Starting phenix.real_space_refine on Wed May 14 07:55:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t25_40980/05_2025/8t25_40980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t25_40980/05_2025/8t25_40980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t25_40980/05_2025/8t25_40980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t25_40980/05_2025/8t25_40980.map" model { file = "/net/cci-nas-00/data/ceres_data/8t25_40980/05_2025/8t25_40980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t25_40980/05_2025/8t25_40980.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 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 6352 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4096 2.51 5 N 1076 2.21 5 O 1199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6408 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4895 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 30, 'TRANS': 564} Chain breaks: 2 Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1513 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 11, 'TRANS': 180} Chain breaks: 1 Time building chain proxies: 4.32, per 1000 atoms: 0.67 Number of scatterers: 6408 At special positions: 0 Unit cell: (101.01, 101.01, 108.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1199 8.00 N 1076 7.00 C 4096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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: 1.39 Conformation dependent library (CDL) restraints added in 844.4 milliseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 55.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.051A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 130 removed outlier: 4.277A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.966A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 219 through 252 removed outlier: 4.358A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.964A pdb=" N LEU A 267 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.532A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix No H-bonds generated for 'chain 'A' and resid 275 through 282' Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.555A pdb=" N SER A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.696A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.988A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.789A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.727A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.705A 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 519 through 534 removed outlier: 3.882A pdb=" N ILE A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.893A pdb=" N GLY A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.598A pdb=" N GLU A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 596 removed outlier: 3.527A pdb=" N LEU A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.097A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.558A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.337A pdb=" N ALA A 348 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS A 359 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP A 350 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ARG A 357 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 352 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.786A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 286 hydrogen bonds defined for protein. 822 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: 1.57 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2073 1.35 - 1.47: 1720 1.47 - 1.59: 2738 1.59 - 1.71: 1 1.71 - 1.84: 58 Bond restraints: 6590 Sorted by residual: bond pdb=" CB PRO A 346 " pdb=" CG PRO A 346 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.20e+00 bond pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.57e+00 bond pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 1.522 1.540 -0.019 1.29e-02 6.01e+03 2.06e+00 bond pdb=" CB LYS A 565 " pdb=" CG LYS A 565 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.28e+00 ... (remaining 6585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 8719 1.72 - 3.44: 184 3.44 - 5.15: 30 5.15 - 6.87: 11 6.87 - 8.59: 5 Bond angle restraints: 8949 Sorted by residual: angle pdb=" CA PRO A 346 " pdb=" N PRO A 346 " pdb=" CD PRO A 346 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" CB LYS A 565 " pdb=" CG LYS A 565 " pdb=" CD LYS A 565 " ideal model delta sigma weight residual 111.30 119.89 -8.59 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA PRO A 321 " pdb=" N PRO A 321 " pdb=" CD PRO A 321 " ideal model delta sigma weight residual 112.00 107.10 4.90 1.40e+00 5.10e-01 1.22e+01 angle pdb=" CA LYS A 470 " pdb=" CB LYS A 470 " pdb=" CG LYS A 470 " ideal model delta sigma weight residual 114.10 120.28 -6.18 2.00e+00 2.50e-01 9.54e+00 angle pdb=" N LEU A 450 " pdb=" CA LEU A 450 " pdb=" C LEU A 450 " ideal model delta sigma weight residual 109.81 116.62 -6.81 2.21e+00 2.05e-01 9.50e+00 ... (remaining 8944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 3268 17.54 - 35.08: 455 35.08 - 52.62: 146 52.62 - 70.16: 17 70.16 - 87.70: 13 Dihedral angle restraints: 3899 sinusoidal: 1590 harmonic: 2309 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 46.44 46.56 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA CYS B 379 " pdb=" C CYS B 379 " pdb=" N TYR B 380 " pdb=" CA TYR B 380 " ideal model delta harmonic sigma weight residual -180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 127.67 -34.67 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 3896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 784 0.054 - 0.109: 119 0.109 - 0.163: 20 0.163 - 0.217: 0 0.217 - 0.272: 1 Chirality restraints: 924 Sorted by residual: chirality pdb=" CB VAL A 582 " pdb=" CA VAL A 582 " pdb=" CG1 VAL A 582 " pdb=" CG2 VAL A 582 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR A 371 " pdb=" CA THR A 371 " pdb=" OG1 THR A 371 " pdb=" CG2 THR A 371 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA LYS A 234 " pdb=" N LYS A 234 " pdb=" C LYS A 234 " pdb=" CB LYS A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 921 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 345 " 0.079 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 346 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 90 " -0.065 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO A 91 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.035 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 321 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.029 5.00e-02 4.00e+02 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 527 2.74 - 3.28: 6393 3.28 - 3.82: 10584 3.82 - 4.36: 11280 4.36 - 4.90: 19478 Nonbonded interactions: 48262 Sorted by model distance: nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 368 " model vdw 2.274 3.040 nonbonded pdb=" OD2 ASP A 435 " pdb=" OH TYR A 541 " model vdw 2.306 3.040 nonbonded pdb=" O SER A 155 " pdb=" NH1 ARG A 161 " model vdw 2.310 3.120 ... (remaining 48257 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 group one per residue 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: 17.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.670 Find NCS groups from input model: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 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 : 0.003 0.114 6596 Z= 0.136 Angle : 0.628 8.588 8961 Z= 0.330 Chirality : 0.041 0.272 924 Planarity : 0.006 0.115 1164 Dihedral : 18.086 87.703 2397 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.44 % Allowed : 29.51 % Favored : 70.06 % 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: -0.27 (0.29), residues: 777 helix: 1.20 (0.27), residues: 365 sheet: 0.41 (1.17), residues: 24 loop : -1.64 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 69 HIS 0.006 0.001 HIS A 417 PHE 0.010 0.001 PHE B 338 TYR 0.015 0.001 TYR B 508 ARG 0.002 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.11418 ( 286) hydrogen bonds : angle 4.62424 ( 822) SS BOND : bond 0.00802 ( 6) SS BOND : angle 1.14799 ( 12) covalent geometry : bond 0.00333 ( 6590) covalent geometry : angle 0.62740 ( 8949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.665 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 77 average time/residue: 0.1814 time to fit residues: 18.8478 Evaluate side-chains 74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.0010 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 0.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 523 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.192422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.173764 restraints weight = 12076.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.176080 restraints weight = 8626.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.177661 restraints weight = 6644.020| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6596 Z= 0.129 Angle : 0.574 10.085 8961 Z= 0.289 Chirality : 0.041 0.169 924 Planarity : 0.005 0.068 1164 Dihedral : 4.156 21.761 861 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.51 % Allowed : 24.42 % Favored : 71.08 % 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: -0.18 (0.29), residues: 777 helix: 1.32 (0.27), residues: 365 sheet: -0.86 (1.01), residues: 27 loop : -1.55 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.006 0.001 HIS A 417 PHE 0.016 0.001 PHE B 338 TYR 0.018 0.001 TYR A 385 ARG 0.004 0.001 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.05395 ( 286) hydrogen bonds : angle 4.37965 ( 822) SS BOND : bond 0.00659 ( 6) SS BOND : angle 1.13512 ( 12) covalent geometry : bond 0.00281 ( 6590) covalent geometry : angle 0.57326 ( 8949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.683 Fit side-chains REVERT: A 512 PHE cc_start: 0.4593 (OUTLIER) cc_final: 0.4243 (t80) REVERT: B 406 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6964 (mm-30) outliers start: 31 outliers final: 16 residues processed: 98 average time/residue: 0.1468 time to fit residues: 20.5382 Evaluate side-chains 88 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 523 GLN Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.189026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.170186 restraints weight = 12135.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.172134 restraints weight = 8633.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.173929 restraints weight = 6771.938| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6596 Z= 0.151 Angle : 0.600 9.357 8961 Z= 0.303 Chirality : 0.043 0.203 924 Planarity : 0.005 0.060 1164 Dihedral : 4.352 23.043 861 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.67 % Allowed : 24.42 % Favored : 69.91 % 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: -0.24 (0.29), residues: 777 helix: 1.40 (0.28), residues: 359 sheet: -1.22 (0.99), residues: 27 loop : -1.66 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.006 0.001 HIS A 417 PHE 0.010 0.001 PHE B 400 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.06223 ( 286) hydrogen bonds : angle 4.45423 ( 822) SS BOND : bond 0.00810 ( 6) SS BOND : angle 1.35396 ( 12) covalent geometry : bond 0.00328 ( 6590) covalent geometry : angle 0.59831 ( 8949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 78 time to evaluate : 0.757 Fit side-chains REVERT: A 169 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6474 (ttm170) REVERT: A 203 TRP cc_start: 0.5763 (OUTLIER) cc_final: 0.5012 (m-10) REVERT: A 438 PHE cc_start: 0.5397 (OUTLIER) cc_final: 0.4762 (t80) REVERT: A 512 PHE cc_start: 0.4885 (OUTLIER) cc_final: 0.4376 (t80) outliers start: 39 outliers final: 24 residues processed: 110 average time/residue: 0.1720 time to fit residues: 25.9285 Evaluate side-chains 98 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 523 GLN B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.183315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.165043 restraints weight = 12415.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.166429 restraints weight = 9490.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.167898 restraints weight = 8216.117| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6596 Z= 0.205 Angle : 0.695 11.057 8961 Z= 0.357 Chirality : 0.046 0.235 924 Planarity : 0.005 0.054 1164 Dihedral : 5.052 26.407 861 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 7.70 % Allowed : 23.84 % Favored : 68.46 % 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: -0.80 (0.29), residues: 777 helix: 0.89 (0.27), residues: 368 sheet: -2.44 (0.72), residues: 41 loop : -1.85 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 165 HIS 0.006 0.001 HIS A 417 PHE 0.015 0.002 PHE B 400 TYR 0.020 0.002 TYR B 351 ARG 0.003 0.001 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.08125 ( 286) hydrogen bonds : angle 4.78952 ( 822) SS BOND : bond 0.00883 ( 6) SS BOND : angle 1.71399 ( 12) covalent geometry : bond 0.00450 ( 6590) covalent geometry : angle 0.69292 ( 8949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 76 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: -0.1122 (OUTLIER) cc_final: -0.1494 (p) REVERT: A 169 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.5916 (ttm170) REVERT: A 183 TYR cc_start: 0.5557 (OUTLIER) cc_final: 0.5188 (t80) REVERT: A 203 TRP cc_start: 0.5996 (OUTLIER) cc_final: 0.5097 (m-10) REVERT: A 401 HIS cc_start: 0.5804 (OUTLIER) cc_final: 0.5428 (m-70) REVERT: A 438 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.4938 (t80) REVERT: A 512 PHE cc_start: 0.5132 (OUTLIER) cc_final: 0.4514 (t80) outliers start: 53 outliers final: 30 residues processed: 121 average time/residue: 0.1701 time to fit residues: 27.7591 Evaluate side-chains 105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 46 optimal weight: 0.0030 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.189289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.171744 restraints weight = 12241.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.172668 restraints weight = 9476.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.174978 restraints weight = 8173.675| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6596 Z= 0.132 Angle : 0.596 11.506 8961 Z= 0.300 Chirality : 0.042 0.176 924 Planarity : 0.004 0.049 1164 Dihedral : 4.566 24.642 861 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.80 % Allowed : 26.74 % Favored : 68.46 % 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: -0.54 (0.29), residues: 777 helix: 1.14 (0.27), residues: 369 sheet: -1.74 (0.85), residues: 32 loop : -1.83 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.008 0.001 HIS A 417 PHE 0.008 0.001 PHE B 338 TYR 0.014 0.001 TYR A 202 ARG 0.004 0.000 ARG A 519 Details of bonding type rmsd hydrogen bonds : bond 0.05880 ( 286) hydrogen bonds : angle 4.52314 ( 822) SS BOND : bond 0.00625 ( 6) SS BOND : angle 1.35985 ( 12) covalent geometry : bond 0.00273 ( 6590) covalent geometry : angle 0.59476 ( 8949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 THR cc_start: -0.1298 (OUTLIER) cc_final: -0.1759 (p) REVERT: A 169 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6027 (ttm170) REVERT: A 438 PHE cc_start: 0.5377 (OUTLIER) cc_final: 0.4873 (t80) REVERT: A 512 PHE cc_start: 0.4833 (OUTLIER) cc_final: 0.4283 (t80) outliers start: 33 outliers final: 19 residues processed: 103 average time/residue: 0.1895 time to fit residues: 26.5050 Evaluate side-chains 99 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.184726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.166447 restraints weight = 12253.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.167880 restraints weight = 8801.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.169146 restraints weight = 7888.638| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6596 Z= 0.184 Angle : 0.666 10.101 8961 Z= 0.338 Chirality : 0.044 0.265 924 Planarity : 0.005 0.047 1164 Dihedral : 4.871 26.853 861 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 6.54 % Allowed : 25.15 % Favored : 68.31 % 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: -0.73 (0.29), residues: 777 helix: 1.06 (0.27), residues: 362 sheet: -2.07 (0.82), residues: 32 loop : -1.95 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 69 HIS 0.006 0.001 HIS A 417 PHE 0.014 0.002 PHE B 429 TYR 0.018 0.002 TYR B 495 ARG 0.006 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.07243 ( 286) hydrogen bonds : angle 4.65861 ( 822) SS BOND : bond 0.00844 ( 6) SS BOND : angle 1.59426 ( 12) covalent geometry : bond 0.00408 ( 6590) covalent geometry : angle 0.66410 ( 8949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 75 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7077 (tt0) cc_final: 0.6804 (tt0) REVERT: A 55 THR cc_start: -0.1289 (OUTLIER) cc_final: -0.1691 (p) REVERT: A 169 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6029 (ttm170) REVERT: A 203 TRP cc_start: 0.5745 (OUTLIER) cc_final: 0.4911 (m-10) REVERT: A 438 PHE cc_start: 0.5591 (OUTLIER) cc_final: 0.4718 (t80) REVERT: A 512 PHE cc_start: 0.5208 (OUTLIER) cc_final: 0.4586 (t80) outliers start: 45 outliers final: 33 residues processed: 114 average time/residue: 0.1722 time to fit residues: 26.5524 Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.185230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.167642 restraints weight = 12223.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.168590 restraints weight = 10023.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.170079 restraints weight = 8927.855| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6596 Z= 0.168 Angle : 0.652 10.649 8961 Z= 0.330 Chirality : 0.044 0.279 924 Planarity : 0.005 0.046 1164 Dihedral : 4.879 27.312 861 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 6.69 % Allowed : 25.58 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.29), residues: 777 helix: 0.98 (0.27), residues: 368 sheet: -2.23 (0.81), residues: 32 loop : -2.00 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 PHE 0.012 0.001 PHE B 429 TYR 0.017 0.002 TYR A 202 ARG 0.005 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.07021 ( 286) hydrogen bonds : angle 4.65405 ( 822) SS BOND : bond 0.00816 ( 6) SS BOND : angle 1.59788 ( 12) covalent geometry : bond 0.00367 ( 6590) covalent geometry : angle 0.65025 ( 8949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 THR cc_start: -0.1236 (OUTLIER) cc_final: -0.1674 (p) REVERT: A 169 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6007 (ttm170) REVERT: A 203 TRP cc_start: 0.5655 (OUTLIER) cc_final: 0.4868 (m-10) REVERT: A 438 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4800 (t80) REVERT: A 512 PHE cc_start: 0.4872 (OUTLIER) cc_final: 0.4294 (t80) REVERT: A 558 MET cc_start: 0.7419 (tpt) cc_final: 0.7182 (tpt) outliers start: 46 outliers final: 35 residues processed: 121 average time/residue: 0.1664 time to fit residues: 27.4842 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 72 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.186583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.168130 restraints weight = 12202.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.169963 restraints weight = 8874.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.171264 restraints weight = 6830.686| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6596 Z= 0.148 Angle : 0.630 10.547 8961 Z= 0.320 Chirality : 0.043 0.265 924 Planarity : 0.005 0.045 1164 Dihedral : 4.762 27.711 861 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.96 % Allowed : 27.03 % Favored : 67.01 % 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: -0.72 (0.29), residues: 777 helix: 1.04 (0.27), residues: 368 sheet: -2.22 (0.83), residues: 32 loop : -1.95 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 69 HIS 0.003 0.001 HIS A 265 PHE 0.014 0.001 PHE B 377 TYR 0.017 0.001 TYR A 202 ARG 0.003 0.000 ARG A 519 Details of bonding type rmsd hydrogen bonds : bond 0.06420 ( 286) hydrogen bonds : angle 4.56114 ( 822) SS BOND : bond 0.00776 ( 6) SS BOND : angle 1.52382 ( 12) covalent geometry : bond 0.00317 ( 6590) covalent geometry : angle 0.62834 ( 8949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 THR cc_start: -0.1315 (OUTLIER) cc_final: -0.1755 (p) REVERT: A 169 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6313 (ttm170) REVERT: A 203 TRP cc_start: 0.5582 (OUTLIER) cc_final: 0.4794 (m-10) REVERT: A 270 MET cc_start: 0.5907 (mtt) cc_final: 0.4736 (mmt) REVERT: A 438 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.4710 (t80) REVERT: A 512 PHE cc_start: 0.4808 (OUTLIER) cc_final: 0.4183 (t80) outliers start: 41 outliers final: 31 residues processed: 110 average time/residue: 0.1670 time to fit residues: 24.9996 Evaluate side-chains 110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 17 optimal weight: 0.0270 chunk 14 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 54 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.189895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.171661 restraints weight = 12233.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.173141 restraints weight = 8739.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.175166 restraints weight = 7134.617| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6596 Z= 0.132 Angle : 0.610 11.045 8961 Z= 0.306 Chirality : 0.043 0.275 924 Planarity : 0.004 0.044 1164 Dihedral : 4.522 26.531 861 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.09 % Allowed : 27.76 % Favored : 67.15 % 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: -0.52 (0.29), residues: 777 helix: 1.23 (0.27), residues: 359 sheet: -2.04 (0.86), residues: 32 loop : -1.80 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 69 HIS 0.002 0.001 HIS A 417 PHE 0.019 0.001 PHE A 72 TYR 0.019 0.001 TYR A 202 ARG 0.003 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.05492 ( 286) hydrogen bonds : angle 4.52583 ( 822) SS BOND : bond 0.00667 ( 6) SS BOND : angle 1.41608 ( 12) covalent geometry : bond 0.00279 ( 6590) covalent geometry : angle 0.60846 ( 8949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 THR cc_start: -0.1518 (OUTLIER) cc_final: -0.1998 (p) REVERT: A 169 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6001 (ttm170) REVERT: A 332 MET cc_start: 0.5081 (mmm) cc_final: 0.4716 (mmm) REVERT: A 438 PHE cc_start: 0.5439 (OUTLIER) cc_final: 0.5009 (t80) REVERT: A 512 PHE cc_start: 0.4857 (OUTLIER) cc_final: 0.4197 (t80) REVERT: A 513 ILE cc_start: 0.8105 (tp) cc_final: 0.7873 (tp) outliers start: 35 outliers final: 28 residues processed: 107 average time/residue: 0.1921 time to fit residues: 27.7498 Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.188481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.170276 restraints weight = 12267.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.172489 restraints weight = 8948.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.173555 restraints weight = 7635.888| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6596 Z= 0.141 Angle : 0.617 10.764 8961 Z= 0.310 Chirality : 0.043 0.270 924 Planarity : 0.005 0.044 1164 Dihedral : 4.528 26.804 861 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.38 % Allowed : 27.33 % Favored : 67.30 % 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: -0.50 (0.29), residues: 777 helix: 1.27 (0.27), residues: 359 sheet: -2.10 (0.86), residues: 32 loop : -1.82 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 69 HIS 0.002 0.001 HIS A 417 PHE 0.017 0.001 PHE A 72 TYR 0.017 0.001 TYR A 202 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.05782 ( 286) hydrogen bonds : angle 4.49031 ( 822) SS BOND : bond 0.00722 ( 6) SS BOND : angle 1.38075 ( 12) covalent geometry : bond 0.00309 ( 6590) covalent geometry : angle 0.61570 ( 8949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 THR cc_start: -0.1588 (OUTLIER) cc_final: -0.2083 (p) REVERT: A 169 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6151 (ttm170) REVERT: A 332 MET cc_start: 0.5175 (mmm) cc_final: 0.4814 (mmm) REVERT: A 438 PHE cc_start: 0.5672 (OUTLIER) cc_final: 0.4852 (t80) REVERT: A 512 PHE cc_start: 0.4803 (OUTLIER) cc_final: 0.4192 (t80) outliers start: 37 outliers final: 29 residues processed: 104 average time/residue: 0.1816 time to fit residues: 25.7392 Evaluate side-chains 106 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 501 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 0.0040 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 0.0370 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.3270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.189655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.171851 restraints weight = 12463.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.173542 restraints weight = 10108.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.175100 restraints weight = 8012.448| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6596 Z= 0.132 Angle : 0.610 10.935 8961 Z= 0.305 Chirality : 0.043 0.281 924 Planarity : 0.004 0.043 1164 Dihedral : 4.469 26.430 861 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.23 % Allowed : 27.18 % Favored : 67.59 % 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: -0.41 (0.29), residues: 777 helix: 1.34 (0.27), residues: 359 sheet: -2.00 (0.87), residues: 32 loop : -1.77 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 69 HIS 0.002 0.001 HIS A 417 PHE 0.018 0.001 PHE A 72 TYR 0.018 0.001 TYR A 202 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.05460 ( 286) hydrogen bonds : angle 4.45733 ( 822) SS BOND : bond 0.00680 ( 6) SS BOND : angle 1.35646 ( 12) covalent geometry : bond 0.00285 ( 6590) covalent geometry : angle 0.60862 ( 8949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2484.10 seconds wall clock time: 44 minutes 42.54 seconds (2682.54 seconds total)