Starting phenix.real_space_refine on Thu Jan 16 18:14:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzb_38792/01_2025/8xzb_38792_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzb_38792/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xzb_38792/01_2025/8xzb_38792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzb_38792/01_2025/8xzb_38792.map" model { file = "/net/cci-nas-00/data/ceres_data/8xzb_38792/01_2025/8xzb_38792_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzb_38792/01_2025/8xzb_38792_neut.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 4.42, per 1000 atoms: 0.69 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: 1.40 Conformation dependent library (CDL) restraints added in 875.4 milliseconds 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: 0.56 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: 1.73 Time building geometry restraints manager: 1.68 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- 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 : 0.007 0.059 6601 Z= 0.442 Angle : 1.640 13.730 8979 Z= 1.182 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 : 19.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (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 TRP 0.015 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.018 0.002 PHE A 512 TYR 0.018 0.002 TYR A 385 ARG 0.003 0.001 ARG A 357 *********************** 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 : 0.721 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: 0.6032 (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: 0.2433 time to fit residues: 43.5727 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 : 0.775 ------------------------------------------------------------------------------- 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 65 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.054737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.039356 restraints weight = 27723.674| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 5.32 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6601 Z= 0.318 Angle : 0.727 10.032 8979 Z= 0.398 Chirality : 0.046 0.218 933 Planarity : 0.006 0.044 1160 Dihedral : 5.901 57.014 869 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.53 % Favored : 98.21 % Rotamer: Outliers : 3.01 % Allowed : 16.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.29), residues: 783 helix: 2.61 (0.26), residues: 383 sheet: 0.83 (0.68), residues: 51 loop : 0.01 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 271 HIS 0.005 0.001 HIS A 265 PHE 0.028 0.002 PHE C 483 TYR 0.024 0.002 TYR A 613 ARG 0.004 0.001 ARG C 395 *********************** 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 88 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 CYS cc_start: 0.9367 (p) cc_final: 0.9158 (p) REVERT: A 194 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8236 (m110) REVERT: A 249 MET cc_start: 0.8876 (tpp) cc_final: 0.8617 (mmt) REVERT: A 481 LYS cc_start: 0.9522 (OUTLIER) cc_final: 0.9268 (ttmt) REVERT: C 334 PHE cc_start: 0.8527 (m-80) cc_final: 0.8286 (m-80) REVERT: C 357 ASN cc_start: 0.9043 (m-40) cc_final: 0.8817 (m110) REVERT: C 411 LYS cc_start: 0.8530 (tppt) cc_final: 0.8238 (tppt) outliers start: 21 outliers final: 11 residues processed: 82 average time/residue: 0.1894 time to fit residues: 21.0301 Evaluate side-chains 72 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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 25 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.040280 restraints weight = 28111.172| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 5.41 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6601 Z= 0.185 Angle : 0.604 10.636 8979 Z= 0.324 Chirality : 0.042 0.236 933 Planarity : 0.004 0.036 1160 Dihedral : 5.300 53.653 865 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.17 % Favored : 97.70 % Rotamer: Outliers : 2.30 % Allowed : 15.64 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.30), residues: 783 helix: 2.64 (0.25), residues: 382 sheet: 0.63 (0.72), residues: 46 loop : 0.14 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.011 0.001 HIS A 401 PHE 0.015 0.001 PHE C 483 TYR 0.028 0.001 TYR A 613 ARG 0.003 0.000 ARG C 395 *********************** 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 81 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8567 (t0) REVERT: A 270 MET cc_start: 0.9181 (tpt) cc_final: 0.8956 (tpt) REVERT: A 481 LYS cc_start: 0.9567 (OUTLIER) cc_final: 0.9310 (ttmt) REVERT: A 512 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.9005 (m-80) REVERT: C 411 LYS cc_start: 0.8537 (tppt) cc_final: 0.8258 (tppt) outliers start: 16 outliers final: 6 residues processed: 78 average time/residue: 0.2109 time to fit residues: 21.6848 Evaluate side-chains 67 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 512 PHE 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 73 optimal weight: 0.0060 chunk 24 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 69 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.2602 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.053751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.038251 restraints weight = 28829.039| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 5.41 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6601 Z= 0.240 Angle : 0.595 11.696 8979 Z= 0.315 Chirality : 0.041 0.189 933 Planarity : 0.004 0.038 1160 Dihedral : 4.918 25.732 861 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.17 % Favored : 97.70 % Rotamer: Outliers : 2.15 % Allowed : 15.78 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.30), residues: 783 helix: 2.58 (0.25), residues: 384 sheet: 0.65 (0.77), residues: 40 loop : 0.17 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.004 0.001 HIS A 401 PHE 0.014 0.001 PHE A 523 TYR 0.025 0.001 TYR A 613 ARG 0.003 0.000 ARG C 395 *********************** 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 73 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9294 (ttmt) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.1972 time to fit residues: 18.2610 Evaluate side-chains 70 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 532 ILE Chi-restraints excluded: chain A residue 579 MET 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 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 58 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 61 optimal weight: 0.0030 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 137 ASN C 424 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.039486 restraints weight = 28199.075| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 5.27 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6601 Z= 0.172 Angle : 0.560 12.242 8979 Z= 0.293 Chirality : 0.040 0.185 933 Planarity : 0.004 0.043 1160 Dihedral : 4.711 23.832 861 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.81 % Favored : 97.06 % Rotamer: Outliers : 2.30 % Allowed : 16.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.30), residues: 783 helix: 2.60 (0.26), residues: 384 sheet: 0.64 (0.79), residues: 40 loop : 0.15 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.002 0.001 HIS A 265 PHE 0.017 0.001 PHE C 361 TYR 0.025 0.001 TYR A 613 ARG 0.003 0.000 ARG C 395 *********************** 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 77 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8759 (t0) REVERT: C 414 ASP cc_start: 0.8675 (p0) cc_final: 0.8289 (p0) REVERT: C 417 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5760 (mpp) REVERT: C 501 PHE cc_start: 0.7341 (p90) cc_final: 0.6324 (t80) outliers start: 16 outliers final: 9 residues processed: 73 average time/residue: 0.1990 time to fit residues: 19.4046 Evaluate side-chains 67 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 417 MET 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 29 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3087 r_free = 0.3087 target = 0.054105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.038538 restraints weight = 28276.913| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 5.36 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6601 Z= 0.206 Angle : 0.559 13.160 8979 Z= 0.292 Chirality : 0.040 0.157 933 Planarity : 0.004 0.045 1160 Dihedral : 4.668 22.005 861 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 16.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.30), residues: 783 helix: 2.62 (0.26), residues: 385 sheet: 0.42 (0.78), residues: 38 loop : 0.12 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.011 0.001 PHE A 523 TYR 0.024 0.001 TYR A 613 ARG 0.004 0.000 ARG C 449 *********************** 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 79 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 501 PHE cc_start: 0.7530 (p90) cc_final: 0.6490 (t80) outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 0.1965 time to fit residues: 19.6336 Evaluate side-chains 66 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 512 PHE Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 366 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 420 VAL 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 48 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 0 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3091 r_free = 0.3091 target = 0.054212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.038686 restraints weight = 28579.247| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 5.31 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6601 Z= 0.182 Angle : 0.561 11.551 8979 Z= 0.291 Chirality : 0.039 0.188 933 Planarity : 0.004 0.045 1160 Dihedral : 4.527 22.121 861 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.68 % Favored : 97.19 % Rotamer: Outliers : 1.87 % Allowed : 17.50 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.30), residues: 783 helix: 2.54 (0.25), residues: 394 sheet: 0.36 (0.79), residues: 40 loop : 0.01 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.005 0.001 HIS A 378 PHE 0.015 0.001 PHE C 361 TYR 0.023 0.001 TYR A 613 ARG 0.006 0.000 ARG C 449 *********************** 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 68 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: C 501 PHE cc_start: 0.7679 (p90) cc_final: 0.6714 (t80) outliers start: 13 outliers final: 11 residues processed: 63 average time/residue: 0.2108 time to fit residues: 17.6589 Evaluate side-chains 65 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 366 CYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 420 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 48 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 = 0.3056 r_free = 0.3056 target = 0.052896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.037467 restraints weight = 29164.032| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 5.38 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6601 Z= 0.234 Angle : 0.573 11.141 8979 Z= 0.301 Chirality : 0.040 0.181 933 Planarity : 0.004 0.044 1160 Dihedral : 4.585 21.212 861 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.58 % Allowed : 17.79 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.30), residues: 783 helix: 2.56 (0.26), residues: 394 sheet: 0.48 (0.81), residues: 38 loop : 0.02 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.022 0.001 PHE C 325 TYR 0.021 0.001 TYR A 613 ARG 0.004 0.000 ARG C 449 *********************** 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 67 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.9182 (tpt) cc_final: 0.8737 (tpp) REVERT: A 376 MET cc_start: 0.9056 (tpp) cc_final: 0.8743 (tpp) REVERT: A 474 MET cc_start: 0.8791 (mmp) cc_final: 0.8498 (mmm) REVERT: C 501 PHE cc_start: 0.7778 (p90) cc_final: 0.6804 (t80) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.2173 time to fit residues: 18.4979 Evaluate side-chains 63 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 401 HIS 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 404 VAL Chi-restraints excluded: chain C residue 420 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 66 optimal weight: 0.8980 chunk 11 optimal weight: 0.0770 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.054934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.039631 restraints weight = 28555.095| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 5.34 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6601 Z= 0.160 Angle : 0.567 11.640 8979 Z= 0.290 Chirality : 0.039 0.181 933 Planarity : 0.004 0.045 1160 Dihedral : 4.426 20.398 861 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.68 % Favored : 97.19 % Rotamer: Outliers : 1.58 % Allowed : 18.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.30), residues: 783 helix: 2.53 (0.26), residues: 394 sheet: 0.54 (0.84), residues: 40 loop : -0.09 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.000 HIS A 265 PHE 0.027 0.001 PHE C 325 TYR 0.022 0.001 TYR A 385 ARG 0.004 0.000 ARG C 449 *********************** 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 69 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9012 (tpp) cc_final: 0.8685 (tpp) REVERT: C 417 MET cc_start: 0.6459 (mpp) cc_final: 0.5503 (mpp) REVERT: C 501 PHE cc_start: 0.7946 (p90) cc_final: 0.7098 (t80) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.2237 time to fit residues: 19.5206 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 : 0.725 ------------------------------------------------------------------------------- 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 364 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 420 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 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.0670 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.053900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.038710 restraints weight = 29360.705| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 5.36 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6601 Z= 0.177 Angle : 0.571 11.135 8979 Z= 0.291 Chirality : 0.039 0.200 933 Planarity : 0.004 0.045 1160 Dihedral : 4.393 19.790 861 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.29 % Allowed : 19.80 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.30), residues: 783 helix: 2.69 (0.26), residues: 387 sheet: 0.40 (0.84), residues: 40 loop : -0.08 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.002 0.001 HIS A 378 PHE 0.023 0.001 PHE C 325 TYR 0.020 0.001 TYR A 385 ARG 0.004 0.000 ARG C 449 ********************** 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 63 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9047 (tpp) cc_final: 0.8739 (tpp) REVERT: C 367 TYR cc_start: 0.9327 (m-80) cc_final: 0.9112 (m-80) REVERT: C 501 PHE cc_start: 0.8017 (p90) cc_final: 0.7116 (t80) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.2233 time to fit residues: 17.5593 Evaluate side-chains 60 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 364 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 420 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 17 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.054968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.039676 restraints weight = 29982.735| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 5.47 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6601 Z= 0.157 Angle : 0.567 10.920 8979 Z= 0.287 Chirality : 0.039 0.177 933 Planarity : 0.004 0.045 1160 Dihedral : 4.316 19.621 861 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.15 % Allowed : 19.66 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.30), residues: 783 helix: 2.68 (0.26), residues: 387 sheet: 0.57 (0.85), residues: 40 loop : -0.13 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.002 0.000 HIS A 378 PHE 0.024 0.001 PHE C 325 TYR 0.022 0.001 TYR A 385 ARG 0.004 0.000 ARG C 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.72 seconds wall clock time: 46 minutes 33.93 seconds (2793.93 seconds total)