Starting phenix.real_space_refine on Sat Aug 3 22:00:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y90_39065/08_2024/8y90_39065.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y90_39065/08_2024/8y90_39065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y90_39065/08_2024/8y90_39065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y90_39065/08_2024/8y90_39065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y90_39065/08_2024/8y90_39065.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y90_39065/08_2024/8y90_39065.cif" } resolution = 3.15 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= 0.045 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 6069 2.51 5 N 1413 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 GLU 382": "OE1" <-> "OE2" 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 PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 587": "NH1" <-> "NH2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "E ARG 607": "NH1" <-> "NH2" Residue "A ARG 81": "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: 9058 Number of models: 1 Model: "" Number of chains: 3 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: 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 26 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX6': 1} Classifications: {'undetermined': 3, 'water': 5} Link IDs: {None: 7} Time building chain proxies: 5.63, per 1000 atoms: 0.62 Number of scatterers: 9058 At special positions: 0 Unit cell: (96.36, 86.87, 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 1534 8.00 N 1413 7.00 C 6069 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: 3.79 Conformation dependent library (CDL) restraints added in 1.6 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: 55 helices and 0 sheets defined 74.6% 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 'E' and resid 61 through 74 removed outlier: 3.758A pdb=" N PHE E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.614A pdb=" N TRP E 128 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 129 " --> pdb=" O THR E 126 " (cutoff:3.500A) Proline residue: E 132 - end of helix Processing helix chain 'E' and resid 135 through 166 removed outlier: 4.094A pdb=" N TYR E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR E 151 " --> pdb=" O TYR E 147 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 234 through 253 Processing helix chain 'E' and resid 255 through 279 removed outlier: 4.132A pdb=" N LYS E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Proline residue: E 270 - end of helix removed outlier: 3.973A pdb=" N PHE E 275 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL E 276 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 277 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 3.784A pdb=" N ILE E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 320 Processing helix chain 'E' and resid 324 through 333 removed outlier: 3.530A 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 removed outlier: 3.614A pdb=" N THR E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 435 removed outlier: 3.557A pdb=" N TRP E 404 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 427 " --> pdb=" O GLY E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 441 Processing helix chain 'E' and resid 441 through 457 Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 464 through 492 removed outlier: 3.985A pdb=" N VAL E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 471 " --> pdb=" O TYR E 467 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP E 473 " --> pdb=" O LEU E 469 " (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: 3.811A pdb=" N ASN E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.931A pdb=" N ALA E 602 " --> pdb=" O HIS E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 616 removed outlier: 4.052A pdb=" N TRP E 614 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.954A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.594A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.516A pdb=" N LEU A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 135 through 167 removed outlier: 3.675A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.632A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 284 removed outlier: 3.727A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.051A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.486A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.567A 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 373 removed outlier: 3.627A pdb=" N ALA A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.860A pdb=" N VAL A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.894A pdb=" N LEU A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.769A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.608A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.211A 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 520 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 580 removed outlier: 3.824A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 598 through 604 removed outlier: 4.375A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.507A 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: 4.030A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1638 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: 2.42 Time building geometry restraints manager: 4.15 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: 2647 1.34 - 1.46: 1907 1.46 - 1.57: 4730 1.57 - 1.69: 1 1.69 - 1.81: 62 Bond restraints: 9347 Sorted by residual: bond pdb=" C01 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 1.449 1.273 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" C03 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 1.450 1.366 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C12 A1LX6 A 701 " pdb=" C13 A1LX6 A 701 " ideal model delta sigma weight residual 1.515 1.582 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C07 A1LX6 A 701 " pdb=" C08 A1LX6 A 701 " ideal model delta sigma weight residual 1.396 1.449 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C11 A1LX6 A 701 " pdb=" C12 A1LX6 A 701 " ideal model delta sigma weight residual 1.398 1.449 -0.051 2.00e-02 2.50e+03 6.49e+00 ... (remaining 9342 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.36: 312 107.36 - 114.01: 5178 114.01 - 120.67: 4134 120.67 - 127.32: 2990 127.32 - 133.98: 140 Bond angle restraints: 12754 Sorted by residual: angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 106.21 109.57 -3.36 1.07e+00 8.73e-01 9.87e+00 angle pdb=" C ASP A 546 " pdb=" CA ASP A 546 " pdb=" CB ASP A 546 " ideal model delta sigma weight residual 110.81 115.78 -4.97 1.60e+00 3.91e-01 9.64e+00 angle pdb=" C LEU A 191 " pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " ideal model delta sigma weight residual 110.92 115.83 -4.91 1.59e+00 3.96e-01 9.55e+00 angle pdb=" C12 A1LX6 A 701 " pdb=" C13 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 113.93 122.76 -8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" N ASP A 546 " pdb=" CA ASP A 546 " pdb=" C ASP A 546 " ideal model delta sigma weight residual 111.11 107.69 3.42 1.20e+00 6.94e-01 8.14e+00 ... (remaining 12749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 4901 16.53 - 33.05: 223 33.05 - 49.58: 76 49.58 - 66.11: 20 66.11 - 82.63: 6 Dihedral angle restraints: 5226 sinusoidal: 1962 harmonic: 3264 Sorted by residual: dihedral pdb=" CA VAL E 374 " pdb=" C VAL E 374 " pdb=" N ASN E 375 " pdb=" CA ASN E 375 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TRP E 128 " pdb=" C TRP E 128 " pdb=" N LYS E 129 " pdb=" CA LYS E 129 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LYS E 373 " pdb=" C LYS E 373 " pdb=" N VAL E 374 " pdb=" CA VAL E 374 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1064 0.038 - 0.076: 304 0.076 - 0.114: 47 0.114 - 0.152: 3 0.152 - 0.189: 1 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C06 A1LX6 A 701 " pdb=" C07 A1LX6 A 701 " pdb=" C14 A1LX6 A 701 " pdb=" O05 A1LX6 A 701 " both_signs ideal model delta sigma weight residual False 2.38 2.19 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA LEU A 269 " pdb=" N LEU A 269 " pdb=" C LEU A 269 " pdb=" CB LEU A 269 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA PRO A 570 " pdb=" N PRO A 570 " pdb=" C PRO A 570 " pdb=" CB PRO A 570 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 1416 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 477 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ALA E 477 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA E 477 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY E 478 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 476 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C ALA E 476 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA E 476 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA E 477 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 475 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C PHE E 475 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE E 475 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA E 476 " -0.015 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 235 2.71 - 3.26: 9740 3.26 - 3.81: 15390 3.81 - 4.35: 19083 4.35 - 4.90: 32295 Nonbonded interactions: 76743 Sorted by model distance: nonbonded pdb=" OH TYR E 205 " pdb=" O LYS E 373 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR E 332 " pdb=" OG1 THR E 429 " model vdw 2.202 3.040 nonbonded pdb=" O ALA E 328 " pdb=" OG SER E 331 " model vdw 2.236 3.040 nonbonded pdb=" O LEU E 471 " pdb=" OG1 THR E 474 " model vdw 2.253 3.040 nonbonded pdb=" O SER A 251 " pdb=" OG SER A 259 " model vdw 2.261 3.040 ... (remaining 76738 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: 2.010 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.460 Find NCS groups from input model: 0.330 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 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 0.176 9347 Z= 0.237 Angle : 0.565 8.828 12754 Z= 0.344 Chirality : 0.034 0.189 1419 Planarity : 0.004 0.038 1554 Dihedral : 11.765 82.634 3150 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 6.09 % Allowed : 8.19 % Favored : 85.71 % 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: -1.83 (0.22), residues: 1126 helix: -0.83 (0.17), residues: 758 sheet: None (None), residues: 0 loop : -1.76 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 128 HIS 0.002 0.000 HIS A 228 PHE 0.008 0.001 PHE E 475 TYR 0.008 0.001 TYR A 98 ARG 0.002 0.000 ARG A 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 371 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 313 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 152 TYR cc_start: 0.6618 (t80) cc_final: 0.5904 (t80) REVERT: E 173 TRP cc_start: 0.5954 (OUTLIER) cc_final: 0.4968 (m-90) REVERT: E 250 PHE cc_start: 0.7255 (m-80) cc_final: 0.6910 (t80) REVERT: E 314 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6423 (mm110) REVERT: E 347 SER cc_start: 0.7763 (m) cc_final: 0.7296 (m) REVERT: A 111 TYR cc_start: 0.7911 (t80) cc_final: 0.7564 (t80) REVERT: A 122 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5884 (mt-10) REVERT: A 147 TYR cc_start: 0.7789 (m-10) cc_final: 0.7303 (m-10) REVERT: A 212 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7167 (mt-10) REVERT: A 263 VAL cc_start: 0.6406 (OUTLIER) cc_final: 0.6124 (m) REVERT: A 397 THR cc_start: 0.8075 (m) cc_final: 0.7710 (p) REVERT: A 418 ASP cc_start: 0.7875 (t0) cc_final: 0.7581 (t0) REVERT: A 490 ILE cc_start: 0.8208 (mt) cc_final: 0.7999 (mp) REVERT: A 519 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8344 (tt) REVERT: A 556 TRP cc_start: 0.6713 (m100) cc_final: 0.6213 (m100) REVERT: A 576 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6866 (tptt) outliers start: 58 outliers final: 12 residues processed: 354 average time/residue: 0.1907 time to fit residues: 94.0780 Evaluate side-chains 195 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 576 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9347 Z= 0.234 Angle : 0.611 12.804 12754 Z= 0.314 Chirality : 0.041 0.206 1419 Planarity : 0.005 0.077 1554 Dihedral : 7.019 58.526 1264 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.67 % Allowed : 14.39 % Favored : 79.94 % 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: -0.48 (0.24), residues: 1126 helix: 0.30 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 80 HIS 0.007 0.001 HIS E 222 PHE 0.020 0.002 PHE E 272 TYR 0.014 0.001 TYR A 575 ARG 0.007 0.001 ARG E 81 *********************** 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 254 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 200 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 152 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6015 (t80) REVERT: E 155 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5923 (mm) REVERT: E 173 TRP cc_start: 0.6346 (OUTLIER) cc_final: 0.5139 (m-90) REVERT: E 250 PHE cc_start: 0.7443 (m-80) cc_final: 0.6756 (t80) REVERT: E 347 SER cc_start: 0.7772 (m) cc_final: 0.6842 (m) REVERT: E 517 TRP cc_start: 0.6293 (m100) cc_final: 0.6087 (m100) REVERT: A 109 LEU cc_start: 0.8210 (mt) cc_final: 0.7979 (mt) REVERT: A 111 TYR cc_start: 0.8049 (t80) cc_final: 0.7318 (t80) REVERT: A 147 TYR cc_start: 0.8012 (m-10) cc_final: 0.7590 (m-10) REVERT: A 418 ASP cc_start: 0.7847 (t0) cc_final: 0.7565 (t0) REVERT: A 556 TRP cc_start: 0.6778 (m100) cc_final: 0.6193 (m100) REVERT: A 576 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6698 (mmmt) outliers start: 54 outliers final: 24 residues processed: 235 average time/residue: 0.1837 time to fit residues: 61.6883 Evaluate side-chains 183 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 100 optimal weight: 0.5980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9347 Z= 0.175 Angle : 0.588 12.668 12754 Z= 0.292 Chirality : 0.039 0.183 1419 Planarity : 0.004 0.044 1554 Dihedral : 5.851 57.802 1246 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.94 % Allowed : 16.60 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1126 helix: 0.53 (0.18), residues: 763 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 80 HIS 0.006 0.001 HIS E 222 PHE 0.021 0.001 PHE E 272 TYR 0.019 0.001 TYR E 249 ARG 0.004 0.000 ARG E 81 *********************** 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 218 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 171 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: E 152 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6141 (t80) REVERT: E 155 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5970 (mm) REVERT: E 173 TRP cc_start: 0.6386 (OUTLIER) cc_final: 0.4965 (m-90) REVERT: E 250 PHE cc_start: 0.7309 (m-80) cc_final: 0.6636 (t80) REVERT: E 259 SER cc_start: 0.7076 (OUTLIER) cc_final: 0.6430 (t) REVERT: E 314 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6364 (mm-40) REVERT: E 347 SER cc_start: 0.7459 (m) cc_final: 0.7017 (m) REVERT: E 518 ARG cc_start: 0.7266 (ptm160) cc_final: 0.6799 (ptm160) REVERT: A 111 TYR cc_start: 0.7911 (t80) cc_final: 0.7211 (t80) REVERT: A 147 TYR cc_start: 0.8038 (m-10) cc_final: 0.7543 (m-10) REVERT: A 391 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: A 418 ASP cc_start: 0.7706 (t0) cc_final: 0.7462 (t0) REVERT: A 556 TRP cc_start: 0.6732 (m100) cc_final: 0.6171 (m100) REVERT: A 588 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8073 (mm) outliers start: 47 outliers final: 27 residues processed: 205 average time/residue: 0.1698 time to fit residues: 51.0948 Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 0.0770 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9347 Z= 0.199 Angle : 0.584 11.205 12754 Z= 0.293 Chirality : 0.040 0.207 1419 Planarity : 0.004 0.039 1554 Dihedral : 5.471 53.656 1240 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.36 % Allowed : 16.81 % 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: 0.21 (0.25), residues: 1126 helix: 0.73 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.99 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 80 HIS 0.003 0.001 HIS E 598 PHE 0.023 0.001 PHE E 272 TYR 0.013 0.001 TYR A 572 ARG 0.003 0.000 ARG E 440 *********************** 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 218 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7134 (t80) cc_final: 0.6857 (t80) REVERT: E 112 MET cc_start: 0.7458 (ttm) cc_final: 0.7231 (ttt) REVERT: E 133 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7738 (m-10) REVERT: E 152 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6573 (t80) REVERT: E 155 ILE cc_start: 0.6209 (OUTLIER) cc_final: 0.5987 (mp) REVERT: E 173 TRP cc_start: 0.6540 (OUTLIER) cc_final: 0.5855 (m-90) REVERT: E 250 PHE cc_start: 0.7361 (m-80) cc_final: 0.6658 (t80) REVERT: E 471 LEU cc_start: 0.4986 (OUTLIER) cc_final: 0.4542 (tt) REVERT: E 518 ARG cc_start: 0.7244 (ptm160) cc_final: 0.6756 (ptm160) REVERT: E 556 TRP cc_start: 0.7053 (m100) cc_final: 0.6787 (m100) REVERT: A 111 TYR cc_start: 0.7930 (t80) cc_final: 0.7125 (t80) REVERT: A 147 TYR cc_start: 0.8215 (m-10) cc_final: 0.7614 (m-10) REVERT: A 323 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7034 (t80) REVERT: A 391 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6823 (m-10) REVERT: A 556 TRP cc_start: 0.6799 (m100) cc_final: 0.6181 (m100) REVERT: A 588 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8077 (mm) outliers start: 51 outliers final: 23 residues processed: 207 average time/residue: 0.1723 time to fit residues: 52.4765 Evaluate side-chains 181 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR 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: 0.8980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.0170 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9347 Z= 0.178 Angle : 0.581 12.679 12754 Z= 0.289 Chirality : 0.040 0.178 1419 Planarity : 0.004 0.065 1554 Dihedral : 5.405 55.416 1239 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.94 % Allowed : 17.96 % 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: 0.30 (0.25), residues: 1126 helix: 0.84 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 264 HIS 0.003 0.000 HIS E 598 PHE 0.031 0.001 PHE A 82 TYR 0.018 0.001 TYR A 572 ARG 0.003 0.000 ARG E 81 *********************** 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 216 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 169 time to evaluate : 0.909 Fit side-chains REVERT: E 111 TYR cc_start: 0.7168 (t80) cc_final: 0.6860 (t80) REVERT: E 133 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: E 152 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6834 (t80) REVERT: E 173 TRP cc_start: 0.6613 (OUTLIER) cc_final: 0.5979 (m-90) REVERT: E 250 PHE cc_start: 0.7260 (m-80) cc_final: 0.6654 (t80) REVERT: E 471 LEU cc_start: 0.4908 (OUTLIER) cc_final: 0.4430 (tt) REVERT: E 518 ARG cc_start: 0.7219 (ptm160) cc_final: 0.6721 (ptm160) REVERT: E 556 TRP cc_start: 0.7044 (m100) cc_final: 0.6776 (m100) REVERT: A 111 TYR cc_start: 0.7957 (t80) cc_final: 0.7208 (t80) REVERT: A 147 TYR cc_start: 0.8254 (m-10) cc_final: 0.7606 (m-10) REVERT: A 323 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7015 (t80) REVERT: A 391 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.7030 (m-10) REVERT: A 556 TRP cc_start: 0.6810 (m100) cc_final: 0.6171 (m100) outliers start: 47 outliers final: 30 residues processed: 205 average time/residue: 0.1749 time to fit residues: 52.0523 Evaluate side-chains 192 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9347 Z= 0.181 Angle : 0.580 11.604 12754 Z= 0.288 Chirality : 0.040 0.187 1419 Planarity : 0.004 0.058 1554 Dihedral : 5.400 56.201 1239 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.41 % Allowed : 20.27 % Favored : 75.32 % 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: 0.46 (0.25), residues: 1126 helix: 0.97 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 264 HIS 0.004 0.001 HIS E 222 PHE 0.022 0.001 PHE A 82 TYR 0.013 0.001 TYR A 572 ARG 0.002 0.000 ARG E 81 *********************** 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 206 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 0.992 Fit side-chains REVERT: E 111 TYR cc_start: 0.7222 (t80) cc_final: 0.6900 (t80) REVERT: E 133 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7718 (m-10) REVERT: E 173 TRP cc_start: 0.6710 (OUTLIER) cc_final: 0.6059 (m-90) REVERT: E 250 PHE cc_start: 0.7197 (m-80) cc_final: 0.6565 (t80) REVERT: E 471 LEU cc_start: 0.4831 (OUTLIER) cc_final: 0.4329 (tt) REVERT: E 518 ARG cc_start: 0.7242 (ptm160) cc_final: 0.6768 (ptm160) REVERT: E 556 TRP cc_start: 0.7028 (m100) cc_final: 0.6752 (m100) REVERT: A 111 TYR cc_start: 0.8005 (t80) cc_final: 0.7181 (t80) REVERT: A 147 TYR cc_start: 0.8297 (m-10) cc_final: 0.7616 (m-10) REVERT: A 216 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7499 (mtp85) REVERT: A 323 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7036 (t80) REVERT: A 391 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.7014 (m-10) REVERT: A 556 TRP cc_start: 0.6844 (m100) cc_final: 0.6186 (m100) outliers start: 42 outliers final: 29 residues processed: 193 average time/residue: 0.1861 time to fit residues: 51.4106 Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9347 Z= 0.167 Angle : 0.572 11.992 12754 Z= 0.282 Chirality : 0.039 0.193 1419 Planarity : 0.004 0.052 1554 Dihedral : 5.358 56.957 1239 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.99 % Allowed : 21.01 % Favored : 75.00 % 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: 0.57 (0.25), residues: 1126 helix: 1.02 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -0.92 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 264 HIS 0.003 0.000 HIS E 222 PHE 0.020 0.001 PHE A 82 TYR 0.014 0.001 TYR A 575 ARG 0.002 0.000 ARG A 121 *********************** 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 203 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 0.904 Fit side-chains REVERT: E 111 TYR cc_start: 0.7234 (t80) cc_final: 0.6888 (t80) REVERT: E 133 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7682 (m-10) REVERT: E 243 VAL cc_start: 0.8788 (t) cc_final: 0.8513 (m) REVERT: E 250 PHE cc_start: 0.7086 (m-80) cc_final: 0.6539 (t80) REVERT: E 264 TRP cc_start: 0.5682 (t60) cc_final: 0.5446 (t60) REVERT: E 471 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4277 (tt) REVERT: E 518 ARG cc_start: 0.7251 (ptm160) cc_final: 0.6766 (ptm160) REVERT: E 556 TRP cc_start: 0.7050 (m100) cc_final: 0.6758 (m100) REVERT: A 111 TYR cc_start: 0.7976 (t80) cc_final: 0.7167 (t80) REVERT: A 147 TYR cc_start: 0.8289 (m-10) cc_final: 0.7644 (m-10) REVERT: A 216 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7486 (mtp85) REVERT: A 299 PHE cc_start: 0.7866 (m-80) cc_final: 0.7627 (m-80) REVERT: A 391 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: A 556 TRP cc_start: 0.6825 (m100) cc_final: 0.6166 (m100) outliers start: 38 outliers final: 29 residues processed: 190 average time/residue: 0.1915 time to fit residues: 52.5900 Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.0770 chunk 73 optimal weight: 0.0470 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9347 Z= 0.163 Angle : 0.589 12.414 12754 Z= 0.288 Chirality : 0.039 0.182 1419 Planarity : 0.004 0.050 1554 Dihedral : 5.252 57.440 1237 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.10 % Allowed : 20.80 % Favored : 75.11 % 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: 0.64 (0.25), residues: 1126 helix: 1.07 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 264 HIS 0.004 0.001 HIS E 222 PHE 0.018 0.001 PHE A 82 TYR 0.014 0.001 TYR A 575 ARG 0.004 0.000 ARG E 440 *********************** 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 204 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 0.956 Fit side-chains REVERT: E 107 MET cc_start: 0.6982 (mmm) cc_final: 0.6461 (tpt) REVERT: E 111 TYR cc_start: 0.7210 (t80) cc_final: 0.6845 (t80) REVERT: E 133 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7586 (m-10) REVERT: E 173 TRP cc_start: 0.6809 (OUTLIER) cc_final: 0.6230 (m-90) REVERT: E 243 VAL cc_start: 0.8751 (t) cc_final: 0.8468 (m) REVERT: E 250 PHE cc_start: 0.7009 (m-80) cc_final: 0.6532 (t80) REVERT: E 264 TRP cc_start: 0.5675 (t60) cc_final: 0.5433 (t60) REVERT: E 471 LEU cc_start: 0.4640 (OUTLIER) cc_final: 0.4152 (tt) REVERT: E 518 ARG cc_start: 0.7258 (ptm160) cc_final: 0.6826 (ptm160) REVERT: E 556 TRP cc_start: 0.7011 (m100) cc_final: 0.6739 (m100) REVERT: A 111 TYR cc_start: 0.7954 (t80) cc_final: 0.7160 (t80) REVERT: A 147 TYR cc_start: 0.8273 (m-10) cc_final: 0.7591 (m-10) REVERT: A 216 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7505 (mtp85) REVERT: A 323 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7009 (t80) REVERT: A 481 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 556 TRP cc_start: 0.6802 (m100) cc_final: 0.6149 (m100) outliers start: 39 outliers final: 30 residues processed: 191 average time/residue: 0.1806 time to fit residues: 50.1295 Evaluate side-chains 188 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR 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: 0.1980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9347 Z= 0.188 Angle : 0.601 11.087 12754 Z= 0.299 Chirality : 0.040 0.193 1419 Planarity : 0.004 0.047 1554 Dihedral : 5.304 58.605 1237 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.10 % Allowed : 21.01 % Favored : 74.89 % 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: 0.63 (0.25), residues: 1126 helix: 1.06 (0.19), residues: 763 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 264 HIS 0.006 0.001 HIS E 280 PHE 0.033 0.001 PHE A 408 TYR 0.017 0.001 TYR A 391 ARG 0.003 0.000 ARG E 440 *********************** 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 194 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: E 107 MET cc_start: 0.6969 (mmm) cc_final: 0.6408 (tpt) REVERT: E 111 TYR cc_start: 0.7251 (t80) cc_final: 0.6865 (t80) REVERT: E 133 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: E 173 TRP cc_start: 0.6851 (OUTLIER) cc_final: 0.6293 (m-90) REVERT: E 243 VAL cc_start: 0.8734 (t) cc_final: 0.8450 (m) REVERT: E 250 PHE cc_start: 0.7031 (m-80) cc_final: 0.6529 (t80) REVERT: E 264 TRP cc_start: 0.5674 (t60) cc_final: 0.5415 (t60) REVERT: E 471 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.4039 (tt) REVERT: E 518 ARG cc_start: 0.7213 (ptm160) cc_final: 0.6774 (ptm160) REVERT: A 111 TYR cc_start: 0.7997 (t80) cc_final: 0.7159 (t80) REVERT: A 147 TYR cc_start: 0.8338 (m-10) cc_final: 0.7727 (m-10) REVERT: A 216 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7525 (mtp85) REVERT: A 323 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 481 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8508 (tp) REVERT: A 556 TRP cc_start: 0.6799 (m100) cc_final: 0.6128 (m100) outliers start: 39 outliers final: 30 residues processed: 183 average time/residue: 0.1837 time to fit residues: 49.1599 Evaluate side-chains 185 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.0000 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.0270 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9347 Z= 0.171 Angle : 0.606 13.187 12754 Z= 0.296 Chirality : 0.040 0.199 1419 Planarity : 0.004 0.048 1554 Dihedral : 5.286 59.584 1237 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.89 % Allowed : 21.64 % Favored : 74.47 % 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: 0.65 (0.25), residues: 1126 helix: 1.07 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 264 HIS 0.008 0.001 HIS E 222 PHE 0.029 0.001 PHE A 408 TYR 0.016 0.001 TYR A 391 ARG 0.005 0.000 ARG E 216 ********************** 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 196 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7253 (t80) cc_final: 0.6881 (t80) REVERT: E 133 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7486 (m-10) REVERT: E 173 TRP cc_start: 0.6900 (OUTLIER) cc_final: 0.6360 (m-90) REVERT: E 243 VAL cc_start: 0.8760 (t) cc_final: 0.8474 (m) REVERT: E 250 PHE cc_start: 0.6910 (m-80) cc_final: 0.6497 (t80) REVERT: E 264 TRP cc_start: 0.5686 (t60) cc_final: 0.5422 (t60) REVERT: E 471 LEU cc_start: 0.4596 (OUTLIER) cc_final: 0.4093 (tt) REVERT: E 518 ARG cc_start: 0.7228 (ptm160) cc_final: 0.6756 (ptm160) REVERT: A 111 TYR cc_start: 0.7952 (t80) cc_final: 0.7143 (t80) REVERT: A 147 TYR cc_start: 0.8274 (m-10) cc_final: 0.7641 (m-10) REVERT: A 216 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7517 (mtp85) REVERT: A 323 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7050 (t80) REVERT: A 481 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8472 (tp) REVERT: A 556 TRP cc_start: 0.6822 (m100) cc_final: 0.6173 (m100) outliers start: 37 outliers final: 28 residues processed: 185 average time/residue: 0.1800 time to fit residues: 48.6069 Evaluate side-chains 184 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 0.0030 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.193409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158706 restraints weight = 13789.891| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.24 r_work: 0.3817 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9347 Z= 0.184 Angle : 0.612 13.185 12754 Z= 0.298 Chirality : 0.040 0.201 1419 Planarity : 0.004 0.087 1554 Dihedral : 5.301 59.817 1237 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.47 % Allowed : 21.95 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1126 helix: 1.10 (0.19), residues: 761 sheet: None (None), residues: 0 loop : -0.84 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 158 HIS 0.003 0.001 HIS E 222 PHE 0.025 0.001 PHE A 408 TYR 0.014 0.001 TYR A 391 ARG 0.003 0.000 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2282.33 seconds wall clock time: 40 minutes 45.08 seconds (2445.08 seconds total)