Starting phenix.real_space_refine on Sat Aug 3 22:06:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/08_2024/8y93_39068.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/08_2024/8y93_39068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/08_2024/8y93_39068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/08_2024/8y93_39068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/08_2024/8y93_39068.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y93_39068/08_2024/8y93_39068.cif" } resolution = 3.0 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= 0.055 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: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 6072 2.51 5 N 1413 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E ARG 440": "NH1" <-> "NH2" Residue "E ARG 442": "NH1" <-> "NH2" Residue "E ARG 500": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E ARG 587": "NH1" <-> "NH2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "E ARG 607": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9055 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "E" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {' CL': 1, ' NA': 1, 'TP0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.65, per 1000 atoms: 0.62 Number of scatterers: 9055 At special positions: 0 Unit cell: (97.09, 85.41, 118.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 40 16.00 Na 1 11.00 O 1528 8.00 N 1413 7.00 C 6072 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: 3.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 72.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.738A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 90 through 93 removed outlier: 3.652A pdb=" N ALA A 93 " --> pdb=" O GLY A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 106 through 120 removed outlier: 4.085A pdb=" N GLU A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 165 removed outlier: 3.644A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.863A pdb=" N CYS A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.838A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.611A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.889A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.505A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 338 through 372 removed outlier: 3.699A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.585A pdb=" N VAL A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.863A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.632A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.151A pdb=" N ARG A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 441' Processing helix chain 'A' and resid 441 through 457 removed outlier: 3.772A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.435A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.918A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.917A pdb=" N VAL A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.792A pdb=" N PHE A 609 " --> pdb=" O ILE A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.031A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 74 removed outlier: 3.792A pdb=" N PHE E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 135 through 166 removed outlier: 4.071A pdb=" N TYR E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 151 " --> pdb=" O TYR E 147 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 234 through 253 Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 269 through 284 removed outlier: 4.462A pdb=" N VAL E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR E 283 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 284 " --> pdb=" O HIS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 4.048A pdb=" N ILE E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.639A pdb=" N ALA E 312 " --> pdb=" O TRP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 333 removed outlier: 3.745A pdb=" N TYR E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 372 Processing helix chain 'E' and resid 385 through 398 Proline residue: E 392 - end of helix Processing helix chain 'E' and resid 400 through 435 Processing helix chain 'E' and resid 435 through 441 Processing helix chain 'E' and resid 441 through 457 Processing helix chain 'E' and resid 464 through 494 removed outlier: 3.958A pdb=" N VAL E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 509 Processing helix chain 'E' and resid 514 through 523 Processing helix chain 'E' and resid 523 through 539 Processing helix chain 'E' and resid 551 through 567 removed outlier: 4.024A pdb=" N ASN E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP E 556 " --> pdb=" O PRO E 552 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 580 Processing helix chain 'E' and resid 583 through 593 Processing helix chain 'E' and resid 598 through 603 removed outlier: 3.933A pdb=" N ALA E 602 " --> pdb=" O HIS E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 616 removed outlier: 4.066A pdb=" N TRP E 614 " --> pdb=" O GLN E 610 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1572 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: 2.44 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1395 1.32 - 1.44: 2870 1.44 - 1.57: 5022 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9349 Sorted by residual: bond pdb=" CA TRP E 128 " pdb=" C TRP E 128 " ideal model delta sigma weight residual 1.530 1.458 0.072 1.14e-02 7.69e+03 4.02e+01 bond pdb=" C3 TP0 A 701 " pdb=" C6 TP0 A 701 " ideal model delta sigma weight residual 1.483 1.555 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CA VAL E 127 " pdb=" C VAL E 127 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.27e-02 6.20e+03 1.18e+01 bond pdb=" CA ILE E 130 " pdb=" C ILE E 130 " ideal model delta sigma weight residual 1.520 1.470 0.050 1.54e-02 4.22e+03 1.07e+01 bond pdb=" CA LYS E 129 " pdb=" C LYS E 129 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.31e-02 5.83e+03 7.81e+00 ... (remaining 9344 not shown) Histogram of bond angle deviations from ideal: 96.19 - 103.75: 107 103.75 - 111.32: 3990 111.32 - 118.88: 3368 118.88 - 126.44: 5070 126.44 - 134.00: 222 Bond angle restraints: 12757 Sorted by residual: angle pdb=" N LYS E 129 " pdb=" CA LYS E 129 " pdb=" C LYS E 129 " ideal model delta sigma weight residual 113.30 96.19 17.11 1.34e+00 5.57e-01 1.63e+02 angle pdb=" N VAL E 127 " pdb=" CA VAL E 127 " pdb=" C VAL E 127 " ideal model delta sigma weight residual 113.16 102.59 10.57 1.49e+00 4.50e-01 5.03e+01 angle pdb=" N ILE E 130 " pdb=" CA ILE E 130 " pdb=" C ILE E 130 " ideal model delta sigma weight residual 112.83 106.53 6.30 9.90e-01 1.02e+00 4.04e+01 angle pdb=" C14 TP0 A 701 " pdb=" N1 TP0 A 701 " pdb=" C20 TP0 A 701 " ideal model delta sigma weight residual 111.01 99.00 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N VAL A 137 " pdb=" CA VAL A 137 " pdb=" C VAL A 137 " ideal model delta sigma weight residual 113.00 108.42 4.58 1.30e+00 5.92e-01 1.24e+01 ... (remaining 12752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.77: 5099 28.77 - 57.55: 111 57.55 - 86.32: 8 86.32 - 115.09: 1 115.09 - 143.87: 2 Dihedral angle restraints: 5221 sinusoidal: 1957 harmonic: 3264 Sorted by residual: dihedral pdb=" C22 TP0 A 701 " pdb=" C21 TP0 A 701 " pdb=" C4 TP0 A 701 " pdb=" C6 TP0 A 701 " ideal model delta sinusoidal sigma weight residual 71.36 -72.51 143.87 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C10 TP0 A 701 " pdb=" C21 TP0 A 701 " pdb=" C4 TP0 A 701 " pdb=" C22 TP0 A 701 " ideal model delta sinusoidal sigma weight residual 108.73 -108.00 -143.27 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C LYS E 129 " pdb=" N LYS E 129 " pdb=" CA LYS E 129 " pdb=" CB LYS E 129 " ideal model delta harmonic sigma weight residual -122.60 -113.18 -9.42 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1156 0.045 - 0.090: 231 0.090 - 0.134: 28 0.134 - 0.179: 1 0.179 - 0.224: 2 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CB VAL E 127 " pdb=" CA VAL E 127 " pdb=" CG1 VAL E 127 " pdb=" CG2 VAL E 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA LYS E 129 " pdb=" N LYS E 129 " pdb=" C LYS E 129 " pdb=" CB LYS E 129 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA TRP E 128 " pdb=" N TRP E 128 " pdb=" C TRP E 128 " pdb=" CB TRP E 128 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 ... (remaining 1415 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 131 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO E 132 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 132 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 132 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 391 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO E 392 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 392 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 392 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 127 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C VAL E 127 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL E 127 " 0.010 2.00e-02 2.50e+03 pdb=" N TRP E 128 " 0.009 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 122 2.68 - 3.24: 9022 3.24 - 3.79: 14631 3.79 - 4.35: 19640 4.35 - 4.90: 32766 Nonbonded interactions: 76181 Sorted by model distance: nonbonded pdb=" C20 TP0 A 701 " pdb=" C29 TP0 A 701 " model vdw 2.127 3.088 nonbonded pdb=" OG SER A 318 " pdb="CL CL A 703 " model vdw 2.227 3.190 nonbonded pdb=" N LYS E 129 " pdb=" N ILE E 130 " model vdw 2.244 2.560 nonbonded pdb=" O SER A 251 " pdb=" OG1 THR A 258 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR E 332 " pdb=" OG1 THR E 429 " model vdw 2.295 3.040 ... (remaining 76176 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' and resid 53 through 617) selection = chain 'E' } 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: 2.660 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.810 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 0.072 9349 Z= 0.194 Angle : 0.603 17.108 12757 Z= 0.367 Chirality : 0.035 0.224 1418 Planarity : 0.004 0.048 1554 Dihedral : 11.793 143.867 3145 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.15 % Allowed : 7.14 % Favored : 87.71 % 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: -1.85 (0.23), residues: 1126 helix: -0.76 (0.18), residues: 730 sheet: None (None), residues: 0 loop : -1.94 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 128 HIS 0.001 0.000 HIS A 280 PHE 0.011 0.001 PHE A 409 TYR 0.007 0.001 TYR A 340 ARG 0.002 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 249 time to evaluate : 1.072 Fit side-chains REVERT: A 147 TYR cc_start: 0.8334 (m-10) cc_final: 0.7725 (m-10) REVERT: A 271 TYR cc_start: 0.8411 (m-80) cc_final: 0.8185 (m-80) REVERT: A 348 SER cc_start: 0.8411 (m) cc_final: 0.8208 (m) REVERT: A 439 LYS cc_start: 0.8491 (mttt) cc_final: 0.8103 (mtpm) REVERT: A 585 TRP cc_start: 0.6791 (m100) cc_final: 0.6542 (m-10) REVERT: A 611 LEU cc_start: 0.8222 (tp) cc_final: 0.7839 (tt) REVERT: E 111 TYR cc_start: 0.8222 (t80) cc_final: 0.7846 (t80) REVERT: E 120 ASN cc_start: 0.8206 (m-40) cc_final: 0.7990 (m-40) REVERT: E 133 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: E 494 TRP cc_start: 0.7747 (m100) cc_final: 0.7422 (m100) outliers start: 49 outliers final: 9 residues processed: 279 average time/residue: 0.7942 time to fit residues: 243.3630 Evaluate side-chains 160 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 205 TYR Chi-restraints excluded: chain E residue 359 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 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 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 184 ASN A 280 HIS A 350 ASN A 507 GLN E 120 ASN E 153 ASN E 337 ASN E 613 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9349 Z= 0.185 Angle : 0.580 10.658 12757 Z= 0.289 Chirality : 0.039 0.170 1418 Planarity : 0.004 0.030 1554 Dihedral : 8.044 140.919 1242 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.52 % Allowed : 17.65 % Favored : 77.84 % 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 (0.25), residues: 1126 helix: 0.43 (0.19), residues: 753 sheet: None (None), residues: 0 loop : -1.46 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 128 HIS 0.006 0.001 HIS E 613 PHE 0.020 0.001 PHE E 275 TYR 0.016 0.001 TYR A 111 ARG 0.005 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8820 (m-40) cc_final: 0.8586 (m110) REVERT: A 348 SER cc_start: 0.8509 (m) cc_final: 0.8269 (m) REVERT: A 439 LYS cc_start: 0.8514 (mttt) cc_final: 0.8100 (mtpm) REVERT: A 585 TRP cc_start: 0.6766 (m100) cc_final: 0.6404 (m-10) REVERT: A 595 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: E 100 LEU cc_start: 0.8190 (tt) cc_final: 0.7137 (mm) REVERT: E 111 TYR cc_start: 0.8435 (t80) cc_final: 0.8140 (t80) REVERT: E 119 TYR cc_start: 0.6590 (t80) cc_final: 0.6289 (t80) REVERT: E 242 MET cc_start: 0.7133 (mtm) cc_final: 0.6885 (mtt) REVERT: E 436 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: E 438 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8204 (mm) outliers start: 43 outliers final: 15 residues processed: 188 average time/residue: 0.7379 time to fit residues: 153.6233 Evaluate side-chains 145 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 438 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 0.0470 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 0.0570 chunk 110 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9349 Z= 0.142 Angle : 0.541 15.919 12757 Z= 0.262 Chirality : 0.038 0.136 1418 Planarity : 0.003 0.028 1554 Dihedral : 7.504 141.359 1233 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.20 % Allowed : 18.59 % Favored : 77.21 % 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: 0.42 (0.25), residues: 1126 helix: 1.04 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -1.17 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 585 HIS 0.007 0.001 HIS E 370 PHE 0.018 0.001 PHE E 454 TYR 0.018 0.001 TYR E 340 ARG 0.010 0.001 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: A 153 ASN cc_start: 0.8828 (m-40) cc_final: 0.8606 (m110) REVERT: A 271 TYR cc_start: 0.8294 (m-80) cc_final: 0.8093 (m-80) REVERT: A 348 SER cc_start: 0.8546 (m) cc_final: 0.8318 (m) REVERT: A 390 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8019 (tm) REVERT: A 439 LYS cc_start: 0.8482 (mttt) cc_final: 0.8075 (mtpm) REVERT: A 502 SER cc_start: 0.8115 (m) cc_final: 0.7834 (p) REVERT: A 585 TRP cc_start: 0.6696 (m100) cc_final: 0.6356 (m-10) REVERT: A 595 GLU cc_start: 0.7822 (mp0) cc_final: 0.7332 (mp0) REVERT: E 100 LEU cc_start: 0.8225 (tt) cc_final: 0.7246 (mm) REVERT: E 112 MET cc_start: 0.8048 (ttm) cc_final: 0.7730 (ttp) REVERT: E 119 TYR cc_start: 0.6764 (t80) cc_final: 0.6217 (t80) REVERT: E 242 MET cc_start: 0.7116 (mtm) cc_final: 0.6827 (mtt) REVERT: E 340 TYR cc_start: 0.7013 (t80) cc_final: 0.6781 (t80) REVERT: E 438 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8173 (mm) REVERT: E 479 THR cc_start: 0.6390 (m) cc_final: 0.5791 (p) REVERT: E 508 MET cc_start: 0.6002 (ttm) cc_final: 0.5774 (ttm) REVERT: E 600 LEU cc_start: 0.7098 (mm) cc_final: 0.6825 (mp) outliers start: 40 outliers final: 11 residues processed: 169 average time/residue: 0.6623 time to fit residues: 126.3694 Evaluate side-chains 138 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 296 HIS Chi-restraints excluded: chain E residue 438 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.0470 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.0030 chunk 102 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 overall best weight: 0.5890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9349 Z= 0.158 Angle : 0.549 15.189 12757 Z= 0.267 Chirality : 0.038 0.133 1418 Planarity : 0.003 0.028 1554 Dihedral : 7.349 141.114 1230 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.20 % Allowed : 18.70 % Favored : 77.10 % 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: 0.66 (0.26), residues: 1126 helix: 1.17 (0.19), residues: 753 sheet: None (None), residues: 0 loop : -1.03 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 585 HIS 0.006 0.001 HIS E 370 PHE 0.022 0.001 PHE E 275 TYR 0.017 0.001 TYR E 340 ARG 0.005 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8843 (m-40) cc_final: 0.8609 (m110) REVERT: A 189 LYS cc_start: 0.7635 (pptt) cc_final: 0.6948 (tttt) REVERT: A 271 TYR cc_start: 0.8321 (m-80) cc_final: 0.8111 (m-80) REVERT: A 390 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8033 (tm) REVERT: A 391 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: A 410 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8555 (m) REVERT: A 439 LYS cc_start: 0.8469 (mttt) cc_final: 0.8062 (mttm) REVERT: A 502 SER cc_start: 0.8168 (m) cc_final: 0.7881 (p) REVERT: A 585 TRP cc_start: 0.6717 (m100) cc_final: 0.6360 (m-10) REVERT: A 595 GLU cc_start: 0.7871 (mp0) cc_final: 0.7384 (mp0) REVERT: E 100 LEU cc_start: 0.8196 (tt) cc_final: 0.7231 (mm) REVERT: E 111 TYR cc_start: 0.8524 (t80) cc_final: 0.8263 (t80) REVERT: E 119 TYR cc_start: 0.6765 (t80) cc_final: 0.6247 (t80) REVERT: E 242 MET cc_start: 0.7113 (mtm) cc_final: 0.6801 (mtt) REVERT: E 257 LYS cc_start: 0.5409 (OUTLIER) cc_final: 0.5175 (mmmt) REVERT: E 337 ASN cc_start: 0.7790 (p0) cc_final: 0.7563 (p0) REVERT: E 438 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8107 (mm) REVERT: E 479 THR cc_start: 0.6396 (m) cc_final: 0.5779 (p) REVERT: E 600 LEU cc_start: 0.6971 (mm) cc_final: 0.6694 (mp) outliers start: 40 outliers final: 18 residues processed: 162 average time/residue: 0.7031 time to fit residues: 127.5008 Evaluate side-chains 147 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 296 HIS Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 528 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9349 Z= 0.178 Angle : 0.560 14.964 12757 Z= 0.271 Chirality : 0.038 0.134 1418 Planarity : 0.004 0.051 1554 Dihedral : 7.341 140.971 1230 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.62 % Allowed : 18.91 % Favored : 76.47 % 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: 0.81 (0.26), residues: 1126 helix: 1.26 (0.19), residues: 755 sheet: None (None), residues: 0 loop : -0.91 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.005 0.001 HIS E 598 PHE 0.023 0.001 PHE E 528 TYR 0.016 0.001 TYR A 575 ARG 0.005 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 130 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8862 (m-40) cc_final: 0.8619 (m110) REVERT: A 390 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8019 (tm) REVERT: A 391 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: A 410 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8562 (m) REVERT: A 439 LYS cc_start: 0.8474 (mttt) cc_final: 0.8067 (mtpm) REVERT: A 502 SER cc_start: 0.8202 (m) cc_final: 0.7915 (p) REVERT: A 585 TRP cc_start: 0.6756 (m100) cc_final: 0.6385 (m-10) REVERT: A 595 GLU cc_start: 0.7909 (mp0) cc_final: 0.7448 (mp0) REVERT: E 100 LEU cc_start: 0.8280 (tt) cc_final: 0.7292 (mm) REVERT: E 111 TYR cc_start: 0.8580 (t80) cc_final: 0.8352 (t80) REVERT: E 119 TYR cc_start: 0.6735 (t80) cc_final: 0.6362 (t80) REVERT: E 242 MET cc_start: 0.7097 (mtm) cc_final: 0.6778 (mtt) REVERT: E 254 LYS cc_start: 0.7491 (tptm) cc_final: 0.7162 (tppp) REVERT: E 257 LYS cc_start: 0.5464 (OUTLIER) cc_final: 0.5210 (mmmt) REVERT: E 337 ASN cc_start: 0.7757 (p0) cc_final: 0.7529 (p0) REVERT: E 438 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8093 (mm) REVERT: E 479 THR cc_start: 0.6471 (m) cc_final: 0.6080 (t) REVERT: E 508 MET cc_start: 0.6055 (ttm) cc_final: 0.5844 (ttm) REVERT: E 600 LEU cc_start: 0.6951 (mm) cc_final: 0.6643 (mp) outliers start: 44 outliers final: 19 residues processed: 161 average time/residue: 0.6576 time to fit residues: 118.9602 Evaluate side-chains 146 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 296 HIS Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 528 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9349 Z= 0.230 Angle : 0.600 16.097 12757 Z= 0.292 Chirality : 0.040 0.188 1418 Planarity : 0.004 0.035 1554 Dihedral : 7.398 140.841 1229 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.52 % Allowed : 19.33 % Favored : 76.16 % 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: 0.80 (0.26), residues: 1126 helix: 1.25 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.87 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.007 0.001 HIS E 370 PHE 0.034 0.002 PHE E 528 TYR 0.018 0.001 TYR E 340 ARG 0.003 0.001 ARG E 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8904 (m-40) cc_final: 0.8685 (m110) REVERT: A 189 LYS cc_start: 0.7618 (pptt) cc_final: 0.6988 (tttm) REVERT: A 390 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8070 (tm) REVERT: A 391 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: A 410 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8597 (m) REVERT: A 439 LYS cc_start: 0.8487 (mttt) cc_final: 0.8063 (mtpm) REVERT: A 585 TRP cc_start: 0.6793 (m100) cc_final: 0.6417 (m-10) REVERT: A 595 GLU cc_start: 0.7962 (mp0) cc_final: 0.7444 (mp0) REVERT: E 112 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7880 (ttp) REVERT: E 119 TYR cc_start: 0.6743 (t80) cc_final: 0.6392 (t80) REVERT: E 242 MET cc_start: 0.7127 (mtm) cc_final: 0.6837 (mtt) REVERT: E 254 LYS cc_start: 0.7520 (tptm) cc_final: 0.7180 (tppp) REVERT: E 257 LYS cc_start: 0.5426 (OUTLIER) cc_final: 0.5132 (mtpm) REVERT: E 436 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8249 (mp10) REVERT: E 438 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8120 (mm) REVERT: E 508 MET cc_start: 0.6019 (ttm) cc_final: 0.5796 (ttm) outliers start: 43 outliers final: 17 residues processed: 156 average time/residue: 0.7460 time to fit residues: 130.0065 Evaluate side-chains 141 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain E residue 438 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9349 Z= 0.169 Angle : 0.577 16.668 12757 Z= 0.279 Chirality : 0.038 0.130 1418 Planarity : 0.003 0.027 1554 Dihedral : 7.302 140.684 1227 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.31 % Allowed : 20.48 % Favored : 75.21 % 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: 0.91 (0.26), residues: 1126 helix: 1.30 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.78 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 80 HIS 0.005 0.001 HIS E 598 PHE 0.018 0.001 PHE E 454 TYR 0.014 0.001 TYR A 575 ARG 0.005 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 118 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8892 (m-40) cc_final: 0.8657 (m110) REVERT: A 189 LYS cc_start: 0.7632 (pptt) cc_final: 0.6969 (tttm) REVERT: A 391 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: A 410 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8596 (m) REVERT: A 439 LYS cc_start: 0.8481 (mttt) cc_final: 0.8054 (mtpm) REVERT: A 585 TRP cc_start: 0.6773 (m100) cc_final: 0.6428 (m-10) REVERT: A 595 GLU cc_start: 0.7964 (mp0) cc_final: 0.7453 (mp0) REVERT: A 611 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7684 (tm) REVERT: E 112 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7876 (ttp) REVERT: E 119 TYR cc_start: 0.6709 (t80) cc_final: 0.6280 (t80) REVERT: E 242 MET cc_start: 0.7094 (mtm) cc_final: 0.6808 (mtt) REVERT: E 254 LYS cc_start: 0.7514 (tptm) cc_final: 0.7191 (tppp) REVERT: E 257 LYS cc_start: 0.5523 (OUTLIER) cc_final: 0.5176 (mtpm) REVERT: E 438 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8088 (mm) REVERT: E 595 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: E 600 LEU cc_start: 0.6991 (mm) cc_final: 0.6670 (mp) outliers start: 41 outliers final: 20 residues processed: 148 average time/residue: 0.7825 time to fit residues: 128.1827 Evaluate side-chains 140 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 595 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.0070 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 0.0770 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9349 Z= 0.153 Angle : 0.584 16.539 12757 Z= 0.278 Chirality : 0.038 0.191 1418 Planarity : 0.003 0.045 1554 Dihedral : 7.292 140.541 1227 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.26 % Allowed : 22.06 % Favored : 74.68 % 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: 1.08 (0.26), residues: 1126 helix: 1.44 (0.19), residues: 751 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 80 HIS 0.005 0.001 HIS E 598 PHE 0.023 0.001 PHE E 454 TYR 0.018 0.001 TYR E 340 ARG 0.003 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8867 (m-40) cc_final: 0.8631 (m110) REVERT: A 189 LYS cc_start: 0.7599 (pptt) cc_final: 0.6951 (tttm) REVERT: A 410 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8586 (m) REVERT: A 439 LYS cc_start: 0.8451 (mttt) cc_final: 0.8030 (mtpm) REVERT: A 585 TRP cc_start: 0.6755 (m100) cc_final: 0.6388 (m-10) REVERT: A 595 GLU cc_start: 0.7935 (mp0) cc_final: 0.7405 (mp0) REVERT: A 611 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7650 (tm) REVERT: E 111 TYR cc_start: 0.8597 (t80) cc_final: 0.8368 (t80) REVERT: E 112 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7848 (ttp) REVERT: E 119 TYR cc_start: 0.6709 (t80) cc_final: 0.6259 (t80) REVERT: E 242 MET cc_start: 0.7079 (mtm) cc_final: 0.6787 (mtt) REVERT: E 254 LYS cc_start: 0.7461 (tptm) cc_final: 0.7155 (tppp) REVERT: E 257 LYS cc_start: 0.5493 (OUTLIER) cc_final: 0.5230 (mmmt) REVERT: E 438 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8015 (mm) REVERT: E 584 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.5103 (tt) REVERT: E 595 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: E 600 LEU cc_start: 0.6935 (mm) cc_final: 0.6627 (mp) outliers start: 31 outliers final: 20 residues processed: 139 average time/residue: 0.7170 time to fit residues: 111.4964 Evaluate side-chains 138 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 180 TRP Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 528 PHE Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 595 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9349 Z= 0.193 Angle : 0.606 18.294 12757 Z= 0.291 Chirality : 0.038 0.172 1418 Planarity : 0.004 0.043 1554 Dihedral : 7.378 140.462 1227 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.99 % Allowed : 21.22 % Favored : 74.79 % 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 (0.26), residues: 1126 helix: 1.45 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -0.69 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 80 HIS 0.004 0.001 HIS E 598 PHE 0.032 0.001 PHE A 275 TYR 0.012 0.001 TYR A 575 ARG 0.003 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8880 (m-40) cc_final: 0.8650 (m110) REVERT: A 189 LYS cc_start: 0.7587 (pptt) cc_final: 0.6924 (tttm) REVERT: A 410 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8590 (m) REVERT: A 439 LYS cc_start: 0.8481 (mttt) cc_final: 0.8049 (mtpm) REVERT: A 585 TRP cc_start: 0.6774 (m100) cc_final: 0.6409 (m-10) REVERT: A 595 GLU cc_start: 0.7945 (mp0) cc_final: 0.7384 (mp0) REVERT: A 597 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: A 611 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7340 (tm) REVERT: E 111 TYR cc_start: 0.8660 (t80) cc_final: 0.8457 (t80) REVERT: E 112 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7856 (ttp) REVERT: E 119 TYR cc_start: 0.6732 (t80) cc_final: 0.6475 (t80) REVERT: E 242 MET cc_start: 0.7118 (mtm) cc_final: 0.6816 (mtt) REVERT: E 254 LYS cc_start: 0.7531 (tptm) cc_final: 0.7200 (tppp) REVERT: E 257 LYS cc_start: 0.5542 (OUTLIER) cc_final: 0.5265 (mmmt) REVERT: E 438 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8029 (mm) REVERT: E 566 MET cc_start: 0.7536 (tpp) cc_final: 0.7272 (mmm) REVERT: E 584 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.5088 (tt) REVERT: E 595 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: E 598 HIS cc_start: 0.5678 (OUTLIER) cc_final: 0.4965 (m-70) REVERT: E 600 LEU cc_start: 0.6970 (mm) cc_final: 0.6656 (mp) outliers start: 38 outliers final: 19 residues processed: 144 average time/residue: 0.7149 time to fit residues: 115.3149 Evaluate side-chains 139 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 595 GLU Chi-restraints excluded: chain E residue 598 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 111 optimal weight: 0.0370 chunk 102 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9349 Z= 0.164 Angle : 0.601 17.695 12757 Z= 0.285 Chirality : 0.038 0.145 1418 Planarity : 0.003 0.035 1554 Dihedral : 7.323 140.335 1227 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.15 % Allowed : 22.48 % Favored : 74.37 % 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: 1.11 (0.26), residues: 1126 helix: 1.43 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 80 HIS 0.003 0.001 HIS E 598 PHE 0.024 0.001 PHE E 275 TYR 0.017 0.001 TYR E 340 ARG 0.003 0.000 ARG A 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 153 ASN cc_start: 0.8870 (m-40) cc_final: 0.8627 (m110) REVERT: A 189 LYS cc_start: 0.7457 (pptt) cc_final: 0.6767 (tttp) REVERT: A 410 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8583 (m) REVERT: A 439 LYS cc_start: 0.8457 (mttt) cc_final: 0.8031 (mtpm) REVERT: A 585 TRP cc_start: 0.6730 (m100) cc_final: 0.6400 (m-10) REVERT: A 595 GLU cc_start: 0.7942 (mp0) cc_final: 0.7368 (mp0) REVERT: E 111 TYR cc_start: 0.8631 (t80) cc_final: 0.8406 (t80) REVERT: E 112 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7823 (ttp) REVERT: E 119 TYR cc_start: 0.6641 (t80) cc_final: 0.6259 (t80) REVERT: E 242 MET cc_start: 0.7080 (mtm) cc_final: 0.6814 (mtt) REVERT: E 254 LYS cc_start: 0.7506 (tptm) cc_final: 0.7178 (tppp) REVERT: E 257 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.5189 (mmmt) REVERT: E 479 THR cc_start: 0.6529 (m) cc_final: 0.5985 (t) REVERT: E 566 MET cc_start: 0.7450 (tpp) cc_final: 0.7200 (mmt) REVERT: E 584 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.5043 (tt) REVERT: E 595 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: E 600 LEU cc_start: 0.6926 (mm) cc_final: 0.6640 (mp) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 0.7130 time to fit residues: 114.5829 Evaluate side-chains 139 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 528 PHE Chi-restraints excluded: chain E residue 584 LEU Chi-restraints excluded: chain E residue 595 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 HIS ** 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 = 0.4205 r_free = 0.4205 target = 0.174873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139585 restraints weight = 12208.479| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.26 r_work: 0.3689 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9349 Z= 0.163 Angle : 0.605 16.833 12757 Z= 0.288 Chirality : 0.039 0.422 1418 Planarity : 0.003 0.031 1554 Dihedral : 7.321 140.385 1227 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.15 % Allowed : 22.48 % Favored : 74.37 % 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: 1.18 (0.26), residues: 1126 helix: 1.45 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.54 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 80 HIS 0.003 0.001 HIS E 598 PHE 0.023 0.001 PHE A 528 TYR 0.013 0.001 TYR A 575 ARG 0.003 0.000 ARG A 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.28 seconds wall clock time: 56 minutes 6.47 seconds (3366.47 seconds total)