Starting phenix.real_space_refine on Thu Jun 27 22:20:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8n_39849/06_2024/8z8n_39849.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8n_39849/06_2024/8z8n_39849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8n_39849/06_2024/8z8n_39849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8n_39849/06_2024/8z8n_39849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8n_39849/06_2024/8z8n_39849.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8n_39849/06_2024/8z8n_39849.pdb" } resolution = 2.79 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= 0.004 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 1345 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 P 14 5.49 5 S 75 5.16 5 C 7868 2.51 5 N 2174 2.21 5 O 2354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12485 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5020 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5254 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 33, 'TRANS': 622} Chain breaks: 3 Chain: "C" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1891 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 16, 'TRANS': 216} Chain breaks: 2 Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Time building chain proxies: 7.04, per 1000 atoms: 0.56 Number of scatterers: 12485 At special positions: 0 Unit cell: (90.7446, 103.323, 137.465, 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) S 75 16.00 P 14 15.00 O 2354 8.00 N 2174 7.00 C 7868 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: 4.87 Conformation dependent library (CDL) restraints added in 2.2 seconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 14 sheets defined 49.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.411A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.669A pdb=" N ILE A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 155 removed outlier: 3.639A pdb=" N ASN A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.569A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 removed outlier: 4.416A pdb=" N ILE A 299 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.032A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.437A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.739A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 516 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.505A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.883A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.544A pdb=" N THR B 5 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.548A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 108 removed outlier: 3.582A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.821A pdb=" N GLU B 117 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.711A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.421A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 removed outlier: 4.239A pdb=" N ALA B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.773A pdb=" N LEU B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.828A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Proline residue: B 338 - end of helix removed outlier: 3.535A pdb=" N SER B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 3.546A pdb=" N VAL B 377 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 removed outlier: 4.073A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.604A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 514 removed outlier: 3.515A pdb=" N ALA B 502 " --> pdb=" O MET B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 588 through 595 removed outlier: 3.502A pdb=" N ARG B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 666 Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 708 removed outlier: 3.933A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.618A pdb=" N SER C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 36 removed outlier: 6.265A pdb=" N THR C 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.741A pdb=" N ARG C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 115 through 122 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 191 through 207 Proline residue: C 202 - end of helix removed outlier: 3.849A pdb=" N LYS C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.985A pdb=" N MET C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.321A pdb=" N ALA A 95 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 117 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS A 97 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.375A pdb=" N ASN B 453 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 238 removed outlier: 4.557A pdb=" N ILE A 450 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 430 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 431 current: chain 'A' and resid 464 through 468 removed outlier: 6.535A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.712A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 430 " --> pdb=" O LEU A 446 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 442 through 451 current: chain 'A' and resid 290 through 291 Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.640A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 removed outlier: 3.506A pdb=" N ASN B 227 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB4, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'C' and resid 151 through 154 537 hydrogen bonds defined for protein. 1509 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: 4.20 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3906 1.34 - 1.45: 1765 1.45 - 1.57: 6971 1.57 - 1.69: 27 1.69 - 1.81: 122 Bond restraints: 12791 Sorted by residual: bond pdb=" CB PRO C 53 " pdb=" CG PRO C 53 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.44e+00 bond pdb=" CG GLU A 150 " pdb=" CD GLU A 150 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" C SER B 463 " pdb=" N PRO B 464 " ideal model delta sigma weight residual 1.334 1.358 -0.025 2.34e-02 1.83e+03 1.10e+00 bond pdb=" CB PRO A 525 " pdb=" CG PRO A 525 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.10e+00 bond pdb=" C VAL B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 ... (remaining 12786 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.59: 515 106.59 - 113.48: 7029 113.48 - 120.37: 4707 120.37 - 127.26: 4942 127.26 - 134.15: 192 Bond angle restraints: 17385 Sorted by residual: angle pdb=" N GLU A 150 " pdb=" CA GLU A 150 " pdb=" CB GLU A 150 " ideal model delta sigma weight residual 110.39 117.27 -6.88 1.66e+00 3.63e-01 1.72e+01 angle pdb=" C LEU A 149 " pdb=" N GLU A 150 " pdb=" CA GLU A 150 " ideal model delta sigma weight residual 120.72 114.70 6.02 1.67e+00 3.59e-01 1.30e+01 angle pdb=" CA GLU A 150 " pdb=" CB GLU A 150 " pdb=" CG GLU A 150 " ideal model delta sigma weight residual 114.10 119.46 -5.36 2.00e+00 2.50e-01 7.19e+00 angle pdb=" C ASN A 155 " pdb=" N ASN A 156 " pdb=" CA ASN A 156 " ideal model delta sigma weight residual 122.82 126.58 -3.76 1.42e+00 4.96e-01 7.03e+00 angle pdb=" C SER B 8 " pdb=" N GLU B 9 " pdb=" CA GLU B 9 " ideal model delta sigma weight residual 121.54 126.57 -5.03 1.91e+00 2.74e-01 6.94e+00 ... (remaining 17380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 7129 17.12 - 34.24: 552 34.24 - 51.36: 87 51.36 - 68.49: 24 68.49 - 85.61: 13 Dihedral angle restraints: 7805 sinusoidal: 3370 harmonic: 4435 Sorted by residual: dihedral pdb=" CA GLU A 81 " pdb=" C GLU A 81 " pdb=" N ARG A 82 " pdb=" CA ARG A 82 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LEU A 157 " pdb=" C LEU A 157 " pdb=" N THR A 158 " pdb=" CA THR A 158 " ideal model delta harmonic sigma weight residual 180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CB GLU C 26 " pdb=" CG GLU C 26 " pdb=" CD GLU C 26 " pdb=" OE1 GLU C 26 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 3.00e+01 1.11e-03 9.85e+00 ... (remaining 7802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1266 0.032 - 0.064: 475 0.064 - 0.096: 133 0.096 - 0.128: 65 0.128 - 0.160: 8 Chirality restraints: 1947 Sorted by residual: chirality pdb=" CA ASN A 156 " pdb=" N ASN A 156 " pdb=" C ASN A 156 " pdb=" CB ASN A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CB ILE B 10 " pdb=" CA ILE B 10 " pdb=" CG1 ILE B 10 " pdb=" CG2 ILE B 10 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA GLU A 150 " pdb=" N GLU A 150 " pdb=" C GLU A 150 " pdb=" CB GLU A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1944 not shown) Planarity restraints: 2169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 52 " 0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO C 53 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 288 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.70e+00 pdb=" N PRO A 289 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO B 97 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.028 5.00e-02 4.00e+02 ... (remaining 2166 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 238 2.67 - 3.23: 12118 3.23 - 3.79: 19892 3.79 - 4.34: 27804 4.34 - 4.90: 45217 Nonbonded interactions: 105269 Sorted by model distance: nonbonded pdb=" OE1 GLU B 141 " pdb=" OH TYR B 176 " model vdw 2.114 2.440 nonbonded pdb=" OG1 THR B 679 " pdb=" OE1 GLU B 682 " model vdw 2.119 2.440 nonbonded pdb=" OG SER A 400 " pdb=" OE1 GLN A 401 " model vdw 2.151 2.440 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.151 2.440 nonbonded pdb=" OD2 ASP A 21 " pdb=" OG1 THR A 24 " model vdw 2.182 2.440 ... (remaining 105264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 2.250 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 35.540 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 0.060 12791 Z= 0.168 Angle : 0.559 9.167 17385 Z= 0.290 Chirality : 0.040 0.160 1947 Planarity : 0.006 0.096 2169 Dihedral : 12.853 85.607 4923 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.21), residues: 1494 helix: 0.75 (0.20), residues: 684 sheet: -0.63 (0.45), residues: 119 loop : -1.21 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 62 HIS 0.006 0.001 HIS A 403 PHE 0.023 0.001 PHE A 483 TYR 0.015 0.001 TYR B 176 ARG 0.009 0.001 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7762 (mp) cc_final: 0.7151 (mp) REVERT: A 142 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7272 (ttmm) REVERT: B 592 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8181 (mmm-85) REVERT: B 656 GLN cc_start: 0.7387 (tp-100) cc_final: 0.7104 (tp-100) REVERT: C 161 GLU cc_start: 0.7366 (mp0) cc_final: 0.6986 (mp0) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 1.4242 time to fit residues: 402.6886 Evaluate side-chains 177 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 0.0470 chunk 118 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 304 ASN B 302 GLN B 429 ASN B 471 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12791 Z= 0.375 Angle : 0.672 9.270 17385 Z= 0.346 Chirality : 0.046 0.158 1947 Planarity : 0.006 0.069 2169 Dihedral : 8.802 75.463 1860 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.51 % Allowed : 10.71 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1494 helix: 0.56 (0.19), residues: 706 sheet: -0.77 (0.46), residues: 113 loop : -1.25 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 62 HIS 0.007 0.001 HIS A 573 PHE 0.029 0.002 PHE A 483 TYR 0.022 0.002 TYR B 533 ARG 0.008 0.001 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: A 160 GLU cc_start: 0.8650 (pm20) cc_final: 0.8449 (pm20) REVERT: A 507 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: B 109 LYS cc_start: 0.8605 (mptp) cc_final: 0.8112 (mtpt) REVERT: B 141 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6722 (tp30) REVERT: B 378 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7217 (ptt-90) REVERT: B 395 MET cc_start: 0.8505 (mtp) cc_final: 0.8229 (mtp) REVERT: B 592 ARG cc_start: 0.8451 (mtt180) cc_final: 0.8207 (mmm-85) REVERT: C 30 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: C 136 THR cc_start: 0.8215 (p) cc_final: 0.8013 (p) REVERT: C 161 GLU cc_start: 0.7541 (mp0) cc_final: 0.7173 (mp0) outliers start: 34 outliers final: 14 residues processed: 216 average time/residue: 1.4092 time to fit residues: 327.5416 Evaluate side-chains 189 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 211 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 172 GLN A 304 ASN B 429 ASN B 656 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12791 Z= 0.215 Angle : 0.572 8.978 17385 Z= 0.292 Chirality : 0.041 0.150 1947 Planarity : 0.005 0.057 2169 Dihedral : 8.721 76.926 1860 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.73 % Allowed : 13.15 % Favored : 84.12 % 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: -0.33 (0.21), residues: 1494 helix: 0.76 (0.20), residues: 712 sheet: -0.68 (0.44), residues: 128 loop : -1.18 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 336 HIS 0.006 0.001 HIS C 169 PHE 0.019 0.001 PHE C 41 TYR 0.019 0.001 TYR B 533 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 183 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8438 (ttp-170) cc_final: 0.8183 (ttm110) REVERT: A 142 LYS cc_start: 0.8276 (tmmt) cc_final: 0.7617 (ttmm) REVERT: A 150 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: A 160 GLU cc_start: 0.8586 (pm20) cc_final: 0.8256 (pm20) REVERT: B 109 LYS cc_start: 0.8607 (mptp) cc_final: 0.8228 (mmtm) REVERT: B 151 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7210 (mmt90) REVERT: B 167 ASP cc_start: 0.7688 (m-30) cc_final: 0.7423 (m-30) REVERT: B 229 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7199 (pmm) REVERT: B 395 MET cc_start: 0.8503 (mtp) cc_final: 0.8284 (mtp) REVERT: B 592 ARG cc_start: 0.8416 (mtt180) cc_final: 0.8161 (mmm-85) REVERT: B 657 ARG cc_start: 0.8149 (ptp-170) cc_final: 0.7938 (ptp-170) REVERT: C 30 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6698 (tp30) REVERT: C 120 ASN cc_start: 0.8046 (m-40) cc_final: 0.7666 (m110) REVERT: C 142 ARG cc_start: 0.7875 (ppt170) cc_final: 0.7636 (ppt90) REVERT: C 161 GLU cc_start: 0.7490 (mp0) cc_final: 0.7128 (mp0) outliers start: 37 outliers final: 10 residues processed: 202 average time/residue: 1.4084 time to fit residues: 307.4754 Evaluate side-chains 184 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 211 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 145 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 304 ASN A 424 GLN B 429 ASN B 656 GLN B 663 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12791 Z= 0.156 Angle : 0.542 9.731 17385 Z= 0.273 Chirality : 0.040 0.156 1947 Planarity : 0.004 0.051 2169 Dihedral : 8.579 77.571 1860 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.95 % Allowed : 14.55 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.21), residues: 1494 helix: 1.05 (0.20), residues: 706 sheet: -0.54 (0.45), residues: 118 loop : -1.15 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.006 0.001 HIS C 169 PHE 0.022 0.001 PHE C 41 TYR 0.023 0.001 TYR C 20 ARG 0.010 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6203 (mp0) REVERT: A 92 ARG cc_start: 0.8412 (ttp-170) cc_final: 0.8162 (ttm110) REVERT: A 124 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 150 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: B 109 LYS cc_start: 0.8570 (mptp) cc_final: 0.8053 (mtpt) REVERT: B 167 ASP cc_start: 0.7717 (m-30) cc_final: 0.7431 (m-30) REVERT: B 229 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7182 (pmm) REVERT: B 378 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7188 (ptt-90) REVERT: B 395 MET cc_start: 0.8497 (mtp) cc_final: 0.8279 (mtp) REVERT: B 657 ARG cc_start: 0.8155 (ptp-170) cc_final: 0.7917 (ptp-170) REVERT: C 30 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6696 (tp30) REVERT: C 120 ASN cc_start: 0.8195 (m-40) cc_final: 0.7691 (m110) REVERT: C 142 ARG cc_start: 0.7841 (ppt170) cc_final: 0.7151 (ppt90) REVERT: C 161 GLU cc_start: 0.7444 (mp0) cc_final: 0.7100 (mp0) REVERT: C 186 ARG cc_start: 0.8138 (mmp80) cc_final: 0.7904 (mmp80) outliers start: 40 outliers final: 11 residues processed: 208 average time/residue: 1.3733 time to fit residues: 307.9722 Evaluate side-chains 185 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 304 ASN A 424 GLN B 429 ASN B 567 HIS B 656 GLN C 209 GLN C 233 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 12791 Z= 0.419 Angle : 0.670 9.827 17385 Z= 0.343 Chirality : 0.046 0.169 1947 Planarity : 0.005 0.052 2169 Dihedral : 8.898 75.144 1860 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.69 % Allowed : 16.10 % Favored : 80.21 % 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: -0.46 (0.21), residues: 1494 helix: 0.67 (0.19), residues: 709 sheet: -0.89 (0.44), residues: 124 loop : -1.23 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 426 HIS 0.006 0.001 HIS A 573 PHE 0.017 0.002 PHE B 529 TYR 0.025 0.002 TYR B 537 ARG 0.009 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7465 (tpp-160) cc_final: 0.6883 (tpp-160) REVERT: A 69 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: A 92 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.8196 (mmm-85) REVERT: A 124 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7153 (mm-30) REVERT: A 150 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: A 168 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: A 397 ARG cc_start: 0.7715 (tpp80) cc_final: 0.7399 (mmt180) REVERT: B 229 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7518 (pmm) REVERT: B 378 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7085 (ptt-90) REVERT: B 395 MET cc_start: 0.8563 (mtp) cc_final: 0.8271 (mtp) REVERT: B 423 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7280 (t70) REVERT: B 593 ARG cc_start: 0.7046 (ttm110) cc_final: 0.6834 (ttp-110) REVERT: B 682 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: C 30 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: C 120 ASN cc_start: 0.8346 (m-40) cc_final: 0.7893 (m110) REVERT: C 137 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6587 (pp20) REVERT: C 142 ARG cc_start: 0.7771 (ppt170) cc_final: 0.7481 (ppt-90) REVERT: C 161 GLU cc_start: 0.7577 (mp0) cc_final: 0.7253 (mp0) REVERT: C 185 LYS cc_start: 0.7591 (tptt) cc_final: 0.7260 (tptt) outliers start: 50 outliers final: 18 residues processed: 205 average time/residue: 1.3624 time to fit residues: 301.1837 Evaluate side-chains 194 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 30.0000 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 531 HIS B 656 GLN C 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12791 Z= 0.207 Angle : 0.584 11.320 17385 Z= 0.296 Chirality : 0.041 0.211 1947 Planarity : 0.004 0.053 2169 Dihedral : 8.780 76.885 1860 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.95 % Allowed : 17.06 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1494 helix: 0.88 (0.20), residues: 710 sheet: -0.66 (0.45), residues: 118 loop : -1.23 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 336 HIS 0.005 0.001 HIS A 573 PHE 0.021 0.001 PHE C 41 TYR 0.021 0.002 TYR C 20 ARG 0.011 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 2.244 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7406 (tpp-160) cc_final: 0.6850 (tpp-160) REVERT: A 69 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: A 92 ARG cc_start: 0.8422 (ttp-170) cc_final: 0.8086 (ttm110) REVERT: A 124 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7123 (mm-30) REVERT: A 150 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: A 168 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: A 357 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7879 (mmmt) REVERT: A 397 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7363 (mmt180) REVERT: B 109 LYS cc_start: 0.8620 (mptp) cc_final: 0.8111 (mtpt) REVERT: B 167 ASP cc_start: 0.7807 (m-30) cc_final: 0.7601 (m-30) REVERT: B 229 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7382 (pmm) REVERT: B 332 MET cc_start: 0.8285 (mmm) cc_final: 0.8005 (mtt) REVERT: B 378 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7171 (ptt-90) REVERT: B 395 MET cc_start: 0.8535 (mtp) cc_final: 0.8324 (mtp) REVERT: B 423 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7255 (t70) REVERT: B 593 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6718 (ttp-110) REVERT: B 657 ARG cc_start: 0.8181 (ptp-170) cc_final: 0.7965 (ptp-170) REVERT: B 682 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: C 30 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6706 (tp30) REVERT: C 120 ASN cc_start: 0.8255 (m-40) cc_final: 0.7919 (m110) REVERT: C 161 GLU cc_start: 0.7529 (mp0) cc_final: 0.7228 (mp0) REVERT: C 185 LYS cc_start: 0.7547 (tptt) cc_final: 0.7289 (tptt) outliers start: 40 outliers final: 13 residues processed: 205 average time/residue: 1.4350 time to fit residues: 318.4182 Evaluate side-chains 187 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 429 ASN B 656 GLN C 209 GLN C 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12791 Z= 0.163 Angle : 0.562 12.045 17385 Z= 0.283 Chirality : 0.040 0.163 1947 Planarity : 0.004 0.050 2169 Dihedral : 8.616 77.568 1860 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.03 % Allowed : 17.06 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1494 helix: 1.11 (0.20), residues: 704 sheet: -0.55 (0.45), residues: 118 loop : -1.20 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.005 0.001 HIS A 573 PHE 0.023 0.001 PHE C 41 TYR 0.024 0.001 TYR C 20 ARG 0.012 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7435 (tpp-160) cc_final: 0.6877 (tpp-160) REVERT: A 69 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: A 92 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8210 (mmm-85) REVERT: A 124 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7006 (mm-30) REVERT: A 150 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: A 357 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7798 (mmmt) REVERT: A 397 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7345 (mmt180) REVERT: B 104 TYR cc_start: 0.8258 (t80) cc_final: 0.8007 (t80) REVERT: B 109 LYS cc_start: 0.8546 (mptp) cc_final: 0.8028 (mtpt) REVERT: B 167 ASP cc_start: 0.7781 (m-30) cc_final: 0.7506 (m-30) REVERT: B 229 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7179 (pmm) REVERT: B 332 MET cc_start: 0.8252 (mmm) cc_final: 0.8037 (mtt) REVERT: B 423 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7270 (t70) REVERT: B 593 ARG cc_start: 0.6930 (ttm110) cc_final: 0.6675 (ttm-80) REVERT: C 120 ASN cc_start: 0.8221 (m-40) cc_final: 0.7856 (m110) REVERT: C 161 GLU cc_start: 0.7488 (mp0) cc_final: 0.7211 (mp0) REVERT: C 185 LYS cc_start: 0.7511 (tptt) cc_final: 0.7302 (tptt) outliers start: 41 outliers final: 15 residues processed: 204 average time/residue: 1.4694 time to fit residues: 321.8771 Evaluate side-chains 190 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 211 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 304 ASN B 429 ASN B 531 HIS B 656 GLN C 209 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12791 Z= 0.189 Angle : 0.577 12.589 17385 Z= 0.292 Chirality : 0.040 0.160 1947 Planarity : 0.004 0.058 2169 Dihedral : 8.586 77.333 1860 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.66 % Allowed : 17.58 % Favored : 79.76 % 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: -0.05 (0.21), residues: 1494 helix: 1.10 (0.20), residues: 706 sheet: -0.61 (0.44), residues: 120 loop : -1.16 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 62 HIS 0.005 0.001 HIS C 169 PHE 0.021 0.001 PHE C 41 TYR 0.022 0.001 TYR C 20 ARG 0.013 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 170 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8203 (mmm-85) REVERT: A 124 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 150 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: A 357 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7854 (mmmt) REVERT: A 397 ARG cc_start: 0.7674 (tpp80) cc_final: 0.7344 (mmt180) REVERT: A 476 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8450 (tm) REVERT: B 104 TYR cc_start: 0.8235 (t80) cc_final: 0.7965 (t80) REVERT: B 109 LYS cc_start: 0.8540 (mptp) cc_final: 0.8015 (mtpt) REVERT: B 167 ASP cc_start: 0.7789 (m-30) cc_final: 0.7500 (m-30) REVERT: B 229 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7191 (pmm) REVERT: B 332 MET cc_start: 0.8254 (mmm) cc_final: 0.8044 (mtt) REVERT: B 593 ARG cc_start: 0.6975 (ttm110) cc_final: 0.6705 (ttm-80) REVERT: C 120 ASN cc_start: 0.8233 (m-40) cc_final: 0.7870 (m110) REVERT: C 161 GLU cc_start: 0.7496 (mp0) cc_final: 0.7221 (mp0) REVERT: C 185 LYS cc_start: 0.7548 (tptt) cc_final: 0.7314 (tptt) REVERT: C 187 LYS cc_start: 0.8676 (ptpp) cc_final: 0.8426 (ptpt) outliers start: 36 outliers final: 19 residues processed: 193 average time/residue: 1.3657 time to fit residues: 284.7309 Evaluate side-chains 191 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 429 ASN B 656 GLN C 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12791 Z= 0.212 Angle : 0.587 13.077 17385 Z= 0.297 Chirality : 0.041 0.170 1947 Planarity : 0.004 0.055 2169 Dihedral : 8.605 77.105 1860 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.81 % Allowed : 17.43 % Favored : 79.76 % 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: -0.08 (0.21), residues: 1494 helix: 1.05 (0.20), residues: 706 sheet: -0.64 (0.44), residues: 120 loop : -1.14 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.005 0.001 HIS A 573 PHE 0.028 0.001 PHE B 479 TYR 0.024 0.002 TYR C 20 ARG 0.014 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8204 (mmm-85) REVERT: A 124 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 150 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: A 357 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7836 (mmmt) REVERT: A 397 ARG cc_start: 0.7675 (tpp80) cc_final: 0.7345 (mmt180) REVERT: A 476 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8440 (tm) REVERT: B 104 TYR cc_start: 0.8221 (t80) cc_final: 0.7975 (t80) REVERT: B 109 LYS cc_start: 0.8545 (mptp) cc_final: 0.8016 (mtpt) REVERT: B 167 ASP cc_start: 0.7815 (m-30) cc_final: 0.7546 (m-30) REVERT: B 229 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7194 (pmm) REVERT: B 443 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8164 (tp) REVERT: B 598 ASN cc_start: 0.7619 (p0) cc_final: 0.7122 (p0) REVERT: B 686 ARG cc_start: 0.7522 (mmm160) cc_final: 0.7311 (mmm-85) REVERT: C 113 GLN cc_start: 0.8502 (mt0) cc_final: 0.7499 (mt0) REVERT: C 120 ASN cc_start: 0.8211 (m-40) cc_final: 0.7864 (m110) REVERT: C 161 GLU cc_start: 0.7508 (mp0) cc_final: 0.7265 (mp0) REVERT: C 185 LYS cc_start: 0.7536 (tptt) cc_final: 0.7309 (tptt) REVERT: C 187 LYS cc_start: 0.8668 (ptpp) cc_final: 0.8438 (ptpt) outliers start: 38 outliers final: 22 residues processed: 197 average time/residue: 1.4139 time to fit residues: 299.4064 Evaluate side-chains 194 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 138 optimal weight: 0.3980 chunk 119 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 127 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 429 ASN B 656 GLN C 113 GLN C 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12791 Z= 0.161 Angle : 0.578 13.523 17385 Z= 0.292 Chirality : 0.040 0.253 1947 Planarity : 0.004 0.064 2169 Dihedral : 8.534 77.854 1860 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.92 % Allowed : 18.61 % Favored : 79.47 % 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: 0.05 (0.22), residues: 1494 helix: 1.19 (0.20), residues: 704 sheet: -0.63 (0.44), residues: 120 loop : -1.08 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.003 0.001 HIS A 573 PHE 0.022 0.001 PHE C 41 TYR 0.025 0.001 TYR C 20 ARG 0.015 0.001 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8200 (mmm-85) REVERT: A 124 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6893 (mm-30) REVERT: A 150 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: A 357 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7779 (mmmt) REVERT: A 397 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7347 (mmt180) REVERT: B 104 TYR cc_start: 0.8189 (t80) cc_final: 0.7866 (t80) REVERT: B 109 LYS cc_start: 0.8532 (mptp) cc_final: 0.8009 (mtpt) REVERT: B 167 ASP cc_start: 0.7769 (m-30) cc_final: 0.7476 (m-30) REVERT: B 229 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7199 (pmm) REVERT: B 598 ASN cc_start: 0.7618 (p0) cc_final: 0.7077 (p0) REVERT: C 120 ASN cc_start: 0.8152 (m-40) cc_final: 0.7821 (m110) REVERT: C 161 GLU cc_start: 0.7473 (mp0) cc_final: 0.7206 (mp0) REVERT: C 187 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8458 (ptpt) outliers start: 26 outliers final: 17 residues processed: 187 average time/residue: 1.4372 time to fit residues: 289.9525 Evaluate side-chains 180 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 473 GLN B 429 ASN B 656 GLN C 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109757 restraints weight = 17476.757| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.14 r_work: 0.3255 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12791 Z= 0.311 Angle : 0.649 13.552 17385 Z= 0.328 Chirality : 0.044 0.291 1947 Planarity : 0.005 0.065 2169 Dihedral : 8.678 76.342 1860 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.14 % Allowed : 18.54 % Favored : 79.32 % 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: -0.14 (0.21), residues: 1494 helix: 1.02 (0.20), residues: 701 sheet: -0.84 (0.43), residues: 131 loop : -1.14 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 62 HIS 0.006 0.001 HIS A 573 PHE 0.030 0.002 PHE B 479 TYR 0.022 0.002 TYR C 20 ARG 0.015 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5225.18 seconds wall clock time: 91 minutes 50.61 seconds (5510.61 seconds total)