Starting phenix.real_space_refine on Sat Aug 23 04:50:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzb_38792/08_2025/8xzb_38792_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzb_38792/08_2025/8xzb_38792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xzb_38792/08_2025/8xzb_38792_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzb_38792/08_2025/8xzb_38792_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xzb_38792/08_2025/8xzb_38792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzb_38792/08_2025/8xzb_38792.map" } resolution = 3.12 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= -0.000 sd= 0.025 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 4271 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4110 2.51 5 N 1058 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s 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: 6412 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4885 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 29, 'TRANS': 566} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.34, per 1000 atoms: 0.21 Number of scatterers: 6412 At special positions: 0 Unit cell: (75.21, 83.49, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 38 16.00 O 1205 8.00 N 1058 7.00 C 4110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.65 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: 0.35 Conformation dependent library (CDL) restraints added in 336.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 56.8% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.534A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.746A pdb=" N THR A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.742A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.572A 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 218 through 252 removed outlier: 3.817A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.521A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.935A pdb=" N GLY A 268 " --> pdb=" O HIS A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.695A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 397 through 414 removed outlier: 4.119A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.512A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.850A 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 503 removed outlier: 3.623A pdb=" N SER A 502 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 503' Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 534 removed outlier: 4.062A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.581A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.552A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 602 removed outlier: 4.636A pdb=" N ASN A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.642A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 395 removed outlier: 3.765A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 392 through 395' Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.310A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.445A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.690A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 386 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 439 through 441 311 hydrogen bonds defined for protein. 924 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: 0.64 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1962 1.33 - 1.45: 1141 1.45 - 1.57: 3437 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 6601 Sorted by residual: bond pdb=" C LYS A 564 " pdb=" N PRO A 565 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.25e-02 6.40e+03 2.26e+01 bond pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 1.518 1.568 -0.049 1.13e-02 7.83e+03 1.91e+01 bond pdb=" CA PRO C 469 " pdb=" C PRO C 469 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.73e+01 bond pdb=" C PRO C 469 " pdb=" N PRO C 470 " ideal model delta sigma weight residual 1.333 1.362 -0.029 7.80e-03 1.64e+04 1.37e+01 bond pdb=" CA GLN A 325 " pdb=" C GLN A 325 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.28e-02 6.10e+03 1.34e+01 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 8279 2.75 - 5.49: 522 5.49 - 8.24: 122 8.24 - 10.98: 44 10.98 - 13.73: 12 Bond angle restraints: 8979 Sorted by residual: angle pdb=" N TYR A 202 " pdb=" CA TYR A 202 " pdb=" C TYR A 202 " ideal model delta sigma weight residual 111.07 97.66 13.41 1.07e+00 8.73e-01 1.57e+02 angle pdb=" N LYS A 112 " pdb=" CA LYS A 112 " pdb=" C LYS A 112 " ideal model delta sigma weight residual 111.36 98.79 12.57 1.09e+00 8.42e-01 1.33e+02 angle pdb=" N GLU C 327 " pdb=" CA GLU C 327 " pdb=" C GLU C 327 " ideal model delta sigma weight residual 111.28 123.82 -12.54 1.09e+00 8.42e-01 1.32e+02 angle pdb=" N PRO C 469 " pdb=" CA PRO C 469 " pdb=" C PRO C 469 " ideal model delta sigma weight residual 110.70 124.43 -13.73 1.22e+00 6.72e-01 1.27e+02 angle pdb=" N GLU A 212 " pdb=" CA GLU A 212 " pdb=" C GLU A 212 " ideal model delta sigma weight residual 111.07 122.83 -11.76 1.07e+00 8.73e-01 1.21e+02 ... (remaining 8974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3375 17.64 - 35.27: 334 35.27 - 52.90: 121 52.90 - 70.54: 41 70.54 - 88.17: 12 Dihedral angle restraints: 3883 sinusoidal: 1561 harmonic: 2322 Sorted by residual: dihedral pdb=" N PRO C 469 " pdb=" C PRO C 469 " pdb=" CA PRO C 469 " pdb=" CB PRO C 469 " ideal model delta harmonic sigma weight residual 115.10 127.99 -12.89 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" N PHE A 512 " pdb=" C PHE A 512 " pdb=" CA PHE A 512 " pdb=" CB PHE A 512 " ideal model delta harmonic sigma weight residual 122.80 110.27 12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C PHE A 512 " pdb=" N PHE A 512 " pdb=" CA PHE A 512 " pdb=" CB PHE A 512 " ideal model delta harmonic sigma weight residual -122.60 -110.20 -12.40 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 3880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 700 0.126 - 0.252: 180 0.252 - 0.378: 40 0.378 - 0.504: 11 0.504 - 0.630: 2 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA PRO C 469 " pdb=" N PRO C 469 " pdb=" C PRO C 469 " pdb=" CB PRO C 469 " both_signs ideal model delta sigma weight residual False 2.72 2.09 0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" CA PHE C 460 " pdb=" N PHE C 460 " pdb=" C PHE C 460 " pdb=" CB PHE C 460 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CA ASN C 473 " pdb=" N ASN C 473 " pdb=" C ASN C 473 " pdb=" CB ASN C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 930 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 468 " -0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 469 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO C 469 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 469 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 332 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C THR C 332 " 0.066 2.00e-02 2.50e+03 pdb=" O THR C 332 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS C 333 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO A 146 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.055 5.00e-02 4.00e+02 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 35 2.53 - 3.12: 5026 3.12 - 3.72: 10271 3.72 - 4.31: 14654 4.31 - 4.90: 23115 Nonbonded interactions: 53101 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 1.941 2.230 nonbonded pdb=" O ASN C 330 " pdb=" OD1 ASN C 330 " model vdw 2.076 3.040 nonbonded pdb=" OD1 ASN C 427 " pdb=" N ILE C 428 " model vdw 2.106 3.120 nonbonded pdb=" OD1 ASP C 351 " pdb=" N TYR C 352 " model vdw 2.188 3.120 nonbonded pdb=" CB TYR C 440 " pdb=" OH TYR C 481 " model vdw 2.198 3.440 ... (remaining 53096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.860 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.011 0.616 6604 Z= 0.645 Angle : 1.655 18.865 8981 Z= 1.187 Chirality : 0.126 0.630 933 Planarity : 0.009 0.114 1160 Dihedral : 17.473 88.173 2390 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.66 % Favored : 97.83 % Rotamer: Outliers : 4.45 % Allowed : 14.49 % Favored : 81.06 % Cbeta Deviations : 1.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.29), residues: 783 helix: 3.39 (0.25), residues: 379 sheet: 2.08 (0.69), residues: 49 loop : 0.02 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 357 TYR 0.018 0.002 TYR A 385 PHE 0.018 0.002 PHE A 512 TRP 0.015 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00669 ( 6601) covalent geometry : angle 1.64010 ( 8979) SS BOND : bond 0.61589 ( 1) SS BOND : angle 14.79944 ( 2) hydrogen bonds : bond 0.24909 ( 311) hydrogen bonds : angle 6.38830 ( 924) metal coordination : bond 0.23436 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 329 PHE cc_start: 0.6610 (t80) cc_final: 0.6031 (t80) REVERT: C 419 CYS cc_start: 0.6266 (m) cc_final: 0.5481 (m) outliers start: 31 outliers final: 2 residues processed: 144 average time/residue: 0.0881 time to fit residues: 15.9590 Evaluate side-chains 62 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain C residue 465 LYS 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: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 96 GLN A 194 ASN A 373 HIS A 401 HIS A 546 ASN A 598 GLN C 330 ASN C 381 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.039420 restraints weight = 28325.936| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 5.28 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6604 Z= 0.236 Angle : 0.737 10.672 8981 Z= 0.403 Chirality : 0.047 0.224 933 Planarity : 0.006 0.044 1160 Dihedral : 5.896 57.072 869 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.66 % Favored : 98.08 % Rotamer: Outliers : 3.16 % Allowed : 15.93 % Favored : 80.92 % 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: 2.00 (0.29), residues: 783 helix: 2.58 (0.26), residues: 383 sheet: 0.84 (0.68), residues: 51 loop : 0.01 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 518 TYR 0.023 0.002 TYR A 613 PHE 0.031 0.002 PHE C 483 TRP 0.015 0.002 TRP A 271 HIS 0.008 0.002 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 6601) covalent geometry : angle 0.73617 ( 8979) SS BOND : bond 0.02506 ( 1) SS BOND : angle 1.68774 ( 2) hydrogen bonds : bond 0.07976 ( 311) hydrogen bonds : angle 5.49500 ( 924) metal coordination : bond 0.01896 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 CYS cc_start: 0.9356 (p) cc_final: 0.9146 (p) REVERT: A 194 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8265 (m110) REVERT: A 481 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9291 (ttmt) REVERT: C 357 ASN cc_start: 0.9029 (m-40) cc_final: 0.8799 (m110) REVERT: C 411 LYS cc_start: 0.8524 (tppt) cc_final: 0.8230 (tppt) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 0.0721 time to fit residues: 8.1032 Evaluate side-chains 74 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 381 ASN C 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.040449 restraints weight = 27938.752| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 5.38 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6604 Z= 0.141 Angle : 0.594 10.427 8981 Z= 0.321 Chirality : 0.041 0.191 933 Planarity : 0.004 0.036 1160 Dihedral : 5.275 53.218 865 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 2.58 % Allowed : 15.64 % Favored : 81.78 % 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: 2.13 (0.30), residues: 783 helix: 2.63 (0.26), residues: 382 sheet: 1.06 (0.74), residues: 47 loop : 0.13 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 395 TYR 0.026 0.001 TYR A 613 PHE 0.015 0.001 PHE C 483 TRP 0.015 0.001 TRP A 163 HIS 0.009 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6601) covalent geometry : angle 0.59400 ( 8979) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.62621 ( 2) hydrogen bonds : bond 0.06582 ( 311) hydrogen bonds : angle 4.96672 ( 924) metal coordination : bond 0.00129 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8543 (t0) REVERT: A 481 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9297 (ttmt) REVERT: C 411 LYS cc_start: 0.8491 (tppt) cc_final: 0.8225 (tppt) outliers start: 18 outliers final: 6 residues processed: 80 average time/residue: 0.0729 time to fit residues: 7.7002 Evaluate side-chains 66 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.040079 restraints weight = 28199.087| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 5.32 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6604 Z= 0.134 Angle : 0.575 12.325 8981 Z= 0.301 Chirality : 0.040 0.192 933 Planarity : 0.004 0.040 1160 Dihedral : 4.818 26.027 861 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 1.72 % Allowed : 15.35 % Favored : 82.93 % 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: 2.12 (0.30), residues: 783 helix: 2.60 (0.25), residues: 384 sheet: 0.93 (0.73), residues: 46 loop : 0.17 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 395 TYR 0.026 0.001 TYR A 613 PHE 0.011 0.001 PHE C 483 TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6601) covalent geometry : angle 0.57459 ( 8979) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.44306 ( 2) hydrogen bonds : bond 0.05911 ( 311) hydrogen bonds : angle 4.87547 ( 924) metal coordination : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.9558 (OUTLIER) cc_final: 0.9293 (ttmt) REVERT: C 501 PHE cc_start: 0.7087 (p90) cc_final: 0.6340 (t80) REVERT: C 502 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8314 (pp20) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.0837 time to fit residues: 7.7901 Evaluate side-chains 67 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 535 HIS C 381 ASN C 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.036506 restraints weight = 29094.645| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 5.37 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6604 Z= 0.202 Angle : 0.610 8.899 8981 Z= 0.327 Chirality : 0.041 0.170 933 Planarity : 0.004 0.043 1160 Dihedral : 4.892 23.218 861 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 15.21 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.30), residues: 783 helix: 2.48 (0.26), residues: 388 sheet: 0.45 (0.77), residues: 40 loop : 0.15 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 518 TYR 0.026 0.002 TYR A 613 PHE 0.017 0.002 PHE A 523 TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6601) covalent geometry : angle 0.60989 ( 8979) SS BOND : bond 0.00461 ( 1) SS BOND : angle 0.72829 ( 2) hydrogen bonds : bond 0.06968 ( 311) hydrogen bonds : angle 4.95434 ( 924) metal coordination : bond 0.00113 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9360 (mmt) cc_final: 0.9148 (mmm) REVERT: A 270 MET cc_start: 0.9321 (tpt) cc_final: 0.8997 (tpp) REVERT: C 401 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7644 (mp10) outliers start: 17 outliers final: 10 residues processed: 71 average time/residue: 0.0886 time to fit residues: 8.3679 Evaluate side-chains 64 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 70 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.037491 restraints weight = 28478.067| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 5.25 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6604 Z= 0.139 Angle : 0.566 12.523 8981 Z= 0.297 Chirality : 0.039 0.164 933 Planarity : 0.004 0.045 1160 Dihedral : 4.702 21.192 861 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 1.87 % Allowed : 15.64 % Favored : 82.50 % 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: 2.00 (0.30), residues: 783 helix: 2.56 (0.26), residues: 385 sheet: 0.49 (0.79), residues: 40 loop : 0.09 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.021 0.001 TYR A 613 PHE 0.013 0.001 PHE C 361 TRP 0.011 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6601) covalent geometry : angle 0.56566 ( 8979) SS BOND : bond 0.00280 ( 1) SS BOND : angle 0.53398 ( 2) hydrogen bonds : bond 0.05870 ( 311) hydrogen bonds : angle 4.65421 ( 924) metal coordination : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9274 (mmt) cc_final: 0.9027 (mmm) REVERT: A 270 MET cc_start: 0.9342 (tpt) cc_final: 0.9057 (tpp) REVERT: A 474 MET cc_start: 0.8763 (mmp) cc_final: 0.8481 (mmm) REVERT: A 481 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9232 (tppt) REVERT: C 401 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7717 (mp10) REVERT: C 501 PHE cc_start: 0.7306 (p90) cc_final: 0.6216 (t80) outliers start: 13 outliers final: 7 residues processed: 65 average time/residue: 0.0968 time to fit residues: 8.3433 Evaluate side-chains 62 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.037709 restraints weight = 29072.964| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 5.52 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6604 Z= 0.126 Angle : 0.541 10.918 8981 Z= 0.284 Chirality : 0.039 0.190 933 Planarity : 0.004 0.044 1160 Dihedral : 4.569 22.327 861 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.68 % Favored : 97.19 % Rotamer: Outliers : 1.29 % Allowed : 17.36 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.30), residues: 783 helix: 2.51 (0.25), residues: 394 sheet: 0.48 (0.82), residues: 40 loop : 0.04 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 449 TYR 0.020 0.001 TYR A 613 PHE 0.013 0.001 PHE C 361 TRP 0.012 0.001 TRP A 163 HIS 0.002 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6601) covalent geometry : angle 0.54079 ( 8979) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.53585 ( 2) hydrogen bonds : bond 0.05373 ( 311) hydrogen bonds : angle 4.51299 ( 924) metal coordination : bond 0.00124 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9291 (mmt) cc_final: 0.9020 (mmm) REVERT: A 270 MET cc_start: 0.9351 (tpt) cc_final: 0.9092 (tpt) REVERT: A 481 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9255 (tppt) REVERT: C 365 LYS cc_start: 0.8120 (tptp) cc_final: 0.7874 (tptt) REVERT: C 401 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7824 (mp10) REVERT: C 501 PHE cc_start: 0.7642 (p90) cc_final: 0.6534 (t80) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.1007 time to fit residues: 7.9698 Evaluate side-chains 60 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.036821 restraints weight = 28613.990| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 5.29 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6604 Z= 0.157 Angle : 0.553 9.915 8981 Z= 0.292 Chirality : 0.039 0.184 933 Planarity : 0.004 0.044 1160 Dihedral : 4.572 20.811 861 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.72 % Allowed : 17.07 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.31), residues: 783 helix: 2.54 (0.26), residues: 391 sheet: 0.73 (0.81), residues: 40 loop : 0.01 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 449 TYR 0.019 0.001 TYR A 613 PHE 0.024 0.001 PHE C 325 TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6601) covalent geometry : angle 0.55340 ( 8979) SS BOND : bond 0.00412 ( 1) SS BOND : angle 0.67737 ( 2) hydrogen bonds : bond 0.05805 ( 311) hydrogen bonds : angle 4.55219 ( 924) metal coordination : bond 0.00130 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 376 MET cc_start: 0.9065 (tpp) cc_final: 0.8762 (tpp) REVERT: A 481 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9274 (tppt) REVERT: C 367 TYR cc_start: 0.9310 (m-80) cc_final: 0.8932 (m-10) REVERT: C 401 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7878 (mp10) REVERT: C 501 PHE cc_start: 0.7666 (p90) cc_final: 0.6594 (t80) REVERT: C 503 LEU cc_start: 0.9317 (tp) cc_final: 0.9105 (tp) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.1059 time to fit residues: 8.7393 Evaluate side-chains 62 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.052371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.036834 restraints weight = 29286.619| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 5.31 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6604 Z= 0.141 Angle : 0.570 10.551 8981 Z= 0.296 Chirality : 0.039 0.176 933 Planarity : 0.004 0.045 1160 Dihedral : 4.531 20.038 861 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.68 % Favored : 97.19 % Rotamer: Outliers : 1.29 % Allowed : 18.22 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.30), residues: 783 helix: 2.50 (0.26), residues: 394 sheet: 0.61 (0.81), residues: 40 loop : -0.09 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 449 TYR 0.019 0.001 TYR A 385 PHE 0.024 0.001 PHE C 325 TRP 0.013 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6601) covalent geometry : angle 0.57022 ( 8979) SS BOND : bond 0.00292 ( 1) SS BOND : angle 0.55963 ( 2) hydrogen bonds : bond 0.05528 ( 311) hydrogen bonds : angle 4.49684 ( 924) metal coordination : bond 0.00099 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9053 (tpp) cc_final: 0.8741 (tpp) REVERT: C 365 LYS cc_start: 0.8183 (tptp) cc_final: 0.7946 (tptp) REVERT: C 401 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7872 (mp10) REVERT: C 501 PHE cc_start: 0.7775 (p90) cc_final: 0.6756 (t80) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.1028 time to fit residues: 8.3275 Evaluate side-chains 60 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.038084 restraints weight = 29272.386| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 5.36 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6604 Z= 0.120 Angle : 0.574 10.649 8981 Z= 0.294 Chirality : 0.039 0.242 933 Planarity : 0.004 0.046 1160 Dihedral : 4.448 20.515 861 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.00 % Allowed : 18.79 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.30), residues: 783 helix: 2.59 (0.26), residues: 387 sheet: 0.55 (0.82), residues: 40 loop : -0.13 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 449 TYR 0.022 0.001 TYR A 385 PHE 0.024 0.001 PHE C 325 TRP 0.016 0.001 TRP A 477 HIS 0.002 0.000 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6601) covalent geometry : angle 0.57395 ( 8979) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.44864 ( 2) hydrogen bonds : bond 0.05032 ( 311) hydrogen bonds : angle 4.41647 ( 924) metal coordination : bond 0.00070 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9059 (tpp) cc_final: 0.8754 (tpp) REVERT: C 365 LYS cc_start: 0.8235 (tptp) cc_final: 0.7945 (tptp) REVERT: C 401 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7893 (mp10) REVERT: C 501 PHE cc_start: 0.7816 (p90) cc_final: 0.6836 (t80) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.0984 time to fit residues: 8.5245 Evaluate side-chains 61 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.0370 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.053447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.038160 restraints weight = 29911.325| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 5.35 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6604 Z= 0.121 Angle : 0.585 13.133 8981 Z= 0.297 Chirality : 0.039 0.175 933 Planarity : 0.004 0.046 1160 Dihedral : 4.426 19.887 861 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.86 % Allowed : 19.37 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.30), residues: 783 helix: 2.61 (0.26), residues: 387 sheet: 0.46 (0.83), residues: 40 loop : -0.15 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 449 TYR 0.021 0.001 TYR A 385 PHE 0.011 0.001 PHE C 325 TRP 0.019 0.001 TRP A 477 HIS 0.002 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6601) covalent geometry : angle 0.58510 ( 8979) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.49165 ( 2) hydrogen bonds : bond 0.04907 ( 311) hydrogen bonds : angle 4.40781 ( 924) metal coordination : bond 0.00063 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1336.07 seconds wall clock time: 23 minutes 44.59 seconds (1424.59 seconds total)