Starting phenix.real_space_refine on Sat Jul 20 13:10:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzd_38793/07_2024/8xzd_38793_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzd_38793/07_2024/8xzd_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzd_38793/07_2024/8xzd_38793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzd_38793/07_2024/8xzd_38793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzd_38793/07_2024/8xzd_38793_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzd_38793/07_2024/8xzd_38793_neut.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: 4.39, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.72 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: 1.83 Time building geometry restraints manager: 2.76 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: 99.05 - 106.82: 329 106.82 - 114.60: 3418 114.60 - 122.38: 4513 122.38 - 130.16: 671 130.16 - 137.93: 75 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 2.440 nonbonded pdb=" OD1 ASN B 477 " pdb=" N LYS B 478 " model vdw 2.378 2.520 ... (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 ========== 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.370 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.620 ------------------------------------------------------------------------------- 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 : 0.018 0.075 6624 Z= 1.165 Angle : 1.680 13.066 9006 Z= 1.177 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.029 0.003 TRP A 163 HIS 0.013 0.002 HIS A 540 PHE 0.029 0.003 PHE B 375 TYR 0.031 0.003 TYR A 183 ARG 0.006 0.001 ARG B 457 *********************** 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 fitting. rotamer outliers: 37 poor density : 311 time to evaluate : 0.723 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: 0.7572 (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: 0.5609 (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: 0.7757 (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: 0.7251 (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: 0.2224 time to fit residues: 91.1194 Evaluate side-chains 267 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 188 ASN A 228 HIS A 330 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6624 Z= 0.199 Angle : 0.610 6.375 9006 Z= 0.341 Chirality : 0.044 0.151 933 Planarity : 0.006 0.058 1168 Dihedral : 6.883 59.699 896 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.02 % Allowed : 19.66 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.30), residues: 787 helix: 2.64 (0.26), residues: 384 sheet: 0.23 (0.94), residues: 27 loop : -0.17 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 163 HIS 0.006 0.002 HIS A 265 PHE 0.015 0.002 PHE A 285 TYR 0.019 0.002 TYR B 451 ARG 0.003 0.000 ARG A 357 *********************** 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 283 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: B 380 TYR cc_start: 0.7612 (m-80) cc_final: 0.7371 (m-10) REVERT: A 143 LEU cc_start: 0.7706 (tp) cc_final: 0.7450 (mt) REVERT: A 166 GLU cc_start: 0.7074 (tp30) cc_final: 0.6859 (tp30) REVERT: A 181 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6284 (mt-10) REVERT: A 209 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 283 VAL cc_start: 0.8142 (t) cc_final: 0.7777 (m) REVERT: A 323 MET cc_start: 0.7563 (mmm) cc_final: 0.7358 (mmt) REVERT: A 376 MET cc_start: 0.6657 (ttm) cc_final: 0.6443 (ttm) REVERT: A 455 MET cc_start: 0.6543 (tmm) cc_final: 0.6232 (tmm) REVERT: A 470 LYS cc_start: 0.7627 (mtpp) cc_final: 0.7415 (mtpp) REVERT: A 562 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7755 (ttpt) outliers start: 28 outliers final: 13 residues processed: 266 average time/residue: 0.2081 time to fit residues: 69.8732 Evaluate side-chains 244 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 250 ASP 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 371 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 491 VAL 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 39 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 526 GLN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6624 Z= 0.212 Angle : 0.569 6.884 9006 Z= 0.308 Chirality : 0.042 0.154 933 Planarity : 0.005 0.050 1168 Dihedral : 5.583 56.828 870 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.58 % Allowed : 21.38 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.30), residues: 787 helix: 2.59 (0.26), residues: 383 sheet: -0.21 (0.87), residues: 27 loop : -0.15 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.016 0.002 PHE B 490 TYR 0.023 0.001 TYR A 385 ARG 0.007 0.001 ARG B 403 *********************** 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 256 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7314 (ttm170) REVERT: A 29 LEU cc_start: 0.7966 (mt) cc_final: 0.7666 (mp) REVERT: A 35 GLU cc_start: 0.7090 (tp30) cc_final: 0.6756 (tp30) REVERT: A 81 LYS cc_start: 0.8384 (mmtp) cc_final: 0.8113 (mmtp) REVERT: A 134 ASN cc_start: 0.7139 (t0) cc_final: 0.6905 (t0) REVERT: A 166 GLU cc_start: 0.7151 (tp30) cc_final: 0.6923 (tp30) REVERT: A 174 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7059 (mtpt) REVERT: A 188 ASN cc_start: 0.7840 (t0) cc_final: 0.7636 (t0) REVERT: A 269 ASP cc_start: 0.6377 (t70) cc_final: 0.6080 (t70) REVERT: A 276 THR cc_start: 0.8200 (p) cc_final: 0.7982 (t) REVERT: A 323 MET cc_start: 0.7607 (mmm) cc_final: 0.7284 (mmt) REVERT: A 362 THR cc_start: 0.7939 (m) cc_final: 0.7469 (p) REVERT: A 455 MET cc_start: 0.6640 (tmm) cc_final: 0.6414 (tmm) REVERT: A 476 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.7925 (t) REVERT: A 496 THR cc_start: 0.8055 (p) cc_final: 0.7846 (t) REVERT: A 562 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7827 (ttmt) outliers start: 18 outliers final: 11 residues processed: 247 average time/residue: 0.2088 time to fit residues: 65.4483 Evaluate side-chains 231 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 218 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 567 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 ASN A 175 GLN A 483 ASN A 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 6624 Z= 0.439 Angle : 0.657 5.853 9006 Z= 0.366 Chirality : 0.048 0.153 933 Planarity : 0.005 0.047 1168 Dihedral : 5.789 53.736 868 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.45 % Allowed : 22.53 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 787 helix: 2.17 (0.26), residues: 379 sheet: 0.52 (1.10), residues: 25 loop : -0.42 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 163 HIS 0.008 0.002 HIS A 102 PHE 0.023 0.002 PHE B 497 TYR 0.027 0.002 TYR A 385 ARG 0.006 0.001 ARG B 403 *********************** 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 262 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 388 ASN cc_start: 0.3119 (OUTLIER) cc_final: 0.2896 (p0) REVERT: B 444 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7924 (mtpp) REVERT: B 460 ASN cc_start: 0.7764 (t0) cc_final: 0.7518 (t0) REVERT: A 134 ASN cc_start: 0.7549 (t0) cc_final: 0.7296 (t0) REVERT: A 161 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7429 (mtt-85) REVERT: A 166 GLU cc_start: 0.7358 (tp30) cc_final: 0.7063 (tp30) REVERT: A 174 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7307 (mppt) REVERT: A 276 THR cc_start: 0.8250 (p) cc_final: 0.8013 (t) REVERT: A 362 THR cc_start: 0.7690 (m) cc_final: 0.7407 (p) REVERT: A 391 LEU cc_start: 0.8245 (mt) cc_final: 0.7939 (mt) REVERT: A 418 LEU cc_start: 0.8485 (mt) cc_final: 0.8280 (mt) REVERT: A 496 THR cc_start: 0.8159 (p) cc_final: 0.7857 (t) outliers start: 31 outliers final: 24 residues processed: 242 average time/residue: 0.1976 time to fit residues: 61.1370 Evaluate side-chains 248 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 476 THR 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 572 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 589 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.0370 chunk 14 optimal weight: 5.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6624 Z= 0.191 Angle : 0.567 6.299 9006 Z= 0.303 Chirality : 0.041 0.154 933 Planarity : 0.005 0.045 1168 Dihedral : 5.257 50.949 868 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.44 % Allowed : 24.96 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 787 helix: 2.35 (0.27), residues: 378 sheet: 0.43 (1.09), residues: 25 loop : -0.38 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.025 0.001 PHE B 497 TYR 0.021 0.001 TYR A 279 ARG 0.008 0.001 ARG B 403 *********************** 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 250 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8473 (t80) cc_final: 0.8244 (t80) REVERT: A 134 ASN cc_start: 0.7411 (t0) cc_final: 0.7178 (t0) REVERT: A 161 ARG cc_start: 0.7718 (mtp180) cc_final: 0.7351 (mtt-85) REVERT: A 166 GLU cc_start: 0.7188 (tp30) cc_final: 0.6887 (tp30) REVERT: A 276 THR cc_start: 0.8139 (p) cc_final: 0.7890 (p) outliers start: 24 outliers final: 16 residues processed: 236 average time/residue: 0.1950 time to fit residues: 58.9385 Evaluate side-chains 236 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 220 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 531 GLN 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 44 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.0270 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 175 GLN A 508 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6624 Z= 0.216 Angle : 0.590 8.953 9006 Z= 0.311 Chirality : 0.042 0.163 933 Planarity : 0.004 0.042 1168 Dihedral : 5.200 49.557 868 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.02 % Allowed : 24.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.30), residues: 787 helix: 2.32 (0.27), residues: 378 sheet: 0.39 (1.11), residues: 25 loop : -0.35 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.026 0.001 PHE B 497 TYR 0.020 0.001 TYR A 385 ARG 0.007 0.000 ARG B 403 *********************** 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 253 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 SER cc_start: 0.9223 (m) cc_final: 0.9022 (m) REVERT: A 35 GLU cc_start: 0.7013 (tp30) cc_final: 0.6800 (tp30) REVERT: A 134 ASN cc_start: 0.7493 (t0) cc_final: 0.7238 (t0) REVERT: A 153 GLU cc_start: 0.7277 (pp20) cc_final: 0.6265 (pp20) REVERT: A 154 ASN cc_start: 0.7662 (m-40) cc_final: 0.7457 (m-40) REVERT: A 161 ARG cc_start: 0.7709 (mtp180) cc_final: 0.7325 (mtt-85) REVERT: A 166 GLU cc_start: 0.7163 (tp30) cc_final: 0.6883 (tp30) REVERT: A 276 THR cc_start: 0.8155 (p) cc_final: 0.7907 (p) outliers start: 28 outliers final: 23 residues processed: 237 average time/residue: 0.1878 time to fit residues: 57.5586 Evaluate side-chains 245 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain A residue 23 ASP 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 142 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 476 THR 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 532 ILE Chi-restraints excluded: chain A residue 572 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6624 Z= 0.238 Angle : 0.604 9.188 9006 Z= 0.316 Chirality : 0.042 0.159 933 Planarity : 0.004 0.040 1168 Dihedral : 5.101 46.913 868 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.02 % Allowed : 24.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.30), residues: 787 helix: 2.28 (0.27), residues: 385 sheet: 0.43 (1.17), residues: 25 loop : -0.45 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.027 0.002 PHE B 497 TYR 0.023 0.002 TYR A 521 ARG 0.008 0.001 ARG B 403 *********************** 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 251 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 223 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8338 (t-100) cc_final: 0.7989 (t-100) REVERT: A 153 GLU cc_start: 0.7249 (pp20) cc_final: 0.6198 (pp20) REVERT: A 154 ASN cc_start: 0.7683 (m-40) cc_final: 0.7460 (m-40) REVERT: A 161 ARG cc_start: 0.7659 (mtp180) cc_final: 0.7323 (mtt-85) REVERT: A 166 GLU cc_start: 0.7143 (tp30) cc_final: 0.6891 (tp30) outliers start: 28 outliers final: 22 residues processed: 235 average time/residue: 0.1858 time to fit residues: 56.4614 Evaluate side-chains 244 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain A residue 23 ASP 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 142 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 476 THR 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 532 ILE Chi-restraints excluded: chain A residue 572 ILE 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 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.0870 chunk 51 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 188 ASN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6624 Z= 0.168 Angle : 0.567 10.396 9006 Z= 0.293 Chirality : 0.040 0.146 933 Planarity : 0.004 0.038 1168 Dihedral : 4.800 43.841 868 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.16 % Allowed : 26.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.30), residues: 787 helix: 2.36 (0.27), residues: 379 sheet: 0.14 (1.05), residues: 25 loop : -0.45 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.002 0.000 HIS A 374 PHE 0.029 0.001 PHE B 497 TYR 0.016 0.001 TYR A 521 ARG 0.007 0.001 ARG B 403 *********************** 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 248 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7009 (tp30) cc_final: 0.6600 (tp30) REVERT: A 69 TRP cc_start: 0.8367 (t-100) cc_final: 0.8056 (t-100) REVERT: A 75 GLU cc_start: 0.7527 (tp30) cc_final: 0.7122 (tp30) REVERT: A 161 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7264 (mtt-85) REVERT: A 166 GLU cc_start: 0.7028 (tp30) cc_final: 0.6753 (tp30) outliers start: 22 outliers final: 17 residues processed: 236 average time/residue: 0.1942 time to fit residues: 59.3120 Evaluate side-chains 235 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 218 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 531 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6624 Z= 0.181 Angle : 0.584 10.881 9006 Z= 0.298 Chirality : 0.040 0.150 933 Planarity : 0.004 0.037 1168 Dihedral : 4.693 40.247 868 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.01 % Allowed : 27.69 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.30), residues: 787 helix: 2.33 (0.27), residues: 386 sheet: 0.04 (1.00), residues: 25 loop : -0.43 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 540 PHE 0.033 0.001 PHE B 497 TYR 0.021 0.001 TYR A 252 ARG 0.007 0.000 ARG B 403 *********************** 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 242 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7070 (tp30) cc_final: 0.6623 (tp30) REVERT: A 69 TRP cc_start: 0.8388 (t-100) cc_final: 0.8101 (t-100) REVERT: A 75 GLU cc_start: 0.7520 (tp30) cc_final: 0.7098 (tp30) REVERT: A 100 LEU cc_start: 0.8451 (tt) cc_final: 0.8185 (tt) REVERT: A 161 ARG cc_start: 0.7606 (mtp180) cc_final: 0.7285 (mtt-85) REVERT: A 166 GLU cc_start: 0.7034 (tp30) cc_final: 0.6746 (tp30) REVERT: A 188 ASN cc_start: 0.7764 (t0) cc_final: 0.7549 (t0) outliers start: 21 outliers final: 19 residues processed: 226 average time/residue: 0.1824 time to fit residues: 54.0383 Evaluate side-chains 239 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 531 GLN 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 77 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN A 188 ASN A 228 HIS ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6624 Z= 0.286 Angle : 0.641 10.664 9006 Z= 0.336 Chirality : 0.044 0.153 933 Planarity : 0.005 0.037 1168 Dihedral : 4.826 37.570 866 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.44 % Allowed : 27.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.30), residues: 787 helix: 2.16 (0.27), residues: 385 sheet: -0.01 (0.96), residues: 25 loop : -0.55 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 163 HIS 0.006 0.001 HIS A 374 PHE 0.035 0.002 PHE B 497 TYR 0.020 0.002 TYR A 385 ARG 0.009 0.001 ARG B 403 ********************** 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 fitting. rotamer outliers: 17 poor density : 227 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8460 (t-100) cc_final: 0.8205 (t-100) REVERT: A 75 GLU cc_start: 0.7600 (tp30) cc_final: 0.7223 (tp30) REVERT: A 100 LEU cc_start: 0.8518 (tt) cc_final: 0.8285 (tt) REVERT: A 161 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7356 (mtt-85) REVERT: A 166 GLU cc_start: 0.7124 (tp30) cc_final: 0.6890 (tp30) outliers start: 17 outliers final: 14 residues processed: 232 average time/residue: 0.1925 time to fit residues: 57.6032 Evaluate side-chains 238 residues out of total 697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 224 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 511 SER 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 17 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097253 restraints weight = 11626.303| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.88 r_work: 0.3079 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6624 Z= 0.320 Angle : 0.654 10.647 9006 Z= 0.344 Chirality : 0.044 0.151 933 Planarity : 0.005 0.040 1168 Dihedral : 4.902 32.516 866 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.15 % Allowed : 28.84 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 787 helix: 2.13 (0.27), residues: 384 sheet: -0.37 (0.92), residues: 27 loop : -0.64 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 163 HIS 0.006 0.001 HIS A 374 PHE 0.036 0.002 PHE B 497 TYR 0.022 0.002 TYR A 252 ARG 0.009 0.001 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1998.05 seconds wall clock time: 35 minutes 57.14 seconds (2157.14 seconds total)