Starting phenix.real_space_refine on Sat Aug 23 10:44:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t25_40980/08_2025/8t25_40980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t25_40980/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t25_40980/08_2025/8t25_40980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t25_40980/08_2025/8t25_40980.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t25_40980/08_2025/8t25_40980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t25_40980/08_2025/8t25_40980.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.50, per 1000 atoms: 0.23 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: 0.58 Conformation dependent library (CDL) restraints added in 389.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.15 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: 0.65 Time building geometry restraints manager: 0.76 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: 15.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.490 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.290 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG A 393 TYR 0.015 0.001 TYR B 508 PHE 0.010 0.001 PHE B 338 TRP 0.020 0.001 TRP A 69 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6590) covalent geometry : angle 0.62740 ( 8949) SS BOND : bond 0.00802 ( 6) SS BOND : angle 1.14799 ( 12) hydrogen bonds : bond 0.11418 ( 286) hydrogen bonds : angle 4.62424 ( 822) *********************** 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 : 0.154 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 77 average time/residue: 0.0783 time to fit residues: 8.0974 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.190913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.172246 restraints weight = 12323.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.174182 restraints weight = 8648.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.175802 restraints weight = 6937.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.176185 restraints weight = 5045.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.176603 restraints weight = 4823.823| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6596 Z= 0.140 Angle : 0.590 10.171 8961 Z= 0.298 Chirality : 0.042 0.174 924 Planarity : 0.005 0.069 1164 Dihedral : 4.257 22.426 861 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.80 % Allowed : 24.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.29), residues: 777 helix: 1.33 (0.28), residues: 365 sheet: -1.14 (1.02), residues: 26 loop : -1.67 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 161 TYR 0.017 0.001 TYR A 385 PHE 0.016 0.001 PHE B 338 TRP 0.016 0.001 TRP A 69 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6590) covalent geometry : angle 0.58928 ( 8949) SS BOND : bond 0.00839 ( 6) SS BOND : angle 1.15446 ( 12) hydrogen bonds : bond 0.05760 ( 286) hydrogen bonds : angle 4.41439 ( 822) *********************** 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 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.327 Fit side-chains REVERT: A 401 HIS cc_start: 0.5219 (OUTLIER) cc_final: 0.4978 (m-70) REVERT: A 438 PHE cc_start: 0.5337 (OUTLIER) cc_final: 0.4903 (t80) REVERT: A 512 PHE cc_start: 0.4725 (OUTLIER) cc_final: 0.4347 (t80) outliers start: 33 outliers final: 15 residues processed: 104 average time/residue: 0.0696 time to fit residues: 10.3022 Evaluate side-chains 91 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 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 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 46 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.188644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.170923 restraints weight = 12235.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.172594 restraints weight = 9785.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.173666 restraints weight = 8626.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.174258 restraints weight = 5910.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.175645 restraints weight = 5404.149| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.1266 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= 0.153 Angle : 0.605 9.592 8961 Z= 0.306 Chirality : 0.043 0.208 924 Planarity : 0.005 0.059 1164 Dihedral : 4.417 23.175 861 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.10 % Allowed : 24.56 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.29), residues: 777 helix: 1.35 (0.28), residues: 359 sheet: -1.28 (0.97), residues: 27 loop : -1.69 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.018 0.002 TYR A 385 PHE 0.011 0.001 PHE B 400 TRP 0.014 0.001 TRP A 69 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6590) covalent geometry : angle 0.60358 ( 8949) SS BOND : bond 0.00586 ( 6) SS BOND : angle 1.35372 ( 12) hydrogen bonds : bond 0.06278 ( 286) hydrogen bonds : angle 4.46489 ( 822) *********************** 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 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.177 Fit side-chains REVERT: A 169 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6440 (ttm170) REVERT: A 203 TRP cc_start: 0.5797 (OUTLIER) cc_final: 0.5072 (m-10) REVERT: A 512 PHE cc_start: 0.4811 (OUTLIER) cc_final: 0.4324 (t80) outliers start: 42 outliers final: 25 residues processed: 113 average time/residue: 0.0719 time to fit residues: 11.1580 Evaluate side-chains 99 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 203 TRP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 MET 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 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 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 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.187322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.169631 restraints weight = 12284.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.170837 restraints weight = 9738.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.172114 restraints weight = 9032.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.172801 restraints weight = 6182.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.173347 restraints weight = 5708.092| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.1630 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= 0.158 Angle : 0.618 8.942 8961 Z= 0.316 Chirality : 0.043 0.232 924 Planarity : 0.005 0.053 1164 Dihedral : 4.562 23.935 861 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.98 % Allowed : 24.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.29), residues: 777 helix: 1.14 (0.27), residues: 368 sheet: -1.36 (0.98), residues: 27 loop : -1.79 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.019 0.002 TYR A 202 PHE 0.010 0.001 PHE B 429 TRP 0.014 0.001 TRP A 165 HIS 0.007 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6590) covalent geometry : angle 0.61678 ( 8949) SS BOND : bond 0.00743 ( 6) SS BOND : angle 1.38385 ( 12) hydrogen bonds : bond 0.06596 ( 286) hydrogen bonds : angle 4.53240 ( 822) *********************** 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 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 75 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: -0.1212 (OUTLIER) cc_final: -0.1657 (p) REVERT: A 169 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6268 (ttm170) REVERT: A 203 TRP cc_start: 0.5693 (OUTLIER) cc_final: 0.4905 (m-10) REVERT: A 512 PHE cc_start: 0.4975 (OUTLIER) cc_final: 0.4401 (t80) outliers start: 48 outliers final: 30 residues processed: 114 average time/residue: 0.0731 time to fit residues: 11.5507 Evaluate side-chains 105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 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 270 MET 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 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 558 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 1 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.189145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.171262 restraints weight = 12420.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.172223 restraints weight = 10466.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.174378 restraints weight = 8488.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.174938 restraints weight = 5898.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.175368 restraints weight = 5464.162| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.1594 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= 0.133 Angle : 0.588 9.954 8961 Z= 0.296 Chirality : 0.042 0.228 924 Planarity : 0.004 0.049 1164 Dihedral : 4.414 23.131 861 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 6.10 % Allowed : 24.71 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.29), residues: 777 helix: 1.22 (0.27), residues: 365 sheet: -1.52 (0.87), residues: 32 loop : -1.71 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.015 0.001 TYR A 202 PHE 0.008 0.001 PHE B 400 TRP 0.017 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6590) covalent geometry : angle 0.58688 ( 8949) SS BOND : bond 0.00651 ( 6) SS BOND : angle 1.29427 ( 12) hydrogen bonds : bond 0.05943 ( 286) hydrogen bonds : angle 4.47095 ( 822) *********************** 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 116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 74 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: -0.1486 (OUTLIER) cc_final: -0.1958 (p) REVERT: A 169 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6237 (ttm170) REVERT: A 203 TRP cc_start: 0.5686 (OUTLIER) cc_final: 0.4902 (m-10) REVERT: A 512 PHE cc_start: 0.4848 (OUTLIER) cc_final: 0.4312 (t80) outliers start: 42 outliers final: 31 residues processed: 107 average time/residue: 0.0701 time to fit residues: 10.2450 Evaluate side-chains 105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 111 ASP 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 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 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 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 558 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 594 THR 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 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.187326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.168776 restraints weight = 11971.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.170825 restraints weight = 8124.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.172808 restraints weight = 6211.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.173023 restraints weight = 4482.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.173779 restraints weight = 4230.133| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6596 Z= 0.154 Angle : 0.616 9.994 8961 Z= 0.311 Chirality : 0.043 0.246 924 Planarity : 0.004 0.047 1164 Dihedral : 4.553 24.780 861 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.83 % Allowed : 24.13 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.29), residues: 777 helix: 1.25 (0.27), residues: 358 sheet: -1.57 (0.86), residues: 32 loop : -1.75 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 255 TYR 0.018 0.001 TYR A 202 PHE 0.010 0.001 PHE B 429 TRP 0.018 0.001 TRP A 69 HIS 0.006 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6590) covalent geometry : angle 0.61407 ( 8949) SS BOND : bond 0.00777 ( 6) SS BOND : angle 1.38173 ( 12) hydrogen bonds : bond 0.06417 ( 286) hydrogen bonds : angle 4.52915 ( 822) *********************** 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 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: -0.1232 (OUTLIER) cc_final: -0.1667 (p) REVERT: A 169 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6123 (ttm170) REVERT: A 203 TRP cc_start: 0.5766 (OUTLIER) cc_final: 0.4911 (m-10) REVERT: A 512 PHE cc_start: 0.5135 (OUTLIER) cc_final: 0.4467 (t80) REVERT: A 530 LEU cc_start: 0.6692 (tp) cc_final: 0.5701 (pp) outliers start: 47 outliers final: 34 residues processed: 114 average time/residue: 0.0625 time to fit residues: 10.1682 Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 111 ASP 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 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 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 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 558 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.0010 chunk 70 optimal weight: 0.0980 chunk 34 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.191503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.173968 restraints weight = 12269.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.175791 restraints weight = 10153.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.177400 restraints weight = 7882.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.177771 restraints weight = 5696.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.178151 restraints weight = 5354.438| |-----------------------------------------------------------------------------| r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6596 Z= 0.125 Angle : 0.581 11.154 8961 Z= 0.292 Chirality : 0.042 0.259 924 Planarity : 0.004 0.046 1164 Dihedral : 4.356 23.854 861 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.38 % Allowed : 25.87 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.29), residues: 777 helix: 1.27 (0.27), residues: 365 sheet: -1.58 (0.85), residues: 32 loop : -1.64 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 255 TYR 0.019 0.001 TYR A 202 PHE 0.007 0.001 PHE B 453 TRP 0.016 0.001 TRP A 69 HIS 0.008 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6590) covalent geometry : angle 0.57974 ( 8949) SS BOND : bond 0.00628 ( 6) SS BOND : angle 1.25296 ( 12) hydrogen bonds : bond 0.05400 ( 286) hydrogen bonds : angle 4.42421 ( 822) *********************** 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 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: -0.1672 (OUTLIER) cc_final: -0.2156 (p) REVERT: A 169 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6231 (ttm170) REVERT: A 512 PHE cc_start: 0.4708 (OUTLIER) cc_final: 0.4188 (t80) outliers start: 37 outliers final: 27 residues processed: 107 average time/residue: 0.0691 time to fit residues: 10.0164 Evaluate side-chains 104 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 198 ASP Chi-restraints excluded: chain A residue 244 VAL 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 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 558 MET 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 490 PHE 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 53 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.188726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.170933 restraints weight = 12270.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.173072 restraints weight = 9833.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.173897 restraints weight = 8381.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.174389 restraints weight = 6050.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.174797 restraints weight = 5494.713| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6596 Z= 0.145 Angle : 0.615 10.781 8961 Z= 0.309 Chirality : 0.043 0.272 924 Planarity : 0.004 0.045 1164 Dihedral : 4.439 25.149 861 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 6.10 % Allowed : 25.73 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.29), residues: 777 helix: 1.20 (0.27), residues: 359 sheet: -1.62 (0.86), residues: 32 loop : -1.65 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.015 0.001 TYR A 202 PHE 0.014 0.001 PHE B 377 TRP 0.019 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6590) covalent geometry : angle 0.61351 ( 8949) SS BOND : bond 0.00688 ( 6) SS BOND : angle 1.32688 ( 12) hydrogen bonds : bond 0.05950 ( 286) hydrogen bonds : angle 4.44444 ( 822) *********************** 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 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: -0.1489 (OUTLIER) cc_final: -0.1953 (p) REVERT: A 169 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6215 (ttm170) REVERT: A 512 PHE cc_start: 0.4918 (OUTLIER) cc_final: 0.4374 (t80) outliers start: 42 outliers final: 33 residues processed: 111 average time/residue: 0.0726 time to fit residues: 11.1339 Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 244 VAL 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 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 558 MET 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 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 478 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.0980 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.187983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.170220 restraints weight = 12393.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.172139 restraints weight = 9659.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.173669 restraints weight = 7926.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.174022 restraints weight = 5614.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.174386 restraints weight = 5863.881| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6596 Z= 0.148 Angle : 0.618 10.913 8961 Z= 0.312 Chirality : 0.043 0.284 924 Planarity : 0.004 0.044 1164 Dihedral : 4.531 25.518 861 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.10 % Allowed : 25.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.29), residues: 777 helix: 1.15 (0.27), residues: 359 sheet: -1.71 (0.86), residues: 32 loop : -1.66 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.015 0.001 TYR A 202 PHE 0.011 0.001 PHE B 377 TRP 0.017 0.001 TRP A 69 HIS 0.007 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6590) covalent geometry : angle 0.61616 ( 8949) SS BOND : bond 0.00718 ( 6) SS BOND : angle 1.40644 ( 12) hydrogen bonds : bond 0.06125 ( 286) hydrogen bonds : angle 4.48849 ( 822) *********************** 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 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 73 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: -0.1566 (OUTLIER) cc_final: -0.1981 (p) REVERT: A 169 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6238 (ttm170) REVERT: A 512 PHE cc_start: 0.4702 (OUTLIER) cc_final: 0.4126 (t80) outliers start: 42 outliers final: 32 residues processed: 106 average time/residue: 0.0732 time to fit residues: 10.5845 Evaluate side-chains 108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 198 ASP Chi-restraints excluded: chain A residue 244 VAL 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 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 558 MET 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 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 495 TYR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.187689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.169344 restraints weight = 12152.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.171655 restraints weight = 8666.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.172748 restraints weight = 7402.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.173436 restraints weight = 5340.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.173627 restraints weight = 5243.138| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.1999 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= 0.148 Angle : 0.631 10.791 8961 Z= 0.317 Chirality : 0.043 0.296 924 Planarity : 0.004 0.044 1164 Dihedral : 4.579 26.521 861 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.96 % Allowed : 25.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.29), residues: 777 helix: 1.13 (0.27), residues: 359 sheet: -1.83 (0.84), residues: 32 loop : -1.68 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.014 0.001 TYR A 202 PHE 0.024 0.001 PHE A 72 TRP 0.018 0.001 TRP A 69 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6590) covalent geometry : angle 0.62906 ( 8949) SS BOND : bond 0.00732 ( 6) SS BOND : angle 1.41228 ( 12) hydrogen bonds : bond 0.06219 ( 286) hydrogen bonds : angle 4.50935 ( 822) ********************** 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 117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: -0.1391 (OUTLIER) cc_final: -0.1837 (p) REVERT: A 169 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5963 (ttm170) REVERT: A 512 PHE cc_start: 0.4810 (OUTLIER) cc_final: 0.4190 (t80) REVERT: A 530 LEU cc_start: 0.6707 (tp) cc_final: 0.5738 (pp) outliers start: 41 outliers final: 35 residues processed: 108 average time/residue: 0.0780 time to fit residues: 11.5159 Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 244 VAL Chi-restraints excluded: chain A residue 256 ILE 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 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 558 MET 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 495 TYR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.186759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.168304 restraints weight = 12306.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.169471 restraints weight = 8854.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.171483 restraints weight = 7450.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.171826 restraints weight = 5417.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.173503 restraints weight = 5156.704| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6596 Z= 0.157 Angle : 0.642 10.904 8961 Z= 0.323 Chirality : 0.044 0.290 924 Planarity : 0.005 0.043 1164 Dihedral : 4.675 27.374 861 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 6.10 % Allowed : 25.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.29), residues: 777 helix: 1.08 (0.27), residues: 362 sheet: -1.89 (0.84), residues: 32 loop : -1.78 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.014 0.001 TYR B 495 PHE 0.023 0.002 PHE A 72 TRP 0.021 0.001 TRP A 69 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6590) covalent geometry : angle 0.63981 ( 8949) SS BOND : bond 0.00833 ( 6) SS BOND : angle 1.48844 ( 12) hydrogen bonds : bond 0.06460 ( 286) hydrogen bonds : angle 4.54871 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.22 seconds wall clock time: 22 minutes 52.99 seconds (1372.99 seconds total)