Starting phenix.real_space_refine on Fri Aug 2 20:15:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ke9_37150/08_2024/8ke9_37150_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ke9_37150/08_2024/8ke9_37150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ke9_37150/08_2024/8ke9_37150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ke9_37150/08_2024/8ke9_37150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ke9_37150/08_2024/8ke9_37150_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ke9_37150/08_2024/8ke9_37150_neut.cif" } resolution = 3.76 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 3 Type Number sf(0) Gaussians C 3105 2.51 5 N 837 2.21 5 O 987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 256": "OD1" <-> "OD2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4929 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1643 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain: "B" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1643 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1643 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 211} Time building chain proxies: 3.21, per 1000 atoms: 0.65 Number of scatterers: 4929 At special positions: 0 Unit cell: (66.34, 142.31, 100.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 987 8.00 N 837 7.00 C 3105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 11 sheets defined 20.3% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 245 through 266 removed outlier: 3.789A pdb=" N VAL A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'B' and resid 247 through 266 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'C' and resid 246 through 267 Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 307 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 330 removed outlier: 4.096A pdb=" N VAL A 454 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 374 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 456 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 372 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY A 458 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 370 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 348 removed outlier: 3.525A pdb=" N PHE A 321 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 458 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 454 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 374 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 456 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 372 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY A 458 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 370 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 423 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 removed outlier: 6.717A pdb=" N VAL A 394 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 404 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA5, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.521A pdb=" N GLY B 458 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 321 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 330 removed outlier: 4.861A pdb=" N VAL B 449 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 380 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU B 451 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA B 378 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP B 453 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG B 376 " --> pdb=" O ASP B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.579A pdb=" N ASN B 436 " --> pdb=" O PHE B 393 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 390 " --> pdb=" O ARG B 407 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG B 407 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 392 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 357 removed outlier: 3.627A pdb=" N ASN B 355 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 345 through 348 removed outlier: 4.177A pdb=" N PHE C 321 " --> pdb=" O GLY C 458 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C 454 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY C 327 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU C 452 " --> pdb=" O GLY C 327 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN C 329 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL C 450 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER C 448 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 380 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 454 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR C 374 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE C 456 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR C 372 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY C 458 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU C 370 " --> pdb=" O GLY C 458 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN C 460 " --> pdb=" O THR C 368 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR C 368 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.755A pdb=" N ASN C 436 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE C 393 " --> pdb=" O ASN C 436 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 438 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA C 390 " --> pdb=" O ARG C 407 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG C 407 " --> pdb=" O ALA C 390 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 392 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 355 through 356 removed outlier: 3.604A pdb=" N ASN C 355 " --> pdb=" O LEU C 362 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 609 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: 1.44 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 813 1.29 - 1.35: 825 1.35 - 1.42: 597 1.42 - 1.49: 799 1.49 - 1.56: 2000 Bond restraints: 5034 Sorted by residual: bond pdb=" C VAL B 273 " pdb=" O VAL B 273 " ideal model delta sigma weight residual 1.237 1.219 0.018 1.19e-02 7.06e+03 2.27e+00 bond pdb=" CA VAL B 273 " pdb=" CB VAL B 273 " ideal model delta sigma weight residual 1.540 1.557 -0.018 1.29e-02 6.01e+03 1.90e+00 bond pdb=" C TYR C 248 " pdb=" O TYR C 248 " ideal model delta sigma weight residual 1.236 1.221 0.015 1.15e-02 7.56e+03 1.77e+00 bond pdb=" C LEU A 270 " pdb=" O LEU A 270 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.21e-02 6.83e+03 1.71e+00 bond pdb=" C VAL A 249 " pdb=" O VAL A 249 " ideal model delta sigma weight residual 1.237 1.222 0.015 1.17e-02 7.31e+03 1.61e+00 ... (remaining 5029 not shown) Histogram of bond angle deviations from ideal: 102.27 - 109.03: 330 109.03 - 115.80: 2864 115.80 - 122.56: 2857 122.56 - 129.32: 802 129.32 - 136.08: 26 Bond angle restraints: 6879 Sorted by residual: angle pdb=" C VAL A 287 " pdb=" N LEU A 288 " pdb=" CA LEU A 288 " ideal model delta sigma weight residual 122.93 136.08 -13.15 1.45e+00 4.76e-01 8.23e+01 angle pdb=" C ASN A 282 " pdb=" N LEU A 283 " pdb=" CA LEU A 283 " ideal model delta sigma weight residual 120.28 131.22 -10.94 1.34e+00 5.57e-01 6.67e+01 angle pdb=" N LEU B 253 " pdb=" CA LEU B 253 " pdb=" C LEU B 253 " ideal model delta sigma weight residual 111.07 105.54 5.53 1.07e+00 8.73e-01 2.67e+01 angle pdb=" N LEU A 270 " pdb=" CA LEU A 270 " pdb=" C LEU A 270 " ideal model delta sigma weight residual 111.37 119.28 -7.91 1.64e+00 3.72e-01 2.33e+01 angle pdb=" N LYS B 267 " pdb=" CA LYS B 267 " pdb=" C LYS B 267 " ideal model delta sigma weight residual 108.45 113.49 -5.04 1.26e+00 6.30e-01 1.60e+01 ... (remaining 6874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2649 17.77 - 35.55: 143 35.55 - 53.32: 47 53.32 - 71.09: 18 71.09 - 88.87: 8 Dihedral angle restraints: 2865 sinusoidal: 1017 harmonic: 1848 Sorted by residual: dihedral pdb=" CA ASN B 284 " pdb=" C ASN B 284 " pdb=" N GLY B 285 " pdb=" CA GLY B 285 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C ASN B 290 " pdb=" N ASN B 290 " pdb=" CA ASN B 290 " pdb=" CB ASN B 290 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C VAL B 273 " pdb=" N VAL B 273 " pdb=" CA VAL B 273 " pdb=" CB VAL B 273 " ideal model delta harmonic sigma weight residual -122.00 -131.19 9.19 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 2862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 793 0.345 - 0.689: 4 0.689 - 1.034: 0 1.034 - 1.379: 0 1.379 - 1.723: 1 Chirality restraints: 798 Sorted by residual: chirality pdb=" CG LEU B 283 " pdb=" CB LEU B 283 " pdb=" CD1 LEU B 283 " pdb=" CD2 LEU B 283 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.42e+01 chirality pdb=" CA LEU B 288 " pdb=" N LEU B 288 " pdb=" C LEU B 288 " pdb=" CB LEU B 288 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA LEU A 288 " pdb=" N LEU A 288 " pdb=" C LEU A 288 " pdb=" CB LEU A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 795 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 273 " -0.005 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C VAL B 273 " 0.019 2.00e-02 2.50e+03 pdb=" O VAL B 273 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN B 274 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 412 " -0.016 5.00e-02 4.00e+02 2.49e-02 9.94e-01 pdb=" N PRO A 413 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 249 " -0.005 2.00e-02 2.50e+03 9.15e-03 8.37e-01 pdb=" C VAL A 249 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL A 249 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN A 250 " -0.005 2.00e-02 2.50e+03 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 87 2.52 - 3.12: 4191 3.12 - 3.71: 8315 3.71 - 4.31: 11712 4.31 - 4.90: 19104 Nonbonded interactions: 43409 Sorted by model distance: nonbonded pdb=" O GLN C 276 " pdb=" OG SER C 279 " model vdw 1.931 3.040 nonbonded pdb=" O GLU B 365 " pdb=" OH TYR B 369 " model vdw 2.001 3.040 nonbonded pdb=" OG1 THR A 340 " pdb=" OD1 ASN A 436 " model vdw 2.019 3.040 nonbonded pdb=" OG SER A 333 " pdb=" OG SER A 335 " model vdw 2.039 3.040 nonbonded pdb=" OG1 THR B 303 " pdb=" OG1 THR C 292 " model vdw 2.050 3.040 ... (remaining 43404 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.850 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5034 Z= 0.203 Angle : 0.704 13.153 6879 Z= 0.417 Chirality : 0.081 1.723 798 Planarity : 0.003 0.030 897 Dihedral : 14.469 88.867 1695 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.71 % Favored : 94.14 % Rotamer: Outliers : 7.55 % Allowed : 6.81 % Favored : 85.64 % 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: -1.09 (0.32), residues: 648 helix: -0.53 (0.41), residues: 132 sheet: 0.26 (0.36), residues: 222 loop : -1.58 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 361 HIS 0.002 0.001 HIS C 310 PHE 0.015 0.001 PHE B 321 TYR 0.007 0.001 TYR A 387 ARG 0.005 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 91 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9393 (m) cc_final: 0.9031 (p) REVERT: A 344 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7116 (m-40) REVERT: A 365 GLU cc_start: 0.8762 (tt0) cc_final: 0.8146 (tt0) REVERT: B 391 LEU cc_start: 0.8550 (mp) cc_final: 0.8014 (tt) REVERT: B 419 LEU cc_start: 0.7695 (mp) cc_final: 0.7341 (tt) REVERT: C 365 GLU cc_start: 0.8504 (tt0) cc_final: 0.8298 (mm-30) REVERT: C 371 ILE cc_start: 0.8179 (mm) cc_final: 0.7833 (mp) REVERT: C 425 LEU cc_start: 0.8647 (mt) cc_final: 0.8371 (mt) outliers start: 41 outliers final: 7 residues processed: 115 average time/residue: 0.1915 time to fit residues: 27.3450 Evaluate side-chains 62 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5034 Z= 0.275 Angle : 0.690 9.387 6879 Z= 0.360 Chirality : 0.046 0.212 798 Planarity : 0.004 0.030 897 Dihedral : 6.927 57.340 724 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.68 % Allowed : 12.71 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.33), residues: 648 helix: 0.45 (0.43), residues: 135 sheet: 0.23 (0.35), residues: 231 loop : -1.31 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 361 HIS 0.004 0.001 HIS B 310 PHE 0.021 0.002 PHE A 434 TYR 0.023 0.002 TYR A 248 ARG 0.006 0.001 ARG C 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 GLU cc_start: 0.8728 (tt0) cc_final: 0.8129 (tt0) REVERT: A 389 ASP cc_start: 0.7247 (t0) cc_final: 0.6425 (t0) REVERT: C 365 GLU cc_start: 0.8693 (tt0) cc_final: 0.8455 (mm-30) REVERT: C 412 TYR cc_start: 0.9085 (m-80) cc_final: 0.8665 (m-80) outliers start: 20 outliers final: 13 residues processed: 64 average time/residue: 0.1973 time to fit residues: 16.5996 Evaluate side-chains 55 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 269 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5034 Z= 0.263 Angle : 0.667 10.272 6879 Z= 0.342 Chirality : 0.045 0.200 798 Planarity : 0.004 0.080 897 Dihedral : 6.142 47.151 715 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.02 % Favored : 93.83 % Rotamer: Outliers : 4.42 % Allowed : 12.89 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.33), residues: 648 helix: 1.14 (0.43), residues: 135 sheet: 0.22 (0.35), residues: 227 loop : -1.18 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 361 HIS 0.003 0.001 HIS C 310 PHE 0.018 0.002 PHE A 393 TYR 0.011 0.002 TYR A 412 ARG 0.009 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 44 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 GLU cc_start: 0.8678 (tt0) cc_final: 0.8062 (tt0) REVERT: A 369 TYR cc_start: 0.8166 (m-80) cc_final: 0.7725 (m-10) REVERT: B 263 LEU cc_start: 0.9248 (mt) cc_final: 0.9037 (pp) REVERT: C 365 GLU cc_start: 0.8814 (tt0) cc_final: 0.8573 (mm-30) REVERT: C 412 TYR cc_start: 0.9152 (m-80) cc_final: 0.8750 (m-80) outliers start: 24 outliers final: 18 residues processed: 60 average time/residue: 0.1274 time to fit residues: 11.0178 Evaluate side-chains 56 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 38 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 269 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 HIS C 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5034 Z= 0.308 Angle : 0.655 8.158 6879 Z= 0.338 Chirality : 0.043 0.161 798 Planarity : 0.004 0.071 897 Dihedral : 6.093 48.605 713 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 5.52 % Allowed : 12.89 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.33), residues: 648 helix: 1.00 (0.44), residues: 135 sheet: 0.17 (0.36), residues: 223 loop : -1.32 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 352 HIS 0.004 0.001 HIS A 310 PHE 0.019 0.002 PHE B 321 TYR 0.019 0.002 TYR A 417 ARG 0.011 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 37 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8324 (mmtt) REVERT: C 412 TYR cc_start: 0.9250 (m-80) cc_final: 0.8860 (m-80) outliers start: 30 outliers final: 19 residues processed: 58 average time/residue: 0.1301 time to fit residues: 10.7037 Evaluate side-chains 54 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 34 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 407 ARG Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 409 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 0.0770 chunk 51 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 40.0000 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN C 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5034 Z= 0.215 Angle : 0.633 13.056 6879 Z= 0.319 Chirality : 0.043 0.139 798 Planarity : 0.004 0.065 897 Dihedral : 5.917 49.434 713 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.02 % Favored : 93.83 % Rotamer: Outliers : 3.68 % Allowed : 15.29 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.33), residues: 648 helix: 1.15 (0.45), residues: 135 sheet: 0.11 (0.37), residues: 213 loop : -1.30 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 361 HIS 0.003 0.001 HIS A 310 PHE 0.018 0.002 PHE A 434 TYR 0.012 0.002 TYR B 248 ARG 0.005 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 33 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9538 (m) cc_final: 0.9271 (p) REVERT: B 267 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8384 (mmtt) REVERT: B 365 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8216 (tm-30) REVERT: C 371 ILE cc_start: 0.7602 (mm) cc_final: 0.7114 (mp) REVERT: C 412 TYR cc_start: 0.9250 (m-80) cc_final: 0.8866 (m-80) outliers start: 20 outliers final: 13 residues processed: 47 average time/residue: 0.1358 time to fit residues: 9.1161 Evaluate side-chains 45 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 31 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 434 PHE Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 50.0000 chunk 32 optimal weight: 0.2980 chunk 58 optimal weight: 20.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5034 Z= 0.205 Angle : 0.636 15.005 6879 Z= 0.318 Chirality : 0.042 0.137 798 Planarity : 0.004 0.056 897 Dihedral : 5.589 48.874 711 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.71 % Favored : 94.14 % Rotamer: Outliers : 3.13 % Allowed : 16.39 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.33), residues: 648 helix: 1.17 (0.45), residues: 135 sheet: 0.16 (0.37), residues: 213 loop : -1.26 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 361 HIS 0.003 0.001 HIS A 310 PHE 0.015 0.002 PHE A 434 TYR 0.014 0.002 TYR C 417 ARG 0.004 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 34 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9560 (m) cc_final: 0.9292 (p) REVERT: B 267 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8443 (mmtt) REVERT: C 371 ILE cc_start: 0.7569 (mm) cc_final: 0.7080 (mp) REVERT: C 412 TYR cc_start: 0.9272 (m-80) cc_final: 0.9023 (m-80) outliers start: 17 outliers final: 11 residues processed: 44 average time/residue: 0.1201 time to fit residues: 7.9255 Evaluate side-chains 45 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 38 optimal weight: 0.0070 chunk 37 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5034 Z= 0.229 Angle : 0.635 12.508 6879 Z= 0.323 Chirality : 0.043 0.240 798 Planarity : 0.004 0.059 897 Dihedral : 5.420 49.950 709 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 3.13 % Allowed : 17.68 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.33), residues: 648 helix: 1.19 (0.46), residues: 135 sheet: 0.20 (0.37), residues: 207 loop : -1.34 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 361 HIS 0.003 0.001 HIS A 310 PHE 0.015 0.002 PHE B 321 TYR 0.013 0.002 TYR C 412 ARG 0.011 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 33 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9589 (m) cc_final: 0.9347 (p) REVERT: B 267 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8486 (mmtt) REVERT: B 365 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 412 TYR cc_start: 0.9278 (m-80) cc_final: 0.8947 (m-80) outliers start: 17 outliers final: 13 residues processed: 44 average time/residue: 0.1370 time to fit residues: 8.7925 Evaluate side-chains 44 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 30 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 41 optimal weight: 40.0000 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 40.0000 chunk 58 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5034 Z= 0.191 Angle : 0.608 12.887 6879 Z= 0.307 Chirality : 0.042 0.197 798 Planarity : 0.004 0.053 897 Dihedral : 5.261 51.367 709 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.29 % Rotamer: Outliers : 2.95 % Allowed : 18.23 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.33), residues: 648 helix: 1.26 (0.45), residues: 135 sheet: 0.31 (0.37), residues: 206 loop : -1.31 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 361 HIS 0.003 0.001 HIS A 310 PHE 0.014 0.001 PHE A 434 TYR 0.013 0.002 TYR C 412 ARG 0.005 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 32 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9585 (m) cc_final: 0.9346 (p) REVERT: B 267 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8536 (mmtt) REVERT: B 365 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 412 TYR cc_start: 0.9286 (m-80) cc_final: 0.8915 (m-80) outliers start: 16 outliers final: 12 residues processed: 42 average time/residue: 0.1460 time to fit residues: 8.8860 Evaluate side-chains 45 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 20.0000 chunk 41 optimal weight: 40.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5034 Z= 0.186 Angle : 0.619 12.876 6879 Z= 0.312 Chirality : 0.043 0.194 798 Planarity : 0.004 0.055 897 Dihedral : 5.210 52.379 709 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.09 % Favored : 94.75 % Rotamer: Outliers : 2.58 % Allowed : 18.78 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.33), residues: 648 helix: 1.10 (0.45), residues: 135 sheet: 0.37 (0.37), residues: 206 loop : -1.26 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 361 HIS 0.003 0.001 HIS A 310 PHE 0.012 0.001 PHE B 321 TYR 0.011 0.002 TYR B 248 ARG 0.005 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 34 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9588 (m) cc_final: 0.9348 (p) REVERT: A 368 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8644 (p) REVERT: B 267 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (mmtt) REVERT: B 365 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 412 TYR cc_start: 0.9281 (m-80) cc_final: 0.8873 (m-10) outliers start: 14 outliers final: 11 residues processed: 43 average time/residue: 0.1437 time to fit residues: 8.7025 Evaluate side-chains 44 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 40.0000 chunk 57 optimal weight: 8.9990 chunk 49 optimal weight: 0.0570 chunk 5 optimal weight: 0.0470 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 overall best weight: 2.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5034 Z= 0.156 Angle : 0.620 13.413 6879 Z= 0.311 Chirality : 0.043 0.185 798 Planarity : 0.003 0.054 897 Dihedral : 5.069 53.350 709 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 2.21 % Allowed : 19.15 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.34), residues: 648 helix: 1.13 (0.45), residues: 135 sheet: 0.39 (0.37), residues: 207 loop : -1.24 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 421 HIS 0.002 0.000 HIS A 310 PHE 0.012 0.001 PHE A 434 TYR 0.016 0.001 TYR B 248 ARG 0.005 0.000 ARG B 407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9578 (m) cc_final: 0.9340 (p) REVERT: A 368 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8761 (p) REVERT: B 267 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8513 (mmtt) REVERT: B 365 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 371 ILE cc_start: 0.7595 (mm) cc_final: 0.7080 (mp) REVERT: C 412 TYR cc_start: 0.9239 (m-80) cc_final: 0.8854 (m-10) outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.2188 time to fit residues: 12.0890 Evaluate side-chains 45 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 40.0000 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 0.0470 chunk 33 optimal weight: 9.9990 overall best weight: 6.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.039061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.031185 restraints weight = 39319.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.032319 restraints weight = 23393.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.033117 restraints weight = 16125.924| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5034 Z= 0.262 Angle : 0.646 13.485 6879 Z= 0.328 Chirality : 0.042 0.166 798 Planarity : 0.004 0.058 897 Dihedral : 5.306 54.513 709 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 2.21 % Allowed : 19.15 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.33), residues: 648 helix: 0.75 (0.45), residues: 135 sheet: 0.30 (0.36), residues: 208 loop : -1.32 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 352 HIS 0.004 0.001 HIS A 310 PHE 0.014 0.002 PHE B 321 TYR 0.014 0.002 TYR C 412 ARG 0.006 0.000 ARG B 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.35 seconds wall clock time: 24 minutes 11.18 seconds (1451.18 seconds total)