025/8xzd_38793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzd_38793/09_2025/8xzd_38793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xzd_38793/09_2025/8xzd_38793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzd_38793/09_2025/8xzd_38793.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5736 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4122 2.51 5 N 1070 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6436 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1550 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4885 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 29, 'TRANS': 566} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.89, per 1000 atoms: 0.29 Number of scatterers: 6436 At special positions: 0 Unit cell: (73.83, 86.25, 120.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1206 8.00 N 1070 7.00 C 4122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.50 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 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 475.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 57.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.589A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.816A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.702A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.664A pdb=" N LYS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.524A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.697A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.911A pdb=" N ASP A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.687A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.709A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.512A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 414 removed outlier: 3.676A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.655A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.516A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.937A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.669A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.689A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.746A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.450A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 873 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: 1.02 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1831 1.33 - 1.46: 1880 1.46 - 1.59: 2855 1.59 - 1.72: 0 1.72 - 1.86: 58 Bond restraints: 6624 Sorted by residual: bond pdb=" CA GLN A 522 " pdb=" C GLN A 522 " ideal model delta sigma weight residual 1.524 1.449 0.075 1.27e-02 6.20e+03 3.47e+01 bond pdb=" CA TYR A 252 " pdb=" C TYR A 252 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.00e-02 1.00e+04 3.38e+01 bond pdb=" CA ASN A 134 " pdb=" C ASN A 134 " ideal model delta sigma weight residual 1.526 1.461 0.065 1.14e-02 7.69e+03 3.25e+01 bond pdb=" CA TRP A 477 " pdb=" C TRP A 477 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.77e+01 bond pdb=" CA TRP A 211 " pdb=" C TRP A 211 " ideal model delta sigma weight residual 1.524 1.459 0.064 1.23e-02 6.61e+03 2.75e+01 ... (remaining 6619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 8183 2.61 - 5.23: 628 5.23 - 7.84: 138 7.84 - 10.45: 42 10.45 - 13.07: 15 Bond angle restraints: 9006 Sorted by residual: angle pdb=" N SER A 339 " pdb=" CA SER A 339 " pdb=" C SER A 339 " ideal model delta sigma weight residual 111.40 124.47 -13.07 1.22e+00 6.72e-01 1.15e+02 angle pdb=" N TYR A 255 " pdb=" CA TYR A 255 " pdb=" C TYR A 255 " ideal model delta sigma weight residual 111.36 122.70 -11.34 1.09e+00 8.42e-01 1.08e+02 angle pdb=" N ALA A 264 " pdb=" CA ALA A 264 " pdb=" C ALA A 264 " ideal model delta sigma weight residual 111.28 122.10 -10.82 1.09e+00 8.42e-01 9.86e+01 angle pdb=" N GLY A 286 " pdb=" CA GLY A 286 " pdb=" C GLY A 286 " ideal model delta sigma weight residual 112.73 124.63 -11.90 1.20e+00 6.94e-01 9.83e+01 angle pdb=" N GLU A 22 " pdb=" CA GLU A 22 " pdb=" C GLU A 22 " ideal model delta sigma weight residual 111.07 100.92 10.15 1.07e+00 8.73e-01 9.00e+01 ... (remaining 9001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3398 17.27 - 34.53: 353 34.53 - 51.80: 93 51.80 - 69.07: 42 69.07 - 86.33: 8 Dihedral angle restraints: 3894 sinusoidal: 1565 harmonic: 2329 Sorted by residual: dihedral pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CA ASN A 195 " pdb=" CB ASN A 195 " ideal model delta harmonic sigma weight residual 122.80 136.62 -13.82 0 2.50e+00 1.60e-01 3.05e+01 dihedral pdb=" C THR A 21 " pdb=" N THR A 21 " pdb=" CA THR A 21 " pdb=" CB THR A 21 " ideal model delta harmonic sigma weight residual -122.00 -108.26 -13.74 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C ASN A 195 " pdb=" N ASN A 195 " pdb=" CA ASN A 195 " pdb=" CB ASN A 195 " ideal model delta harmonic sigma weight residual -122.60 -135.97 13.37 0 2.50e+00 1.60e-01 2.86e+01 ... (remaining 3891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 636 0.137 - 0.274: 229 0.274 - 0.411: 51 0.411 - 0.547: 16 0.547 - 0.684: 1 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA ASN A 195 " pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CB ASN A 195 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA LEU A 450 " pdb=" N LEU A 450 " pdb=" C LEU A 450 " pdb=" CB LEU A 450 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CA GLU A 145 " pdb=" N GLU A 145 " pdb=" C GLU A 145 " pdb=" CB GLU A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 ... (remaining 930 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 410 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ILE B 410 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE B 410 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA B 411 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 234 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO A 235 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 79 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C LEU A 79 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU A 79 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 80 " -0.017 2.00e-02 2.50e+03 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 116 2.62 - 3.19: 6205 3.19 - 3.76: 9700 3.76 - 4.33: 13152 4.33 - 4.90: 21079 Nonbonded interactions: 50252 Sorted by model distance: nonbonded pdb=" O ARG A 393 " pdb=" OD1 ASN A 394 " model vdw 2.052 3.040 nonbonded pdb=" CE2 TYR A 381 " pdb=" CE2 TYR A 385 " model vdw 2.314 3.640 nonbonded pdb=" N ASN A 397 " pdb=" O ASN A 397 " model vdw 2.334 2.496 nonbonded pdb=" O SER A 122 " pdb=" OG1 THR A 125 " model vdw 2.353 3.040 nonbonded pdb=" OD1 ASN B 477 " pdb=" N LYS B 478 " model vdw 2.378 3.120 ... (remaining 50247 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 : 0.019 0.468 6627 Z= 1.362 Angle : 1.706 22.501 9008 Z= 1.185 Chirality : 0.152 0.684 933 Planarity : 0.009 0.075 1168 Dihedral : 16.407 86.332 2397 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 5.31 % Allowed : 13.06 % Favored : 81.64 % Cbeta Deviations : 1.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.29), residues: 787 helix: 3.20 (0.25), residues: 370 sheet: 0.73 (0.98), residues: 27 loop : 0.10 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 457 TYR 0.031 0.003 TYR A 183 PHE 0.029 0.003 PHE B 375 TRP 0.029 0.003 TRP A 163 HIS 0.013 0.002 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.01796 ( 6624) covalent geometry : angle 1.68015 ( 9006) SS BOND : bond 0.46752 ( 1) SS BOND : angle 20.00262 ( 2) hydrogen bonds : bond 0.30578 ( 304) hydrogen bonds : angle 7.74407 ( 873) metal coordination : bond 0.14965 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 500 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7571 (p) REVERT: A 37 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6887 (mt-10) REVERT: A 38 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: A 39 LEU cc_start: 0.7957 (mp) cc_final: 0.7705 (mm) REVERT: A 53 ASN cc_start: 0.5984 (t0) cc_final: 0.5610 (t0) REVERT: A 181 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6675 (mt-10) REVERT: A 208 GLU cc_start: 0.6843 (tt0) cc_final: 0.6634 (tt0) REVERT: A 283 VAL cc_start: 0.8621 (t) cc_final: 0.8254 (m) REVERT: A 336 PRO cc_start: 0.7962 (Cg_exo) cc_final: 0.7756 (Cg_endo) REVERT: A 358 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7058 (tt) REVERT: A 462 MET cc_start: 0.7460 (mtt) cc_final: 0.7250 (mtt) REVERT: A 495 GLU cc_start: 0.7141 (tp30) cc_final: 0.6591 (mm-30) REVERT: A 520 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 532 ILE cc_start: 0.8639 (mt) cc_final: 0.8057 (mt) outliers start: 37 outliers final: 9 residues processed: 325 average time/residue: 0.0999 time to fit residues: 41.0989 Evaluate side-chains 267 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 553 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 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: B 414 GLN B 450 ASN B 474 GLN A 89 GLN A 228 HIS A 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104042 restraints weight = 11626.434| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.84 r_work: 0.3192 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6627 Z= 0.171 Angle : 0.624 6.180 9008 Z= 0.348 Chirality : 0.044 0.155 933 Planarity : 0.006 0.057 1168 Dihedral : 6.911 58.538 896 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.44 % Allowed : 19.51 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.30), residues: 787 helix: 2.50 (0.26), residues: 384 sheet: 0.37 (0.96), residues: 27 loop : -0.14 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.020 0.002 TYR B 451 PHE 0.015 0.002 PHE A 285 TRP 0.016 0.002 TRP A 163 HIS 0.006 0.002 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6624) covalent geometry : angle 0.62390 ( 9006) SS BOND : bond 0.00240 ( 1) SS BOND : angle 1.17772 ( 2) hydrogen bonds : bond 0.07445 ( 304) hydrogen bonds : angle 5.22681 ( 873) metal coordination : bond 0.00600 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8466 (tttm) cc_final: 0.8102 (tttm) REVERT: B 380 TYR cc_start: 0.8186 (m-80) cc_final: 0.7724 (m-10) REVERT: B 403 ARG cc_start: 0.8141 (ttm170) cc_final: 0.7722 (ttm-80) REVERT: B 509 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7847 (mtt180) REVERT: A 21 THR cc_start: 0.8256 (m) cc_final: 0.8043 (p) REVERT: A 34 TYR cc_start: 0.7887 (m-10) cc_final: 0.7685 (m-80) REVERT: A 35 GLU cc_start: 0.8472 (tp30) cc_final: 0.7913 (tp30) REVERT: A 38 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7136 (pm20) REVERT: A 87 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 121 ASN cc_start: 0.8477 (m-40) cc_final: 0.8258 (m-40) REVERT: A 134 ASN cc_start: 0.8280 (t0) cc_final: 0.8042 (t0) REVERT: A 142 LEU cc_start: 0.8391 (mt) cc_final: 0.8120 (mt) REVERT: A 148 LEU cc_start: 0.8307 (mt) cc_final: 0.8090 (mt) REVERT: A 152 MET cc_start: 0.8429 (mmt) cc_final: 0.8025 (mmt) REVERT: A 153 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7727 (pp20) REVERT: A 156 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8192 (mtmm) REVERT: A 161 ARG cc_start: 0.8492 (mtt-85) cc_final: 0.7981 (mtt-85) REVERT: A 166 GLU cc_start: 0.8003 (tp30) cc_final: 0.7662 (tp30) REVERT: A 174 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8268 (tppt) REVERT: A 190 MET cc_start: 0.8303 (tmm) cc_final: 0.8012 (tmm) REVERT: A 208 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: A 209 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7418 (mm-30) REVERT: A 283 VAL cc_start: 0.8637 (t) cc_final: 0.8352 (m) REVERT: A 312 GLU cc_start: 0.8123 (tt0) cc_final: 0.7877 (tm-30) REVERT: A 322 ASN cc_start: 0.6320 (p0) cc_final: 0.5772 (p0) REVERT: A 400 PHE cc_start: 0.8208 (m-10) cc_final: 0.7806 (m-80) REVERT: A 439 LEU cc_start: 0.8420 (mt) cc_final: 0.8137 (mm) REVERT: A 455 MET cc_start: 0.7986 (tmm) cc_final: 0.7596 (tmm) REVERT: A 462 MET cc_start: 0.8581 (mtt) cc_final: 0.8303 (mtp) REVERT: A 496 THR cc_start: 0.8479 (p) cc_final: 0.7954 (t) REVERT: A 534 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8412 (mmmm) REVERT: A 553 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8288 (tptm) REVERT: A 562 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8456 (ttmt) REVERT: A 585 LEU cc_start: 0.8830 (mp) cc_final: 0.8552 (mm) outliers start: 24 outliers final: 10 residues processed: 267 average time/residue: 0.0928 time to fit residues: 31.5030 Evaluate side-chains 246 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103106 restraints weight = 11705.238| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.89 r_work: 0.3169 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6627 Z= 0.144 Angle : 0.549 6.324 9008 Z= 0.299 Chirality : 0.042 0.140 933 Planarity : 0.005 0.048 1168 Dihedral : 6.188 59.510 877 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.58 % Allowed : 21.66 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.30), residues: 787 helix: 2.49 (0.26), residues: 384 sheet: 0.27 (0.93), residues: 25 loop : -0.15 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 600 TYR 0.021 0.001 TYR A 385 PHE 0.017 0.002 PHE B 497 TRP 0.011 0.001 TRP A 606 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6624) covalent geometry : angle 0.54887 ( 9006) SS BOND : bond 0.00333 ( 1) SS BOND : angle 1.49543 ( 2) hydrogen bonds : bond 0.06129 ( 304) hydrogen bonds : angle 4.72750 ( 873) metal coordination : bond 0.00312 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8503 (tttm) cc_final: 0.8133 (tttm) REVERT: B 378 LYS cc_start: 0.8253 (pttt) cc_final: 0.7810 (pttt) REVERT: B 380 TYR cc_start: 0.8044 (m-80) cc_final: 0.7743 (m-10) REVERT: B 403 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7707 (ttm-80) REVERT: B 460 ASN cc_start: 0.7878 (t0) cc_final: 0.7641 (t0) REVERT: B 462 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8351 (mmmt) REVERT: A 30 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 34 TYR cc_start: 0.7845 (m-10) cc_final: 0.7471 (m-80) REVERT: A 35 GLU cc_start: 0.8423 (tp30) cc_final: 0.8027 (tp30) REVERT: A 38 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: A 81 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8587 (mmtp) REVERT: A 142 LEU cc_start: 0.8383 (mt) cc_final: 0.8133 (mt) REVERT: A 152 MET cc_start: 0.8542 (mmt) cc_final: 0.8110 (mmt) REVERT: A 153 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7668 (pp20) REVERT: A 161 ARG cc_start: 0.8521 (mtt-85) cc_final: 0.8080 (mtt-85) REVERT: A 166 GLU cc_start: 0.7932 (tp30) cc_final: 0.7576 (tp30) REVERT: A 174 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8196 (ttmm) REVERT: A 188 ASN cc_start: 0.8414 (t0) cc_final: 0.8028 (t0) REVERT: A 190 MET cc_start: 0.8305 (tmm) cc_final: 0.8070 (tmm) REVERT: A 208 GLU cc_start: 0.8070 (tt0) cc_final: 0.7860 (tt0) REVERT: A 305 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7777 (mtp85) REVERT: A 312 GLU cc_start: 0.8103 (tt0) cc_final: 0.7860 (tm-30) REVERT: A 322 ASN cc_start: 0.6321 (p0) cc_final: 0.5760 (p0) REVERT: A 347 THR cc_start: 0.8498 (m) cc_final: 0.8033 (p) REVERT: A 362 THR cc_start: 0.8662 (m) cc_final: 0.8255 (p) REVERT: A 371 THR cc_start: 0.8515 (m) cc_final: 0.8280 (p) REVERT: A 439 LEU cc_start: 0.8436 (mt) cc_final: 0.8161 (mm) REVERT: A 455 MET cc_start: 0.7992 (tmm) cc_final: 0.7532 (tmm) REVERT: A 462 MET cc_start: 0.8569 (mtt) cc_final: 0.8238 (mtp) REVERT: A 527 GLU cc_start: 0.8446 (tt0) cc_final: 0.8063 (tp30) REVERT: A 553 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8273 (tptp) REVERT: A 562 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8484 (ttmt) outliers start: 18 outliers final: 10 residues processed: 236 average time/residue: 0.0976 time to fit residues: 29.4549 Evaluate side-chains 229 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 483 ASN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104126 restraints weight = 11675.906| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.88 r_work: 0.3171 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6627 Z= 0.127 Angle : 0.521 5.718 9008 Z= 0.279 Chirality : 0.040 0.147 933 Planarity : 0.004 0.042 1168 Dihedral : 5.885 58.882 877 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.58 % Allowed : 24.25 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.30), residues: 787 helix: 2.52 (0.26), residues: 378 sheet: 0.43 (0.98), residues: 25 loop : -0.19 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.020 0.001 TYR A 385 PHE 0.020 0.001 PHE B 497 TRP 0.011 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6624) covalent geometry : angle 0.52081 ( 9006) SS BOND : bond 0.00218 ( 1) SS BOND : angle 1.39096 ( 2) hydrogen bonds : bond 0.05310 ( 304) hydrogen bonds : angle 4.52291 ( 873) metal coordination : bond 0.00150 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8527 (tttm) cc_final: 0.8132 (tttm) REVERT: B 403 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7713 (ttm-80) REVERT: B 462 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8295 (mmmt) REVERT: A 30 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 34 TYR cc_start: 0.7843 (m-10) cc_final: 0.7428 (m-80) REVERT: A 35 GLU cc_start: 0.8410 (tp30) cc_final: 0.8052 (tp30) REVERT: A 38 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: A 75 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8088 (tp30) REVERT: A 81 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8579 (tppt) REVERT: A 142 LEU cc_start: 0.8392 (mt) cc_final: 0.8145 (mt) REVERT: A 152 MET cc_start: 0.8554 (mmt) cc_final: 0.8150 (mmt) REVERT: A 153 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7756 (pp20) REVERT: A 161 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.8091 (mtt-85) REVERT: A 166 GLU cc_start: 0.7940 (tp30) cc_final: 0.7552 (tp30) REVERT: A 174 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8200 (mttm) REVERT: A 188 ASN cc_start: 0.8432 (t0) cc_final: 0.8071 (t0) REVERT: A 190 MET cc_start: 0.8313 (tmm) cc_final: 0.8087 (tmm) REVERT: A 197 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7112 (mt-10) REVERT: A 279 TYR cc_start: 0.8479 (t80) cc_final: 0.8240 (t80) REVERT: A 305 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7669 (ttt-90) REVERT: A 322 ASN cc_start: 0.6306 (p0) cc_final: 0.5895 (p0) REVERT: A 347 THR cc_start: 0.8506 (m) cc_final: 0.8151 (p) REVERT: A 362 THR cc_start: 0.8549 (m) cc_final: 0.8194 (p) REVERT: A 371 THR cc_start: 0.8487 (m) cc_final: 0.8223 (p) REVERT: A 439 LEU cc_start: 0.8458 (mt) cc_final: 0.8171 (mm) REVERT: A 455 MET cc_start: 0.8087 (tmm) cc_final: 0.7541 (tmm) REVERT: A 462 MET cc_start: 0.8589 (mtt) cc_final: 0.8273 (mtp) REVERT: A 527 GLU cc_start: 0.8388 (tt0) cc_final: 0.8181 (tp30) REVERT: A 553 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8233 (tptp) REVERT: A 562 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8633 (ttpt) outliers start: 18 outliers final: 9 residues processed: 239 average time/residue: 0.0902 time to fit residues: 27.9591 Evaluate side-chains 229 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 553 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN A 63 ASN A 325 GLN A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098792 restraints weight = 11797.446| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.93 r_work: 0.3093 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6627 Z= 0.179 Angle : 0.550 6.241 9008 Z= 0.300 Chirality : 0.042 0.167 933 Planarity : 0.005 0.040 1168 Dihedral : 5.721 58.406 875 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.58 % Allowed : 26.26 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.30), residues: 787 helix: 2.33 (0.26), residues: 385 sheet: 0.71 (1.09), residues: 25 loop : -0.29 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 600 TYR 0.021 0.002 TYR A 385 PHE 0.024 0.002 PHE B 497 TRP 0.012 0.002 TRP A 163 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6624) covalent geometry : angle 0.54973 ( 9006) SS BOND : bond 0.00100 ( 1) SS BOND : angle 1.34986 ( 2) hydrogen bonds : bond 0.06437 ( 304) hydrogen bonds : angle 4.57172 ( 873) metal coordination : bond 0.00549 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.7935 (m-80) cc_final: 0.7491 (m-80) REVERT: B 356 LYS cc_start: 0.8611 (tttm) cc_final: 0.8237 (tttm) REVERT: B 400 PHE cc_start: 0.7738 (p90) cc_final: 0.7485 (p90) REVERT: B 403 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7834 (ttm-80) REVERT: B 444 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8414 (mtpp) REVERT: B 462 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8321 (mmmt) REVERT: A 35 GLU cc_start: 0.8502 (tp30) cc_final: 0.8199 (tp30) REVERT: A 38 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: A 72 PHE cc_start: 0.8912 (t80) cc_final: 0.8657 (t80) REVERT: A 75 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8238 (tp30) REVERT: A 81 LYS cc_start: 0.8919 (mmtp) cc_final: 0.8548 (mmtp) REVERT: A 142 LEU cc_start: 0.8434 (mt) cc_final: 0.8169 (mt) REVERT: A 152 MET cc_start: 0.8665 (mmt) cc_final: 0.8303 (mmt) REVERT: A 153 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7692 (pp20) REVERT: A 161 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8096 (mtt-85) REVERT: A 162 LEU cc_start: 0.8367 (tp) cc_final: 0.8123 (tt) REVERT: A 166 GLU cc_start: 0.8046 (tp30) cc_final: 0.7633 (tp30) REVERT: A 190 MET cc_start: 0.8364 (tmm) cc_final: 0.8113 (tmm) REVERT: A 197 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 207 TYR cc_start: 0.8466 (m-80) cc_final: 0.8069 (m-80) REVERT: A 279 TYR cc_start: 0.8587 (t80) cc_final: 0.8326 (t80) REVERT: A 322 ASN cc_start: 0.5992 (p0) cc_final: 0.5605 (p0) REVERT: A 325 GLN cc_start: 0.8163 (mp10) cc_final: 0.7939 (mm-40) REVERT: A 357 ARG cc_start: 0.8304 (ttm170) cc_final: 0.8059 (mtp85) REVERT: A 371 THR cc_start: 0.8590 (m) cc_final: 0.8259 (p) REVERT: A 397 ASN cc_start: 0.8272 (p0) cc_final: 0.8024 (p0) REVERT: A 441 LYS cc_start: 0.8866 (tttt) cc_final: 0.8592 (tttm) REVERT: A 455 MET cc_start: 0.8183 (tmm) cc_final: 0.7859 (tmm) REVERT: A 462 MET cc_start: 0.8639 (mtt) cc_final: 0.8338 (mtp) REVERT: A 527 GLU cc_start: 0.8394 (tt0) cc_final: 0.8191 (tp30) REVERT: A 562 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8645 (ttpt) outliers start: 18 outliers final: 14 residues processed: 242 average time/residue: 0.0906 time to fit residues: 28.5184 Evaluate side-chains 249 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.0970 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099738 restraints weight = 11793.858| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.92 r_work: 0.3126 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6627 Z= 0.134 Angle : 0.524 6.874 9008 Z= 0.282 Chirality : 0.041 0.187 933 Planarity : 0.004 0.042 1168 Dihedral : 5.297 59.988 871 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.58 % Allowed : 26.97 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.30), residues: 787 helix: 2.33 (0.26), residues: 389 sheet: 0.78 (1.13), residues: 25 loop : -0.22 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 600 TYR 0.018 0.001 TYR A 385 PHE 0.026 0.001 PHE B 497 TRP 0.011 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6624) covalent geometry : angle 0.52330 ( 9006) SS BOND : bond 0.00196 ( 1) SS BOND : angle 1.51624 ( 2) hydrogen bonds : bond 0.05559 ( 304) hydrogen bonds : angle 4.48313 ( 873) metal coordination : bond 0.00348 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.7954 (m-80) cc_final: 0.7526 (m-80) REVERT: B 356 LYS cc_start: 0.8607 (tttm) cc_final: 0.8209 (tttm) REVERT: B 400 PHE cc_start: 0.7647 (p90) cc_final: 0.7353 (p90) REVERT: B 403 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7832 (ttm-80) REVERT: B 405 ASN cc_start: 0.8756 (p0) cc_final: 0.8491 (p0) REVERT: B 408 SER cc_start: 0.9095 (m) cc_final: 0.8794 (t) REVERT: B 444 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8420 (mtpp) REVERT: B 462 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8291 (mmmt) REVERT: A 35 GLU cc_start: 0.8406 (tp30) cc_final: 0.8192 (tp30) REVERT: A 75 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8313 (tp30) REVERT: A 142 LEU cc_start: 0.8431 (mt) cc_final: 0.8173 (mt) REVERT: A 144 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8128 (tp) REVERT: A 152 MET cc_start: 0.8626 (mmt) cc_final: 0.8337 (mmt) REVERT: A 153 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7682 (pp20) REVERT: A 161 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8097 (mtt-85) REVERT: A 166 GLU cc_start: 0.7979 (tp30) cc_final: 0.7546 (tp30) REVERT: A 190 MET cc_start: 0.8324 (tmm) cc_final: 0.8096 (tmm) REVERT: A 197 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7176 (mt-10) REVERT: A 207 TYR cc_start: 0.8417 (m-80) cc_final: 0.8080 (m-80) REVERT: A 279 TYR cc_start: 0.8558 (t80) cc_final: 0.8342 (t80) REVERT: A 322 ASN cc_start: 0.5975 (p0) cc_final: 0.5604 (p0) REVERT: A 325 GLN cc_start: 0.8189 (mp10) cc_final: 0.7971 (mm-40) REVERT: A 332 MET cc_start: 0.8295 (ttp) cc_final: 0.8072 (ptp) REVERT: A 347 THR cc_start: 0.8488 (m) cc_final: 0.8081 (p) REVERT: A 357 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7593 (mtt180) REVERT: A 360 MET cc_start: 0.8265 (ttp) cc_final: 0.7874 (ttt) REVERT: A 371 THR cc_start: 0.8519 (m) cc_final: 0.8170 (p) REVERT: A 397 ASN cc_start: 0.8166 (p0) cc_final: 0.7951 (p0) REVERT: A 441 LYS cc_start: 0.8832 (tttt) cc_final: 0.8618 (tttm) REVERT: A 455 MET cc_start: 0.8172 (tmm) cc_final: 0.7806 (tmm) REVERT: A 462 MET cc_start: 0.8654 (mtt) cc_final: 0.8333 (mtp) REVERT: A 474 MET cc_start: 0.7633 (mmm) cc_final: 0.7408 (mmm) REVERT: A 516 TYR cc_start: 0.8651 (t80) cc_final: 0.8398 (t80) REVERT: A 527 GLU cc_start: 0.8360 (tt0) cc_final: 0.8159 (tp30) REVERT: A 595 LEU cc_start: 0.8547 (mt) cc_final: 0.8192 (mp) outliers start: 18 outliers final: 12 residues processed: 242 average time/residue: 0.0827 time to fit residues: 26.3086 Evaluate side-chains 237 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 589 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 508 ASN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100499 restraints weight = 11722.933| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.91 r_work: 0.3142 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6627 Z= 0.124 Angle : 0.532 9.501 9008 Z= 0.280 Chirality : 0.041 0.226 933 Planarity : 0.004 0.041 1168 Dihedral : 4.948 59.270 868 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.87 % Allowed : 27.12 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.30), residues: 787 helix: 2.41 (0.26), residues: 386 sheet: 0.93 (1.21), residues: 25 loop : -0.28 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 600 TYR 0.018 0.001 TYR A 385 PHE 0.026 0.001 PHE B 497 TRP 0.010 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6624) covalent geometry : angle 0.53171 ( 9006) SS BOND : bond 0.00153 ( 1) SS BOND : angle 1.42816 ( 2) hydrogen bonds : bond 0.05165 ( 304) hydrogen bonds : angle 4.45242 ( 873) metal coordination : bond 0.00270 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.7954 (m-80) cc_final: 0.7520 (m-80) REVERT: B 356 LYS cc_start: 0.8613 (tttm) cc_final: 0.8241 (tttm) REVERT: B 400 PHE cc_start: 0.7620 (p90) cc_final: 0.7334 (p90) REVERT: B 403 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7884 (ttm-80) REVERT: B 408 SER cc_start: 0.9068 (m) cc_final: 0.8743 (t) REVERT: B 444 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8417 (mtpp) REVERT: B 462 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8286 (mmmt) REVERT: A 35 GLU cc_start: 0.8396 (tp30) cc_final: 0.8157 (tp30) REVERT: A 69 TRP cc_start: 0.8769 (t-100) cc_final: 0.8511 (t-100) REVERT: A 75 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8344 (tp30) REVERT: A 142 LEU cc_start: 0.8437 (mt) cc_final: 0.8182 (mt) REVERT: A 152 MET cc_start: 0.8656 (mmt) cc_final: 0.8384 (mmt) REVERT: A 153 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: A 161 ARG cc_start: 0.8524 (mtt-85) cc_final: 0.8107 (mtt-85) REVERT: A 166 GLU cc_start: 0.7957 (tp30) cc_final: 0.7517 (tp30) REVERT: A 174 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8208 (mmtt) REVERT: A 207 TYR cc_start: 0.8424 (m-80) cc_final: 0.8072 (m-80) REVERT: A 279 TYR cc_start: 0.8565 (t80) cc_final: 0.8351 (t80) REVERT: A 322 ASN cc_start: 0.6090 (p0) cc_final: 0.5716 (p0) REVERT: A 325 GLN cc_start: 0.8184 (mp10) cc_final: 0.7971 (mm-40) REVERT: A 347 THR cc_start: 0.8487 (m) cc_final: 0.8059 (p) REVERT: A 357 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7628 (mtt180) REVERT: A 360 MET cc_start: 0.8215 (ttp) cc_final: 0.7819 (ttt) REVERT: A 366 MET cc_start: 0.7268 (mtp) cc_final: 0.7040 (mtm) REVERT: A 371 THR cc_start: 0.8478 (m) cc_final: 0.8112 (p) REVERT: A 397 ASN cc_start: 0.8086 (p0) cc_final: 0.7879 (p0) REVERT: A 455 MET cc_start: 0.8179 (tmm) cc_final: 0.7929 (tmm) REVERT: A 462 MET cc_start: 0.8652 (mtt) cc_final: 0.8316 (mtp) REVERT: A 474 MET cc_start: 0.7678 (mmm) cc_final: 0.7465 (mmm) REVERT: A 516 TYR cc_start: 0.8643 (t80) cc_final: 0.8395 (t80) REVERT: A 595 LEU cc_start: 0.8529 (mt) cc_final: 0.8186 (mp) outliers start: 20 outliers final: 13 residues processed: 242 average time/residue: 0.0886 time to fit residues: 27.6355 Evaluate side-chains 240 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 589 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 228 HIS A 330 ASN A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098979 restraints weight = 11740.919| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.91 r_work: 0.3120 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6627 Z= 0.150 Angle : 0.574 9.901 9008 Z= 0.300 Chirality : 0.041 0.227 933 Planarity : 0.005 0.065 1168 Dihedral : 4.978 58.305 868 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.01 % Allowed : 26.97 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.30), residues: 787 helix: 2.40 (0.27), residues: 386 sheet: 0.72 (1.13), residues: 25 loop : -0.32 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 457 TYR 0.019 0.001 TYR A 385 PHE 0.029 0.002 PHE B 497 TRP 0.010 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6624) covalent geometry : angle 0.57375 ( 9006) SS BOND : bond 0.00136 ( 1) SS BOND : angle 1.41594 ( 2) hydrogen bonds : bond 0.05667 ( 304) hydrogen bonds : angle 4.52933 ( 873) metal coordination : bond 0.00414 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.7989 (m-80) cc_final: 0.7520 (m-80) REVERT: B 357 ARG cc_start: 0.7501 (mmm-85) cc_final: 0.6549 (tpp-160) REVERT: B 400 PHE cc_start: 0.7635 (p90) cc_final: 0.7366 (p90) REVERT: B 403 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7860 (ttm-80) REVERT: B 408 SER cc_start: 0.9120 (m) cc_final: 0.8820 (t) REVERT: B 409 GLN cc_start: 0.8269 (mt0) cc_final: 0.8006 (tt0) REVERT: B 444 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8428 (mtpp) REVERT: B 462 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8291 (mmmt) REVERT: A 35 GLU cc_start: 0.8416 (tp30) cc_final: 0.8167 (tp30) REVERT: A 69 TRP cc_start: 0.8782 (t-100) cc_final: 0.8535 (t-100) REVERT: A 75 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8382 (tp30) REVERT: A 86 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8012 (mp0) REVERT: A 126 ILE cc_start: 0.8995 (mt) cc_final: 0.8698 (tt) REVERT: A 142 LEU cc_start: 0.8457 (mt) cc_final: 0.8223 (mt) REVERT: A 152 MET cc_start: 0.8675 (mmt) cc_final: 0.8419 (mmt) REVERT: A 153 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: A 161 ARG cc_start: 0.8551 (mtt-85) cc_final: 0.8134 (mtt-85) REVERT: A 166 GLU cc_start: 0.7965 (tp30) cc_final: 0.7539 (tp30) REVERT: A 207 TYR cc_start: 0.8435 (m-80) cc_final: 0.8025 (m-80) REVERT: A 322 ASN cc_start: 0.6135 (p0) cc_final: 0.5722 (p0) REVERT: A 325 GLN cc_start: 0.8190 (mp10) cc_final: 0.7970 (mm-40) REVERT: A 347 THR cc_start: 0.8484 (m) cc_final: 0.8030 (p) REVERT: A 357 ARG cc_start: 0.8287 (ttm170) cc_final: 0.7671 (mtt180) REVERT: A 366 MET cc_start: 0.7334 (mtp) cc_final: 0.7112 (ttm) REVERT: A 371 THR cc_start: 0.8517 (m) cc_final: 0.8179 (p) REVERT: A 436 ILE cc_start: 0.8337 (mm) cc_final: 0.8121 (tt) REVERT: A 455 MET cc_start: 0.8199 (tmm) cc_final: 0.7526 (tmm) REVERT: A 470 LYS cc_start: 0.8262 (mtpp) cc_final: 0.8023 (ttmm) REVERT: A 516 TYR cc_start: 0.8676 (t80) cc_final: 0.8434 (t80) REVERT: A 553 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8343 (mmtt) REVERT: A 595 LEU cc_start: 0.8540 (mt) cc_final: 0.8182 (mp) outliers start: 21 outliers final: 15 residues processed: 234 average time/residue: 0.0918 time to fit residues: 27.7869 Evaluate side-chains 238 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 589 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.097753 restraints weight = 11821.041| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.87 r_work: 0.3099 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6627 Z= 0.181 Angle : 0.589 10.337 9008 Z= 0.312 Chirality : 0.042 0.190 933 Planarity : 0.005 0.040 1168 Dihedral : 5.055 58.106 868 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.59 % Allowed : 26.54 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.30), residues: 787 helix: 2.25 (0.26), residues: 389 sheet: 0.70 (1.04), residues: 25 loop : -0.46 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 600 TYR 0.020 0.001 TYR A 385 PHE 0.030 0.002 PHE B 497 TRP 0.011 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6624) covalent geometry : angle 0.58833 ( 9006) SS BOND : bond 0.00146 ( 1) SS BOND : angle 1.51947 ( 2) hydrogen bonds : bond 0.06306 ( 304) hydrogen bonds : angle 4.56682 ( 873) metal coordination : bond 0.00525 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.7976 (m-80) cc_final: 0.7523 (m-10) REVERT: B 400 PHE cc_start: 0.7641 (p90) cc_final: 0.7396 (p90) REVERT: B 403 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7839 (ttm-80) REVERT: B 408 SER cc_start: 0.9119 (m) cc_final: 0.8766 (t) REVERT: B 409 GLN cc_start: 0.8275 (mt0) cc_final: 0.8042 (tt0) REVERT: B 410 ILE cc_start: 0.8715 (mm) cc_final: 0.8515 (mm) REVERT: B 444 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8421 (mtpp) REVERT: B 462 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8309 (mmmt) REVERT: A 35 GLU cc_start: 0.8445 (tp30) cc_final: 0.8200 (tp30) REVERT: A 69 TRP cc_start: 0.8821 (t-100) cc_final: 0.8588 (t-100) REVERT: A 75 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8434 (tp30) REVERT: A 126 ILE cc_start: 0.9036 (mt) cc_final: 0.8740 (tt) REVERT: A 152 MET cc_start: 0.8682 (mmt) cc_final: 0.8453 (mmt) REVERT: A 153 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: A 161 ARG cc_start: 0.8550 (mtt-85) cc_final: 0.8129 (mtt-85) REVERT: A 166 GLU cc_start: 0.8008 (tp30) cc_final: 0.7549 (tp30) REVERT: A 174 LYS cc_start: 0.8545 (mttm) cc_final: 0.8314 (mmtt) REVERT: A 207 TYR cc_start: 0.8440 (m-80) cc_final: 0.8018 (m-80) REVERT: A 322 ASN cc_start: 0.6140 (p0) cc_final: 0.5710 (p0) REVERT: A 325 GLN cc_start: 0.8184 (mp10) cc_final: 0.7967 (mm-40) REVERT: A 357 ARG cc_start: 0.8313 (ttm170) cc_final: 0.7664 (mtt180) REVERT: A 360 MET cc_start: 0.8219 (ttp) cc_final: 0.7815 (ttt) REVERT: A 371 THR cc_start: 0.8552 (m) cc_final: 0.8154 (p) REVERT: A 436 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8137 (tt) REVERT: A 455 MET cc_start: 0.8206 (tmm) cc_final: 0.7953 (tmm) REVERT: A 462 MET cc_start: 0.8721 (mtt) cc_final: 0.8476 (mtp) REVERT: A 474 MET cc_start: 0.7746 (mmm) cc_final: 0.7506 (mmm) REVERT: A 516 TYR cc_start: 0.8723 (t80) cc_final: 0.8502 (t80) REVERT: A 553 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8286 (mmtt) REVERT: A 595 LEU cc_start: 0.8571 (mt) cc_final: 0.8210 (mp) outliers start: 25 outliers final: 17 residues processed: 233 average time/residue: 0.0904 time to fit residues: 27.3751 Evaluate side-chains 245 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 589 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.0070 chunk 1 optimal weight: 0.0030 chunk 77 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.0952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103099 restraints weight = 11713.052| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.91 r_work: 0.3192 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6627 Z= 0.121 Angle : 0.567 9.877 9008 Z= 0.296 Chirality : 0.040 0.153 933 Planarity : 0.004 0.044 1168 Dihedral : 4.681 53.876 868 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.15 % Allowed : 28.12 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.30), residues: 787 helix: 2.34 (0.27), residues: 385 sheet: 0.63 (0.89), residues: 33 loop : -0.34 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 600 TYR 0.015 0.001 TYR A 50 PHE 0.030 0.001 PHE B 497 TRP 0.009 0.001 TRP A 48 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6624) covalent geometry : angle 0.56696 ( 9006) SS BOND : bond 0.00169 ( 1) SS BOND : angle 1.45500 ( 2) hydrogen bonds : bond 0.04289 ( 304) hydrogen bonds : angle 4.47603 ( 873) metal coordination : bond 0.00087 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.7959 (m-80) cc_final: 0.7504 (m-10) REVERT: B 354 ASN cc_start: 0.6603 (m-40) cc_final: 0.6399 (m-40) REVERT: B 403 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7867 (ttm-80) REVERT: B 408 SER cc_start: 0.9036 (m) cc_final: 0.8719 (t) REVERT: B 409 GLN cc_start: 0.8158 (mt0) cc_final: 0.7863 (tt0) REVERT: B 444 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8381 (mtpp) REVERT: B 462 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8270 (mmmt) REVERT: A 35 GLU cc_start: 0.8250 (tp30) cc_final: 0.7982 (tp30) REVERT: A 69 TRP cc_start: 0.8787 (t-100) cc_final: 0.8568 (t-100) REVERT: A 75 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8360 (tp30) REVERT: A 86 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8135 (mm-30) REVERT: A 153 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7555 (pp20) REVERT: A 161 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.8079 (mtt-85) REVERT: A 166 GLU cc_start: 0.7883 (tp30) cc_final: 0.7448 (tp30) REVERT: A 174 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8137 (mmtt) REVERT: A 209 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7401 (mm-30) REVERT: A 266 LEU cc_start: 0.8745 (mt) cc_final: 0.8501 (tt) REVERT: A 322 ASN cc_start: 0.6061 (p0) cc_final: 0.5713 (p0) REVERT: A 347 THR cc_start: 0.8427 (m) cc_final: 0.7980 (p) REVERT: A 360 MET cc_start: 0.8210 (ttp) cc_final: 0.7741 (ttt) REVERT: A 371 THR cc_start: 0.8286 (m) cc_final: 0.7970 (p) REVERT: A 455 MET cc_start: 0.8134 (tmm) cc_final: 0.7853 (tmm) REVERT: A 462 MET cc_start: 0.8721 (mtt) cc_final: 0.8490 (mtp) REVERT: A 470 LYS cc_start: 0.8539 (ttpp) cc_final: 0.8127 (ttpp) REVERT: A 472 GLN cc_start: 0.7974 (mt0) cc_final: 0.7725 (mt0) REVERT: A 474 MET cc_start: 0.7676 (mmm) cc_final: 0.7423 (mmm) REVERT: A 516 TYR cc_start: 0.8623 (t80) cc_final: 0.8414 (t80) REVERT: A 595 LEU cc_start: 0.8494 (mt) cc_final: 0.8163 (mp) REVERT: A 597 GLU cc_start: 0.8244 (tt0) cc_final: 0.7882 (tt0) outliers start: 15 outliers final: 10 residues processed: 234 average time/residue: 0.0874 time to fit residues: 26.6731 Evaluate side-chains 233 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 531 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 59 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 0.0670 overall best weight: 1.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099380 restraints weight = 11685.189| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.91 r_work: 0.3128 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6627 Z= 0.161 Angle : 0.601 9.642 9008 Z= 0.313 Chirality : 0.042 0.217 933 Planarity : 0.004 0.037 1168 Dihedral : 4.581 52.555 866 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.43 % Allowed : 29.84 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.30), residues: 787 helix: 2.26 (0.27), residues: 389 sheet: 0.68 (1.02), residues: 25 loop : -0.39 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 600 TYR 0.018 0.001 TYR A 385 PHE 0.032 0.002 PHE B 497 TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6624) covalent geometry : angle 0.60101 ( 9006) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.48031 ( 2) hydrogen bonds : bond 0.05577 ( 304) hydrogen bonds : angle 4.54412 ( 873) metal coordination : bond 0.00474 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1639.22 seconds wall clock time: 28 minutes 47.36 seconds (1727.36 seconds total)