Starting phenix.real_space_refine on Fri Jan 19 01:58:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhb_33193/01_2024/7xhb_33193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhb_33193/01_2024/7xhb_33193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhb_33193/01_2024/7xhb_33193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhb_33193/01_2024/7xhb_33193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhb_33193/01_2024/7xhb_33193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xhb_33193/01_2024/7xhb_33193_updated.pdb" } resolution = 3.33 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= 0.001 sd= 0.061 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 P 2 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 6473 2.51 5 N 1727 2.21 5 O 1873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 106": "NH1" <-> "NH2" Residue "Y PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 213": "NH1" <-> "NH2" Residue "Y ARG 252": "NH1" <-> "NH2" Residue "Y ARG 301": "NH1" <-> "NH2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10122 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6107 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 15, 'TRANS': 749} Chain: "Y" Number of atoms: 3198 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 3194 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 20, 'TRANS': 386} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 407, 3194 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 20, 'TRANS': 386} Chain breaks: 2 bond proxies already assigned to first conformer: 3261 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "B" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 309 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY Y 145 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY Y 145 " occ=0.50 Time building chain proxies: 7.20, per 1000 atoms: 0.71 Number of scatterers: 10122 At special positions: 0 Unit cell: (98.115, 119.215, 128.71, 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) S 46 16.00 P 2 15.00 Mg 1 11.99 O 1873 8.00 N 1727 7.00 C 6473 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 2.4 seconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 6 sheets defined 58.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 15 through 32 Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 106 through 118 removed outlier: 4.883A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 131 through 146 removed outlier: 4.813A pdb=" N ILE A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.861A pdb=" N MET A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 232 through 243 removed outlier: 4.466A pdb=" N THR A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 302 through 305 No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.457A pdb=" N ASN A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.941A pdb=" N THR A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 464 through 473 removed outlier: 4.046A pdb=" N GLU A 467 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 470 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 471 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 473 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 removed outlier: 3.836A pdb=" N ARG A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 572 through 619 removed outlier: 3.889A pdb=" N GLN A 598 " --> pdb=" O LYS A 594 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 642 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 681 through 700 Processing helix chain 'A' and resid 706 through 744 removed outlier: 4.902A pdb=" N HIS A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU A 740 " --> pdb=" O GLN A 736 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG A 741 " --> pdb=" O GLY A 737 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA A 742 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR A 743 " --> pdb=" O HIS A 739 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 776 removed outlier: 3.687A pdb=" N PHE A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 9 Processing helix chain 'Y' and resid 12 through 33 Processing helix chain 'Y' and resid 41 through 47 Processing helix chain 'Y' and resid 75 through 86 Processing helix chain 'Y' and resid 93 through 100 Processing helix chain 'Y' and resid 104 through 135 removed outlier: 3.749A pdb=" N LEU Y 126 " --> pdb=" O PHE Y 122 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 172 removed outlier: 3.554A pdb=" N ALA Y 172 " --> pdb=" O GLU Y 168 " (cutoff:3.500A) Processing helix chain 'Y' and resid 178 through 188 removed outlier: 3.507A pdb=" N ILE Y 182 " --> pdb=" O GLY Y 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 202 removed outlier: 4.341A pdb=" N TYR Y 199 " --> pdb=" O LEU Y 195 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA Y 200 " --> pdb=" O ASN Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 235 Processing helix chain 'Y' and resid 272 through 282 Processing helix chain 'Y' and resid 284 through 288 Processing helix chain 'Y' and resid 295 through 303 Processing helix chain 'Y' and resid 309 through 330 removed outlier: 4.130A pdb=" N ILE Y 314 " --> pdb=" O VAL Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 333 through 342 Processing helix chain 'Y' and resid 355 through 380 removed outlier: 3.958A pdb=" N LEU Y 369 " --> pdb=" O TYR Y 365 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL Y 370 " --> pdb=" O ARG Y 366 " (cutoff:3.500A) Processing helix chain 'Y' and resid 383 through 386 No H-bonds generated for 'chain 'Y' and resid 383 through 386' Processing helix chain 'Y' and resid 399 through 418 removed outlier: 4.918A pdb=" N ILE Y 404 " --> pdb=" O SER Y 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL Y 405 " --> pdb=" O LEU Y 402 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL Y 406 " --> pdb=" O LEU Y 403 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL Y 408 " --> pdb=" O VAL Y 405 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU Y 410 " --> pdb=" O GLY Y 407 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR Y 412 " --> pdb=" O ALA Y 409 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU Y 417 " --> pdb=" O LYS Y 414 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER Y 418 " --> pdb=" O GLN Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 423 No H-bonds generated for 'chain 'Y' and resid 420 through 423' Processing helix chain 'E' and resid 3 through 17 removed outlier: 4.024A pdb=" N LYS E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 58 Processing helix chain 'B' and resid 4 through 22 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 99 Processing sheet with id= B, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.628A pdb=" N ILE A 172 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 124 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N SER A 175 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A 126 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS A 202 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS A 125 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 204 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 127 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE A 206 " --> pdb=" O VAL A 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 306 through 309 removed outlier: 3.535A pdb=" N GLN A 312 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 533 through 537 removed outlier: 6.686A pdb=" N LEU A 505 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLN A 536 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 507 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLN A 457 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 221 through 225 removed outlier: 3.780A pdb=" N ALA A 353 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY A 225 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR A 351 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'Y' and resid 238 through 241 521 hydrogen bonds defined for protein. 1524 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: 3.03 Time building geometry restraints manager: 4.10 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: 3081 1.34 - 1.46: 1670 1.46 - 1.58: 5452 1.58 - 1.69: 3 1.69 - 1.81: 91 Bond restraints: 10297 Sorted by residual: bond pdb=" CA GLN Y 396 " pdb=" CB GLN Y 396 " ideal model delta sigma weight residual 1.527 1.575 -0.048 1.75e-02 3.27e+03 7.59e+00 bond pdb=" CB ASP Y 48 " pdb=" CG ASP Y 48 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.31e+00 bond pdb=" CA THR A 410 " pdb=" CB THR A 410 " ideal model delta sigma weight residual 1.530 1.563 -0.033 1.69e-02 3.50e+03 3.84e+00 bond pdb=" C ILE Y 191 " pdb=" N PRO Y 192 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.23e-02 6.61e+03 3.82e+00 bond pdb=" N PRO Y 392 " pdb=" CA PRO Y 392 " ideal model delta sigma weight residual 1.465 1.502 -0.037 2.03e-02 2.43e+03 3.32e+00 ... (remaining 10292 not shown) Histogram of bond angle deviations from ideal: 88.81 - 98.39: 5 98.39 - 107.97: 372 107.97 - 117.55: 6994 117.55 - 127.13: 6466 127.13 - 136.71: 70 Bond angle restraints: 13907 Sorted by residual: angle pdb=" N LEU A 221 " pdb=" CA LEU A 221 " pdb=" C LEU A 221 " ideal model delta sigma weight residual 108.20 88.81 19.39 1.71e+00 3.42e-01 1.29e+02 angle pdb=" N ILE A 222 " pdb=" CA ILE A 222 " pdb=" C ILE A 222 " ideal model delta sigma weight residual 108.11 96.86 11.25 1.40e+00 5.10e-01 6.46e+01 angle pdb=" N TYR B 50 " pdb=" CA TYR B 50 " pdb=" C TYR B 50 " ideal model delta sigma weight residual 108.73 95.68 13.05 1.63e+00 3.76e-01 6.41e+01 angle pdb=" C GLN Y 47 " pdb=" N ASP Y 48 " pdb=" CA ASP Y 48 " ideal model delta sigma weight residual 125.66 136.71 -11.05 1.85e+00 2.92e-01 3.57e+01 angle pdb=" N ALA B 47 " pdb=" CA ALA B 47 " pdb=" C ALA B 47 " ideal model delta sigma weight residual 108.20 118.34 -10.14 1.71e+00 3.42e-01 3.52e+01 ... (remaining 13902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 6007 23.47 - 46.95: 193 46.95 - 70.42: 4 70.42 - 93.89: 7 93.89 - 117.37: 1 Dihedral angle restraints: 6212 sinusoidal: 2531 harmonic: 3681 Sorted by residual: dihedral pdb=" CA LEU Y 391 " pdb=" C LEU Y 391 " pdb=" N PRO Y 392 " pdb=" CA PRO Y 392 " ideal model delta harmonic sigma weight residual -180.00 -133.78 -46.22 0 5.00e+00 4.00e-02 8.54e+01 dihedral pdb=" CA HIS Y 308 " pdb=" C HIS Y 308 " pdb=" N PRO Y 309 " pdb=" CA PRO Y 309 " ideal model delta harmonic sigma weight residual -180.00 -148.43 -31.57 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" C5' ADP A1002 " pdb=" O5' ADP A1002 " pdb=" PA ADP A1002 " pdb=" O2A ADP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 -177.36 117.37 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 6209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1227 0.068 - 0.135: 307 0.135 - 0.203: 38 0.203 - 0.270: 11 0.270 - 0.338: 4 Chirality restraints: 1587 Sorted by residual: chirality pdb=" CB VAL Y 331 " pdb=" CA VAL Y 331 " pdb=" CG1 VAL Y 331 " pdb=" CG2 VAL Y 331 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA THR A 410 " pdb=" N THR A 410 " pdb=" C THR A 410 " pdb=" CB THR A 410 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU A 221 " pdb=" N LEU A 221 " pdb=" C LEU A 221 " pdb=" CB LEU A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1584 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Y 284 " 0.055 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO Y 285 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO Y 285 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Y 285 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 241 " -0.013 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C VAL A 241 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 241 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 242 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 174 " 0.013 2.00e-02 2.50e+03 1.67e-02 5.61e+00 pdb=" CG TYR A 174 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 174 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 174 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 174 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 174 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 174 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 174 " 0.001 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 156 2.67 - 3.23: 9340 3.23 - 3.79: 15947 3.79 - 4.34: 20840 4.34 - 4.90: 33818 Nonbonded interactions: 80101 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O2B ADP A1002 " model vdw 2.115 2.170 nonbonded pdb=" O ILE A 639 " pdb=" OG1 THR A 643 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR A 436 " pdb=" OG1 THR A 441 " model vdw 2.289 2.440 nonbonded pdb=" OD1 ASN A 460 " pdb=" OG1 THR A 484 " model vdw 2.300 2.440 nonbonded pdb=" O PRO Y 268 " pdb=" NE2 GLN Y 330 " model vdw 2.322 2.520 ... (remaining 80096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 9.110 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.630 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.006 0.063 10297 Z= 0.363 Angle : 1.082 19.391 13907 Z= 0.596 Chirality : 0.061 0.338 1587 Planarity : 0.007 0.082 1778 Dihedral : 11.156 117.367 3846 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 0.19 % Allowed : 4.16 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -3.95 (0.18), residues: 1261 helix: -2.28 (0.14), residues: 809 sheet: -2.31 (0.53), residues: 73 loop : -3.03 (0.25), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 98 HIS 0.016 0.002 HIS A 297 PHE 0.040 0.003 PHE A 48 TYR 0.040 0.003 TYR A 174 ARG 0.005 0.001 ARG A 735 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 1.044 Fit side-chains REVERT: A 33 TYR cc_start: 0.6443 (m-10) cc_final: 0.5895 (m-80) REVERT: A 400 ARG cc_start: 0.6653 (ptt90) cc_final: 0.5597 (ptm-80) REVERT: A 531 ASP cc_start: 0.7900 (m-30) cc_final: 0.7694 (p0) REVERT: A 563 MET cc_start: 0.3124 (ppp) cc_final: 0.2515 (mmp) REVERT: A 573 MET cc_start: 0.6587 (ptp) cc_final: 0.5850 (ppp) REVERT: A 671 LEU cc_start: 0.8352 (tp) cc_final: 0.8151 (tp) REVERT: A 690 ASP cc_start: 0.8064 (m-30) cc_final: 0.7682 (m-30) REVERT: Y 116 PHE cc_start: 0.8456 (t80) cc_final: 0.8193 (t80) REVERT: Y 365 TYR cc_start: 0.5433 (m-10) cc_final: 0.5223 (m-10) REVERT: E 3 ARG cc_start: 0.7175 (ttm170) cc_final: 0.6843 (ttt90) REVERT: E 24 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8285 (ptmm) REVERT: B 4 LYS cc_start: 0.3563 (pttp) cc_final: 0.2883 (mttm) outliers start: 2 outliers final: 1 residues processed: 278 average time/residue: 0.2495 time to fit residues: 93.1058 Evaluate side-chains 167 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 203 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 622 ASN Y 196 ASN Y 236 GLN ** Y 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 308 HIS Y 339 ASN Y 355 ASN Y 387 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10297 Z= 0.225 Angle : 0.686 11.942 13907 Z= 0.350 Chirality : 0.044 0.214 1587 Planarity : 0.005 0.067 1778 Dihedral : 6.447 103.997 1401 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.85 % Allowed : 11.38 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.22), residues: 1261 helix: -0.46 (0.17), residues: 808 sheet: -2.05 (0.55), residues: 73 loop : -2.70 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 652 HIS 0.008 0.001 HIS A 297 PHE 0.021 0.002 PHE Y 112 TYR 0.015 0.002 TYR Y 130 ARG 0.008 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8032 (m-30) cc_final: 0.7705 (p0) REVERT: A 563 MET cc_start: 0.3016 (ppp) cc_final: 0.2518 (mmp) REVERT: A 573 MET cc_start: 0.6774 (ptp) cc_final: 0.6501 (ppp) REVERT: A 584 ARG cc_start: 0.7759 (ttp-170) cc_final: 0.6864 (ptt180) REVERT: A 690 ASP cc_start: 0.8094 (m-30) cc_final: 0.7758 (m-30) REVERT: Y 183 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7902 (mp) REVERT: Y 372 SER cc_start: 0.7171 (m) cc_final: 0.6847 (p) REVERT: E 3 ARG cc_start: 0.7316 (ttm170) cc_final: 0.7013 (tmt170) REVERT: E 9 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7971 (mmtt) REVERT: E 24 LYS cc_start: 0.8681 (ptpp) cc_final: 0.8346 (mmmt) REVERT: B 4 LYS cc_start: 0.3688 (pttp) cc_final: 0.3013 (mttt) outliers start: 20 outliers final: 9 residues processed: 188 average time/residue: 0.2142 time to fit residues: 58.1891 Evaluate side-chains 170 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain Y residue 319 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 0.0470 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN Y 244 GLN ** Y 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10297 Z= 0.289 Angle : 0.685 9.801 13907 Z= 0.348 Chirality : 0.044 0.202 1587 Planarity : 0.005 0.064 1778 Dihedral : 6.156 102.342 1399 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.22 % Allowed : 12.86 % Favored : 84.92 % 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: -1.17 (0.23), residues: 1261 helix: 0.14 (0.18), residues: 799 sheet: -1.98 (0.55), residues: 79 loop : -2.37 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 98 HIS 0.009 0.001 HIS A 297 PHE 0.023 0.002 PHE E 8 TYR 0.023 0.002 TYR Y 245 ARG 0.005 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 MET cc_start: 0.8113 (ppp) cc_final: 0.7875 (ppp) REVERT: A 531 ASP cc_start: 0.8103 (m-30) cc_final: 0.7713 (p0) REVERT: A 563 MET cc_start: 0.3321 (ppp) cc_final: 0.2692 (mmp) REVERT: A 573 MET cc_start: 0.6632 (ptp) cc_final: 0.6126 (ppp) REVERT: A 584 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7384 (ttp-170) REVERT: A 688 ILE cc_start: 0.8932 (mm) cc_final: 0.8683 (mp) REVERT: A 690 ASP cc_start: 0.8018 (m-30) cc_final: 0.7667 (m-30) REVERT: A 706 GLU cc_start: 0.7236 (pm20) cc_final: 0.6490 (pm20) REVERT: A 763 MET cc_start: 0.7981 (ttt) cc_final: 0.7748 (ttt) REVERT: Y 183 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7975 (mp) REVERT: E 3 ARG cc_start: 0.7452 (ttm170) cc_final: 0.7075 (tmt170) REVERT: E 24 LYS cc_start: 0.8732 (ptpp) cc_final: 0.8454 (mmmt) REVERT: B 4 LYS cc_start: 0.3815 (pttp) cc_final: 0.3123 (mttt) outliers start: 24 outliers final: 16 residues processed: 175 average time/residue: 0.2040 time to fit residues: 51.7831 Evaluate side-chains 165 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 108 optimal weight: 0.0570 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 0.0040 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 238 ASN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN Y 197 GLN Y 308 HIS Y 387 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10297 Z= 0.192 Angle : 0.636 8.187 13907 Z= 0.319 Chirality : 0.043 0.205 1587 Planarity : 0.004 0.064 1778 Dihedral : 5.801 94.624 1399 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.94 % Allowed : 15.36 % Favored : 82.70 % 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 (0.23), residues: 1261 helix: 0.55 (0.19), residues: 796 sheet: -1.70 (0.56), residues: 87 loop : -2.18 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 98 HIS 0.007 0.001 HIS A 297 PHE 0.025 0.002 PHE E 8 TYR 0.016 0.001 TYR A 115 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8081 (m-30) cc_final: 0.7665 (p0) REVERT: A 563 MET cc_start: 0.3426 (ppp) cc_final: 0.2664 (mmp) REVERT: A 573 MET cc_start: 0.7159 (ptp) cc_final: 0.6721 (ppp) REVERT: A 688 ILE cc_start: 0.8934 (mm) cc_final: 0.8650 (mt) REVERT: A 690 ASP cc_start: 0.8042 (m-30) cc_final: 0.7714 (m-30) REVERT: Y 183 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8039 (mp) REVERT: Y 390 ASN cc_start: 0.7217 (m-40) cc_final: 0.6866 (p0) REVERT: Y 417 GLU cc_start: 0.8085 (pt0) cc_final: 0.7733 (mt-10) REVERT: E 3 ARG cc_start: 0.7416 (ttm170) cc_final: 0.6977 (tmt170) REVERT: E 9 LYS cc_start: 0.8298 (mmtt) cc_final: 0.8059 (mmtt) REVERT: E 24 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8433 (mmmt) REVERT: B 4 LYS cc_start: 0.3969 (pttp) cc_final: 0.3226 (mttm) outliers start: 21 outliers final: 14 residues processed: 175 average time/residue: 0.2169 time to fit residues: 55.8749 Evaluate side-chains 168 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 108 optimal weight: 0.0470 chunk 30 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10297 Z= 0.178 Angle : 0.633 11.098 13907 Z= 0.315 Chirality : 0.042 0.240 1587 Planarity : 0.004 0.065 1778 Dihedral : 5.621 90.158 1399 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.85 % Allowed : 15.54 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1261 helix: 0.73 (0.19), residues: 792 sheet: -1.56 (0.57), residues: 79 loop : -1.97 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 165 HIS 0.008 0.001 HIS Y 308 PHE 0.025 0.002 PHE E 8 TYR 0.012 0.001 TYR Y 130 ARG 0.006 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8091 (m-30) cc_final: 0.7680 (p0) REVERT: A 563 MET cc_start: 0.3636 (ppp) cc_final: 0.2787 (mmp) REVERT: A 573 MET cc_start: 0.7187 (ptp) cc_final: 0.6769 (ppp) REVERT: A 584 ARG cc_start: 0.7590 (ptm160) cc_final: 0.6697 (ptt90) REVERT: A 690 ASP cc_start: 0.8040 (m-30) cc_final: 0.7781 (m-30) REVERT: Y 183 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8007 (mp) REVERT: Y 417 GLU cc_start: 0.8063 (pt0) cc_final: 0.7714 (mt-10) REVERT: E 3 ARG cc_start: 0.7358 (ttm170) cc_final: 0.7012 (ttp80) REVERT: E 24 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8524 (mmmt) REVERT: B 4 LYS cc_start: 0.3982 (pttp) cc_final: 0.3216 (mttm) outliers start: 20 outliers final: 14 residues processed: 170 average time/residue: 0.2020 time to fit residues: 50.8250 Evaluate side-chains 161 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 120 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10297 Z= 0.197 Angle : 0.632 11.369 13907 Z= 0.313 Chirality : 0.042 0.200 1587 Planarity : 0.004 0.065 1778 Dihedral : 5.517 88.059 1399 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.04 % Allowed : 16.19 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1261 helix: 0.83 (0.19), residues: 793 sheet: -1.51 (0.57), residues: 79 loop : -1.81 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 165 HIS 0.007 0.001 HIS A 297 PHE 0.028 0.002 PHE E 43 TYR 0.017 0.001 TYR A 115 ARG 0.004 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 HIS cc_start: 0.7590 (m-70) cc_final: 0.6802 (m90) REVERT: A 531 ASP cc_start: 0.8126 (m-30) cc_final: 0.7659 (p0) REVERT: A 563 MET cc_start: 0.3726 (ppp) cc_final: 0.2642 (mmp) REVERT: A 573 MET cc_start: 0.7229 (ptp) cc_final: 0.6773 (ppp) REVERT: A 584 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7001 (ptt90) REVERT: A 688 ILE cc_start: 0.8956 (mm) cc_final: 0.8653 (mt) REVERT: A 690 ASP cc_start: 0.8045 (m-30) cc_final: 0.7723 (m-30) REVERT: Y 183 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8057 (mp) REVERT: E 3 ARG cc_start: 0.7455 (ttm170) cc_final: 0.7036 (ttp80) REVERT: B 4 LYS cc_start: 0.3983 (pttp) cc_final: 0.3237 (mttt) outliers start: 22 outliers final: 16 residues processed: 174 average time/residue: 0.2014 time to fit residues: 51.5083 Evaluate side-chains 169 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 0.0470 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10297 Z= 0.212 Angle : 0.637 11.962 13907 Z= 0.317 Chirality : 0.042 0.185 1587 Planarity : 0.004 0.066 1778 Dihedral : 5.487 85.880 1399 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.22 % Allowed : 16.84 % Favored : 80.94 % 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: -0.11 (0.24), residues: 1261 helix: 0.90 (0.19), residues: 788 sheet: -1.44 (0.59), residues: 79 loop : -1.72 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 165 HIS 0.009 0.001 HIS Y 308 PHE 0.029 0.002 PHE E 43 TYR 0.013 0.001 TYR Y 245 ARG 0.012 0.000 ARG Y 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 513 HIS cc_start: 0.7223 (m-70) cc_final: 0.6642 (m90) REVERT: A 531 ASP cc_start: 0.8116 (m-30) cc_final: 0.7620 (p0) REVERT: A 563 MET cc_start: 0.3770 (ppp) cc_final: 0.2437 (tpt) REVERT: A 573 MET cc_start: 0.7215 (ptp) cc_final: 0.6685 (ppp) REVERT: A 584 ARG cc_start: 0.7441 (ptm160) cc_final: 0.7023 (ptt90) REVERT: A 680 GLU cc_start: 0.7142 (pm20) cc_final: 0.6932 (pp20) REVERT: A 690 ASP cc_start: 0.8026 (m-30) cc_final: 0.7707 (m-30) REVERT: Y 183 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8120 (mp) REVERT: Y 308 HIS cc_start: 0.5253 (OUTLIER) cc_final: 0.4835 (m-70) REVERT: E 3 ARG cc_start: 0.7381 (ttm170) cc_final: 0.6978 (ttp80) REVERT: E 9 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7927 (mmtt) REVERT: E 53 GLN cc_start: 0.7908 (mm110) cc_final: 0.7687 (mm-40) REVERT: B 4 LYS cc_start: 0.3990 (pttp) cc_final: 0.3243 (mttt) outliers start: 24 outliers final: 16 residues processed: 181 average time/residue: 0.2069 time to fit residues: 54.3886 Evaluate side-chains 173 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 109 optimal weight: 0.0010 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN Y 133 ASN Y 308 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10297 Z= 0.203 Angle : 0.646 11.427 13907 Z= 0.318 Chirality : 0.043 0.195 1587 Planarity : 0.004 0.065 1778 Dihedral : 5.393 81.998 1399 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.85 % Allowed : 17.95 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1261 helix: 0.95 (0.19), residues: 783 sheet: -0.94 (0.64), residues: 71 loop : -1.60 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 98 HIS 0.007 0.001 HIS A 297 PHE 0.032 0.002 PHE E 43 TYR 0.013 0.001 TYR Y 130 ARG 0.011 0.000 ARG Y 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8126 (m-30) cc_final: 0.7611 (p0) REVERT: A 563 MET cc_start: 0.3583 (ppp) cc_final: 0.2268 (tpt) REVERT: A 573 MET cc_start: 0.7098 (ptp) cc_final: 0.6553 (ppp) REVERT: A 584 ARG cc_start: 0.7338 (ptm160) cc_final: 0.7007 (ptt90) REVERT: A 690 ASP cc_start: 0.8009 (m-30) cc_final: 0.7690 (m-30) REVERT: Y 72 MET cc_start: 0.5894 (tpp) cc_final: 0.5615 (tpp) REVERT: Y 183 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8120 (mp) REVERT: Y 258 HIS cc_start: 0.6874 (m-70) cc_final: 0.6616 (m170) REVERT: Y 308 HIS cc_start: 0.5720 (OUTLIER) cc_final: 0.5291 (m-70) REVERT: E 3 ARG cc_start: 0.7383 (ttm170) cc_final: 0.6939 (ttp80) REVERT: E 9 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7994 (mmtt) REVERT: E 53 GLN cc_start: 0.7929 (mm110) cc_final: 0.7699 (mm-40) REVERT: B 4 LYS cc_start: 0.4081 (pttp) cc_final: 0.3245 (mttt) outliers start: 20 outliers final: 15 residues processed: 172 average time/residue: 0.2066 time to fit residues: 52.5620 Evaluate side-chains 170 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.0270 chunk 115 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 101 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN Y 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10297 Z= 0.169 Angle : 0.645 12.717 13907 Z= 0.316 Chirality : 0.042 0.177 1587 Planarity : 0.004 0.065 1778 Dihedral : 5.308 78.017 1399 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.67 % Allowed : 18.59 % Favored : 79.74 % 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: 0.10 (0.24), residues: 1261 helix: 0.99 (0.19), residues: 782 sheet: -0.86 (0.65), residues: 70 loop : -1.53 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 98 HIS 0.007 0.001 HIS Y 308 PHE 0.035 0.002 PHE E 43 TYR 0.014 0.001 TYR Y 130 ARG 0.010 0.000 ARG Y 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 HIS cc_start: 0.7576 (m-70) cc_final: 0.7232 (m-70) REVERT: A 531 ASP cc_start: 0.8107 (m-30) cc_final: 0.7595 (p0) REVERT: A 563 MET cc_start: 0.3782 (ppp) cc_final: 0.2296 (tpt) REVERT: A 573 MET cc_start: 0.7138 (ptp) cc_final: 0.6321 (ppp) REVERT: A 690 ASP cc_start: 0.8047 (m-30) cc_final: 0.7742 (m-30) REVERT: Y 72 MET cc_start: 0.5922 (tpp) cc_final: 0.5648 (tpp) REVERT: Y 183 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8107 (mp) REVERT: Y 258 HIS cc_start: 0.6867 (m-70) cc_final: 0.6617 (m170) REVERT: Y 308 HIS cc_start: 0.5538 (OUTLIER) cc_final: 0.5229 (m-70) REVERT: E 3 ARG cc_start: 0.7346 (ttm170) cc_final: 0.6932 (ttp80) REVERT: E 53 GLN cc_start: 0.7911 (mm110) cc_final: 0.7648 (mm-40) REVERT: B 4 LYS cc_start: 0.4060 (pttp) cc_final: 0.3225 (mttt) outliers start: 18 outliers final: 13 residues processed: 169 average time/residue: 0.1960 time to fit residues: 48.8224 Evaluate side-chains 165 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain Y residue 319 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.0030 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 0.0060 chunk 78 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN Y 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10297 Z= 0.172 Angle : 0.654 11.783 13907 Z= 0.319 Chirality : 0.042 0.164 1587 Planarity : 0.004 0.065 1778 Dihedral : 5.181 73.045 1399 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.11 % Allowed : 18.87 % Favored : 80.02 % 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: 0.13 (0.24), residues: 1261 helix: 1.05 (0.19), residues: 782 sheet: -1.26 (0.59), residues: 79 loop : -1.50 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 98 HIS 0.006 0.001 HIS A 297 PHE 0.037 0.001 PHE E 43 TYR 0.016 0.001 TYR Y 130 ARG 0.010 0.000 ARG Y 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.8095 (m-30) cc_final: 0.7569 (p0) REVERT: A 563 MET cc_start: 0.3813 (ppp) cc_final: 0.2256 (tpt) REVERT: A 573 MET cc_start: 0.7055 (ptp) cc_final: 0.6189 (ppp) REVERT: A 690 ASP cc_start: 0.8034 (m-30) cc_final: 0.7737 (m-30) REVERT: Y 72 MET cc_start: 0.5927 (tpp) cc_final: 0.5635 (tpp) REVERT: Y 104 MET cc_start: 0.7793 (mmm) cc_final: 0.7564 (mmm) REVERT: Y 183 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8123 (mp) REVERT: Y 258 HIS cc_start: 0.6750 (m-70) cc_final: 0.6509 (m170) REVERT: Y 308 HIS cc_start: 0.5602 (OUTLIER) cc_final: 0.5216 (m-70) REVERT: E 3 ARG cc_start: 0.7365 (ttm170) cc_final: 0.6981 (ttp80) REVERT: E 53 GLN cc_start: 0.7950 (mm110) cc_final: 0.7678 (mm-40) REVERT: B 4 LYS cc_start: 0.4054 (pttp) cc_final: 0.3241 (mttt) outliers start: 12 outliers final: 10 residues processed: 169 average time/residue: 0.1925 time to fit residues: 48.3043 Evaluate side-chains 162 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain Y residue 113 THR Chi-restraints excluded: chain Y residue 183 ILE Chi-restraints excluded: chain Y residue 308 HIS Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.196338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142863 restraints weight = 12480.878| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.52 r_work: 0.3606 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10297 Z= 0.197 Angle : 0.662 11.904 13907 Z= 0.323 Chirality : 0.043 0.192 1587 Planarity : 0.004 0.065 1778 Dihedral : 5.160 71.360 1399 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.20 % Allowed : 19.24 % Favored : 79.56 % 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: 0.12 (0.24), residues: 1261 helix: 1.00 (0.19), residues: 787 sheet: -0.95 (0.63), residues: 70 loop : -1.52 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 98 HIS 0.010 0.001 HIS Y 308 PHE 0.036 0.002 PHE E 43 TYR 0.015 0.001 TYR Y 130 ARG 0.014 0.000 ARG Y 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.80 seconds wall clock time: 48 minutes 4.98 seconds (2884.98 seconds total)