Starting phenix.real_space_refine on Fri Mar 15 02:34:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/03_2024/6qwl_4660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/03_2024/6qwl_4660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/03_2024/6qwl_4660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/03_2024/6qwl_4660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/03_2024/6qwl_4660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/03_2024/6qwl_4660.pdb" } resolution = 4.1 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= 1.000 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: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 74 5.16 5 C 6498 2.51 5 N 1787 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 260": "OE1" <-> "OE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 549": "NH1" <-> "NH2" Residue "E ARG 574": "NH1" <-> "NH2" Residue "E GLU 585": "OE1" <-> "OE2" Residue "E TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 657": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K ASP 169": "OD1" <-> "OD2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "K GLU 256": "OE1" <-> "OE2" Residue "K GLU 311": "OE1" <-> "OE2" Residue "K ASP 438": "OD1" <-> "OD2" Residue "K PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 460": "OE1" <-> "OE2" Residue "K ASP 521": "OD1" <-> "OD2" Residue "Q ASP 65": "OD1" <-> "OD2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 179": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10408 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4084 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain: "K" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4206 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 514} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1565 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "T" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 4, 'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 7} Chain: "W" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 11} Time building chain proxies: 6.15, per 1000 atoms: 0.59 Number of scatterers: 10408 At special positions: 0 Unit cell: (99.36, 104.76, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 26 15.00 O 2023 8.00 N 1787 7.00 C 6498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 1.9 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 50.2% alpha, 7.8% beta 6 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 222 through 232 Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.846A pdb=" N ASP E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 3.584A pdb=" N ILE E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 removed outlier: 4.179A pdb=" N GLU E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 317 Processing helix chain 'E' and resid 332 through 345 removed outlier: 3.900A pdb=" N LEU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS E 338 " --> pdb=" O ASN E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.627A pdb=" N LYS E 363 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.809A pdb=" N VAL E 379 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 410 Processing helix chain 'E' and resid 429 through 447 removed outlier: 3.511A pdb=" N ASN E 447 " --> pdb=" O VAL E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 472 Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.513A pdb=" N TRP E 533 " --> pdb=" O SER E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 572 removed outlier: 3.509A pdb=" N GLU E 572 " --> pdb=" O LYS E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 596 removed outlier: 3.636A pdb=" N GLN E 579 " --> pdb=" O ARG E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 605 removed outlier: 3.702A pdb=" N LYS E 605 " --> pdb=" O LYS E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 646 removed outlier: 3.581A pdb=" N TYR E 644 " --> pdb=" O CYS E 640 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 646 " --> pdb=" O MET E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 670 removed outlier: 3.734A pdb=" N GLU E 652 " --> pdb=" O ASN E 648 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG E 660 " --> pdb=" O ALA E 656 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU E 661 " --> pdb=" O GLU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 688 Processing helix chain 'E' and resid 693 through 714 removed outlier: 3.513A pdb=" N ILE E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 11 removed outlier: 3.839A pdb=" N LEU K 8 " --> pdb=" O PRO K 5 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 17 Processing helix chain 'K' and resid 37 through 48 Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 85 through 98 Processing helix chain 'K' and resid 101 through 116 removed outlier: 3.743A pdb=" N MET K 115 " --> pdb=" O MET K 111 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 123 removed outlier: 3.973A pdb=" N LEU K 122 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR K 123 " --> pdb=" O ASP K 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 119 through 123' Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 152 through 154 No H-bonds generated for 'chain 'K' and resid 152 through 154' Processing helix chain 'K' and resid 162 through 172 removed outlier: 3.851A pdb=" N PHE K 166 " --> pdb=" O GLY K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 176 Processing helix chain 'K' and resid 214 through 223 removed outlier: 3.922A pdb=" N ALA K 221 " --> pdb=" O TYR K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 264 removed outlier: 4.462A pdb=" N GLY K 250 " --> pdb=" O ILE K 246 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE K 251 " --> pdb=" O GLN K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 326 removed outlier: 3.751A pdb=" N PHE K 318 " --> pdb=" O ASN K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 329 No H-bonds generated for 'chain 'K' and resid 327 through 329' Processing helix chain 'K' and resid 330 through 338 removed outlier: 3.535A pdb=" N ARG K 334 " --> pdb=" O PRO K 330 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER K 338 " --> pdb=" O ARG K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 344 Processing helix chain 'K' and resid 377 through 381 removed outlier: 4.068A pdb=" N TYR K 381 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 393 removed outlier: 3.636A pdb=" N ARG K 386 " --> pdb=" O ASN K 382 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 396 No H-bonds generated for 'chain 'K' and resid 394 through 396' Processing helix chain 'K' and resid 413 through 426 Processing helix chain 'K' and resid 454 through 471 Processing helix chain 'K' and resid 518 through 537 removed outlier: 4.165A pdb=" N ASN K 536 " --> pdb=" O ASN K 532 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY K 537 " --> pdb=" O MET K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 558 removed outlier: 3.680A pdb=" N GLN K 548 " --> pdb=" O GLN K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 571 through 582 removed outlier: 3.825A pdb=" N ILE K 575 " --> pdb=" O ARG K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 589 through 593 Processing helix chain 'K' and resid 607 through 612 Processing helix chain 'K' and resid 616 through 624 Processing helix chain 'Q' and resid 64 through 69 removed outlier: 3.941A pdb=" N ARG Q 69 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 105 removed outlier: 4.079A pdb=" N ASN Q 102 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY Q 105 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.133A pdb=" N TYR Q 117 " --> pdb=" O PHE Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 129 Processing helix chain 'Q' and resid 157 through 170 Processing helix chain 'Q' and resid 178 through 193 removed outlier: 5.077A pdb=" N GLU Q 186 " --> pdb=" O TRP Q 182 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU Q 187 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 198 removed outlier: 4.225A pdb=" N GLY Q 197 " --> pdb=" O LYS Q 194 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR Q 198 " --> pdb=" O LEU Q 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 194 through 198' Processing helix chain 'Q' and resid 201 through 214 removed outlier: 3.594A pdb=" N VAL Q 214 " --> pdb=" O GLU Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 233 Processing helix chain 'Q' and resid 233 through 238 Processing sheet with id=AA1, first strand: chain 'E' and resid 373 through 374 removed outlier: 6.659A pdb=" N GLN E 373 " --> pdb=" O LYS K 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 480 through 486 removed outlier: 4.799A pdb=" N ILE E 481 " --> pdb=" O TYR E 497 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN E 483 " --> pdb=" O MET E 495 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET E 495 " --> pdb=" O ASN E 483 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 499 " --> pdb=" O PHE E 519 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 521 through 522 removed outlier: 3.923A pdb=" N TYR E 554 " --> pdb=" O SER E 522 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR E 537 " --> pdb=" O CYS E 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 521 through 522 removed outlier: 3.923A pdb=" N TYR E 554 " --> pdb=" O SER E 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 623 through 627 removed outlier: 3.859A pdb=" N GLY E 618 " --> pdb=" O VAL E 625 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY E 627 " --> pdb=" O SER E 616 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER E 616 " --> pdb=" O GLY E 627 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN K 2 " --> pdb=" O THR E 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'K' and resid 128 through 129 Processing sheet with id=AA8, first strand: chain 'K' and resid 178 through 181 Processing sheet with id=AA9, first strand: chain 'K' and resid 435 through 437 removed outlier: 3.721A pdb=" N MET K 300 " --> pdb=" O VAL K 450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 348 through 350 Processing sheet with id=AB2, first strand: chain 'Q' and resid 73 through 74 Processing sheet with id=AB3, first strand: chain 'Q' and resid 131 through 135 removed outlier: 5.691A pdb=" N ILE Q 245 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 143 through 148 removed outlier: 3.845A pdb=" N ARG Q 218 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2799 1.33 - 1.46: 2522 1.46 - 1.58: 5173 1.58 - 1.70: 50 1.70 - 1.83: 124 Bond restraints: 10668 Sorted by residual: bond pdb=" CB TRP E 340 " pdb=" CG TRP E 340 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.09e+00 bond pdb=" CA ILE E 479 " pdb=" C ILE E 479 " ideal model delta sigma weight residual 1.525 1.506 0.019 8.80e-03 1.29e+04 4.60e+00 bond pdb=" CG MET E 407 " pdb=" SD MET E 407 " ideal model delta sigma weight residual 1.803 1.751 0.052 2.50e-02 1.60e+03 4.33e+00 bond pdb=" CB ASN E 560 " pdb=" CG ASN E 560 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.09e+00 bond pdb=" C ILE E 479 " pdb=" N PRO E 480 " ideal model delta sigma weight residual 1.333 1.312 0.021 1.17e-02 7.31e+03 3.27e+00 ... (remaining 10663 not shown) Histogram of bond angle deviations from ideal: 96.95 - 104.44: 300 104.44 - 111.92: 4875 111.92 - 119.41: 4086 119.41 - 126.90: 5068 126.90 - 134.38: 194 Bond angle restraints: 14523 Sorted by residual: angle pdb=" N ILE E 347 " pdb=" CA ILE E 347 " pdb=" C ILE E 347 " ideal model delta sigma weight residual 112.12 107.85 4.27 8.40e-01 1.42e+00 2.58e+01 angle pdb=" N LYS K 393 " pdb=" CA LYS K 393 " pdb=" C LYS K 393 " ideal model delta sigma weight residual 109.81 119.35 -9.54 2.21e+00 2.05e-01 1.86e+01 angle pdb=" C3' G T 2 " pdb=" O3' G T 2 " pdb=" P C T 3 " ideal model delta sigma weight residual 120.20 126.48 -6.28 1.50e+00 4.44e-01 1.75e+01 angle pdb=" N GLY E 367 " pdb=" CA GLY E 367 " pdb=" C GLY E 367 " ideal model delta sigma weight residual 113.18 122.07 -8.89 2.37e+00 1.78e-01 1.41e+01 angle pdb=" C ASN K 153 " pdb=" N ASP K 154 " pdb=" CA ASP K 154 " ideal model delta sigma weight residual 122.08 127.43 -5.35 1.47e+00 4.63e-01 1.32e+01 ... (remaining 14518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 6302 35.58 - 71.16: 183 71.16 - 106.74: 16 106.74 - 142.32: 1 142.32 - 177.90: 1 Dihedral angle restraints: 6503 sinusoidal: 2917 harmonic: 3586 Sorted by residual: dihedral pdb=" O4' U T 6 " pdb=" C1' U T 6 " pdb=" N1 U T 6 " pdb=" C2 U T 6 " ideal model delta sinusoidal sigma weight residual -128.00 49.90 -177.90 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLU K 399 " pdb=" C GLU K 399 " pdb=" N GLY K 400 " pdb=" CA GLY K 400 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA THR E 366 " pdb=" C THR E 366 " pdb=" N GLY E 367 " pdb=" CA GLY E 367 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 6500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1098 0.056 - 0.112: 404 0.112 - 0.168: 94 0.168 - 0.224: 27 0.224 - 0.280: 2 Chirality restraints: 1625 Sorted by residual: chirality pdb=" CB VAL K 116 " pdb=" CA VAL K 116 " pdb=" CG1 VAL K 116 " pdb=" CG2 VAL K 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB THR K 401 " pdb=" CA THR K 401 " pdb=" OG1 THR K 401 " pdb=" CG2 THR K 401 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU Q 79 " pdb=" CB LEU Q 79 " pdb=" CD1 LEU Q 79 " pdb=" CD2 LEU Q 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1622 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE Q 70 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO Q 71 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO Q 71 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 71 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 605 " -0.048 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO K 606 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO K 606 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 606 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 405 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO K 406 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO K 406 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO K 406 " 0.040 5.00e-02 4.00e+02 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1704 2.75 - 3.29: 10241 3.29 - 3.83: 18346 3.83 - 4.36: 19733 4.36 - 4.90: 32328 Nonbonded interactions: 82352 Sorted by model distance: nonbonded pdb=" O ASP K 553 " pdb=" OG1 THR K 557 " model vdw 2.214 2.440 nonbonded pdb=" O LEU K 114 " pdb=" OG1 THR K 117 " model vdw 2.244 2.440 nonbonded pdb=" O SER E 215 " pdb=" OG SER E 215 " model vdw 2.251 2.440 nonbonded pdb=" O ALA E 362 " pdb=" OG1 THR E 366 " model vdw 2.257 2.440 nonbonded pdb=" OG SER E 328 " pdb=" OE1 GLU E 329 " model vdw 2.269 2.440 ... (remaining 82347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.220 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 34.020 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.008 0.077 10668 Z= 0.493 Angle : 1.013 9.537 14523 Z= 0.547 Chirality : 0.062 0.280 1625 Planarity : 0.008 0.075 1767 Dihedral : 17.049 177.903 4191 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.85 % Favored : 89.07 % Rotamer: Outliers : 0.93 % Allowed : 12.05 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.18), residues: 1226 helix: -2.72 (0.16), residues: 530 sheet: -3.72 (0.51), residues: 73 loop : -3.44 (0.20), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 364 HIS 0.016 0.002 HIS K 99 PHE 0.035 0.003 PHE E 604 TYR 0.029 0.003 TYR K 554 ARG 0.007 0.001 ARG K 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.7373 (tpp) cc_final: 0.7093 (tpp) REVERT: E 271 ASN cc_start: 0.8572 (t0) cc_final: 0.8185 (t0) REVERT: E 473 MET cc_start: 0.5168 (ttm) cc_final: 0.4880 (ttt) REVERT: E 477 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8172 (ptpp) REVERT: E 483 ASN cc_start: 0.8372 (t0) cc_final: 0.8082 (t0) REVERT: E 584 MET cc_start: 0.8118 (ttp) cc_final: 0.7561 (tmm) REVERT: E 599 MET cc_start: 0.4518 (mmt) cc_final: 0.3800 (mpp) REVERT: E 659 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8147 (ttm110) REVERT: K 65 MET cc_start: 0.8627 (mtt) cc_final: 0.8235 (mtm) REVERT: K 111 MET cc_start: 0.8449 (mtm) cc_final: 0.7766 (mtp) REVERT: K 114 LEU cc_start: 0.8625 (tp) cc_final: 0.8328 (tp) REVERT: K 163 LEU cc_start: 0.8817 (tt) cc_final: 0.8383 (tp) REVERT: K 174 LEU cc_start: 0.8699 (pt) cc_final: 0.8393 (pt) REVERT: K 217 TYR cc_start: 0.7725 (t80) cc_final: 0.7292 (t80) REVERT: K 300 MET cc_start: 0.7350 (mtm) cc_final: 0.6749 (mtm) REVERT: K 331 ILE cc_start: 0.8242 (mp) cc_final: 0.8036 (tp) REVERT: K 412 MET cc_start: 0.7646 (ptp) cc_final: 0.7430 (ptt) REVERT: K 459 MET cc_start: 0.8121 (mmt) cc_final: 0.7652 (mmt) REVERT: K 538 MET cc_start: 0.7336 (ttm) cc_final: 0.6566 (ttm) REVERT: Q 166 MET cc_start: 0.4454 (mtt) cc_final: 0.3921 (mmt) REVERT: Q 233 MET cc_start: 0.5615 (mmm) cc_final: 0.5024 (mmm) outliers start: 10 outliers final: 2 residues processed: 179 average time/residue: 0.2405 time to fit residues: 59.3729 Evaluate side-chains 116 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.0570 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 349 ASN ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN E 643 HIS ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 261 ASN ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 544 GLN ** K 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 HIS Q 235 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10668 Z= 0.167 Angle : 0.622 7.816 14523 Z= 0.324 Chirality : 0.043 0.203 1625 Planarity : 0.005 0.064 1767 Dihedral : 14.906 176.756 1738 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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: -3.33 (0.21), residues: 1226 helix: -1.14 (0.20), residues: 544 sheet: -3.58 (0.48), residues: 82 loop : -3.09 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 533 HIS 0.005 0.001 HIS E 643 PHE 0.023 0.001 PHE E 604 TYR 0.016 0.001 TYR E 497 ARG 0.005 0.000 ARG Q 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.7430 (tpp) cc_final: 0.7107 (tpp) REVERT: E 271 ASN cc_start: 0.8637 (t0) cc_final: 0.8236 (t0) REVERT: E 285 MET cc_start: 0.8189 (mtt) cc_final: 0.7985 (ttm) REVERT: E 473 MET cc_start: 0.5188 (ttm) cc_final: 0.4447 (ttp) REVERT: E 483 ASN cc_start: 0.8312 (t0) cc_final: 0.8108 (t0) REVERT: E 544 LEU cc_start: 0.8620 (mt) cc_final: 0.8409 (tp) REVERT: E 584 MET cc_start: 0.8179 (ttp) cc_final: 0.7562 (tmm) REVERT: E 659 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8096 (ttm110) REVERT: K 111 MET cc_start: 0.8443 (mtm) cc_final: 0.7732 (mtp) REVERT: K 217 TYR cc_start: 0.7681 (t80) cc_final: 0.7288 (t80) REVERT: K 300 MET cc_start: 0.6257 (mtm) cc_final: 0.5395 (mtm) REVERT: K 392 LEU cc_start: 0.7694 (tp) cc_final: 0.7317 (tt) REVERT: K 459 MET cc_start: 0.7981 (mmt) cc_final: 0.7398 (mmt) REVERT: K 602 ASN cc_start: 0.7621 (m110) cc_final: 0.7121 (m110) REVERT: Q 166 MET cc_start: 0.4317 (mtt) cc_final: 0.3715 (mmt) REVERT: Q 217 ARG cc_start: 0.7650 (mtt-85) cc_final: 0.7161 (mtp85) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2283 time to fit residues: 51.7014 Evaluate side-chains 126 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 101 optimal weight: 0.0870 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.0270 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 ASN E 467 ASN E 595 GLN E 648 ASN E 693 ASN ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10668 Z= 0.148 Angle : 0.569 8.554 14523 Z= 0.292 Chirality : 0.041 0.167 1625 Planarity : 0.004 0.055 1767 Dihedral : 14.505 177.213 1738 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.28 % Allowed : 4.26 % Favored : 95.46 % 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: -2.47 (0.23), residues: 1226 helix: -0.24 (0.22), residues: 544 sheet: -3.27 (0.47), residues: 91 loop : -2.79 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 533 HIS 0.005 0.001 HIS Q 184 PHE 0.022 0.001 PHE E 604 TYR 0.011 0.001 TYR K 556 ARG 0.002 0.000 ARG E 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 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: 3 poor density : 170 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 271 ASN cc_start: 0.8697 (t0) cc_final: 0.8270 (t0) REVERT: E 473 MET cc_start: 0.5088 (ttm) cc_final: 0.4387 (ttp) REVERT: E 477 LYS cc_start: 0.8210 (ptpp) cc_final: 0.7988 (ptpp) REVERT: E 483 ASN cc_start: 0.8298 (t0) cc_final: 0.8068 (t0) REVERT: E 581 MET cc_start: 0.8098 (ttm) cc_final: 0.7532 (tpp) REVERT: E 659 ARG cc_start: 0.8432 (ttm110) cc_final: 0.8077 (ttm110) REVERT: K 111 MET cc_start: 0.8424 (mtm) cc_final: 0.7872 (mtp) REVERT: K 217 TYR cc_start: 0.7710 (t80) cc_final: 0.7420 (t80) REVERT: K 247 GLN cc_start: 0.8704 (mp10) cc_final: 0.8501 (mm-40) REVERT: K 300 MET cc_start: 0.6273 (mtp) cc_final: 0.5959 (mtp) REVERT: K 392 LEU cc_start: 0.7634 (tp) cc_final: 0.7142 (tt) REVERT: K 415 MET cc_start: 0.7588 (mmt) cc_final: 0.7040 (mmt) REVERT: K 459 MET cc_start: 0.7949 (mmt) cc_final: 0.7458 (mmt) REVERT: K 602 ASN cc_start: 0.7553 (m110) cc_final: 0.7058 (m110) REVERT: Q 166 MET cc_start: 0.4109 (mtt) cc_final: 0.3519 (mmt) REVERT: Q 217 ARG cc_start: 0.7653 (mtt-85) cc_final: 0.7410 (mtp85) outliers start: 3 outliers final: 0 residues processed: 173 average time/residue: 0.2171 time to fit residues: 53.8684 Evaluate side-chains 131 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN E 467 ASN ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 ASN E 666 GLN E 693 ASN ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 310 ASN K 561 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10668 Z= 0.166 Angle : 0.575 9.528 14523 Z= 0.298 Chirality : 0.041 0.165 1625 Planarity : 0.004 0.051 1767 Dihedral : 14.415 177.595 1738 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.19 % Allowed : 3.43 % Favored : 96.39 % 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: -2.07 (0.23), residues: 1226 helix: 0.09 (0.22), residues: 545 sheet: -3.39 (0.50), residues: 81 loop : -2.54 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 533 HIS 0.003 0.001 HIS Q 184 PHE 0.025 0.001 PHE E 604 TYR 0.018 0.001 TYR E 644 ARG 0.004 0.000 ARG Q 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 473 MET cc_start: 0.5050 (ttm) cc_final: 0.4331 (ttp) REVERT: E 477 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7867 (ptpp) REVERT: E 483 ASN cc_start: 0.8386 (t0) cc_final: 0.8159 (t0) REVERT: E 582 GLN cc_start: 0.8183 (pt0) cc_final: 0.7903 (pt0) REVERT: E 659 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8102 (ttm110) REVERT: K 65 MET cc_start: 0.8238 (mtt) cc_final: 0.7944 (mtt) REVERT: K 111 MET cc_start: 0.8349 (mtm) cc_final: 0.7797 (mtp) REVERT: K 217 TYR cc_start: 0.7664 (t80) cc_final: 0.7441 (t80) REVERT: K 300 MET cc_start: 0.6415 (mtp) cc_final: 0.6020 (mtp) REVERT: K 415 MET cc_start: 0.7581 (mmt) cc_final: 0.7104 (mmt) REVERT: K 459 MET cc_start: 0.7932 (mmt) cc_final: 0.7453 (mmt) REVERT: K 526 MET cc_start: 0.7944 (tpp) cc_final: 0.7651 (tpp) REVERT: K 602 ASN cc_start: 0.7662 (m110) cc_final: 0.7185 (m110) REVERT: Q 166 MET cc_start: 0.4038 (mtt) cc_final: 0.3450 (mmt) REVERT: Q 217 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7158 (mtp85) outliers start: 2 outliers final: 1 residues processed: 166 average time/residue: 0.2162 time to fit residues: 51.3322 Evaluate side-chains 131 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 HIS ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 663 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10668 Z= 0.179 Angle : 0.588 8.848 14523 Z= 0.303 Chirality : 0.042 0.220 1625 Planarity : 0.004 0.051 1767 Dihedral : 14.289 177.815 1738 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: -1.89 (0.24), residues: 1226 helix: 0.28 (0.23), residues: 539 sheet: -3.31 (0.51), residues: 83 loop : -2.45 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 533 HIS 0.005 0.001 HIS K 99 PHE 0.024 0.001 PHE E 604 TYR 0.019 0.001 TYR E 361 ARG 0.002 0.000 ARG Q 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 326 MET cc_start: 0.6699 (tmm) cc_final: 0.6435 (tmm) REVERT: E 473 MET cc_start: 0.5131 (ttm) cc_final: 0.4363 (ttp) REVERT: E 582 GLN cc_start: 0.8148 (pt0) cc_final: 0.7914 (pt0) REVERT: E 659 ARG cc_start: 0.8433 (ttm110) cc_final: 0.8016 (mtp180) REVERT: K 111 MET cc_start: 0.8320 (mtm) cc_final: 0.7785 (mtp) REVERT: K 217 TYR cc_start: 0.7677 (t80) cc_final: 0.7416 (t80) REVERT: K 247 GLN cc_start: 0.8722 (mp10) cc_final: 0.8447 (mm-40) REVERT: K 300 MET cc_start: 0.6249 (mtp) cc_final: 0.5847 (mtp) REVERT: K 415 MET cc_start: 0.7566 (mmt) cc_final: 0.7068 (mmt) REVERT: K 459 MET cc_start: 0.7858 (mmt) cc_final: 0.7347 (mmt) REVERT: K 556 TYR cc_start: 0.8230 (t80) cc_final: 0.7901 (t80) REVERT: K 602 ASN cc_start: 0.7831 (m110) cc_final: 0.7348 (m110) REVERT: Q 163 ASN cc_start: 0.7352 (t0) cc_final: 0.6848 (t0) REVERT: Q 166 MET cc_start: 0.3785 (mtt) cc_final: 0.3269 (mmt) REVERT: Q 218 ARG cc_start: 0.9060 (tpp-160) cc_final: 0.8843 (tpp80) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2121 time to fit residues: 47.8504 Evaluate side-chains 128 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10668 Z= 0.223 Angle : 0.613 9.770 14523 Z= 0.317 Chirality : 0.043 0.171 1625 Planarity : 0.004 0.049 1767 Dihedral : 14.270 177.762 1738 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: -1.86 (0.24), residues: 1226 helix: 0.30 (0.23), residues: 539 sheet: -3.41 (0.50), residues: 82 loop : -2.43 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 364 HIS 0.004 0.001 HIS E 506 PHE 0.024 0.002 PHE E 604 TYR 0.017 0.002 TYR E 361 ARG 0.002 0.000 ARG E 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 271 ASN cc_start: 0.8701 (t0) cc_final: 0.8354 (t0) REVERT: E 386 MET cc_start: 0.6464 (tpt) cc_final: 0.6232 (mmm) REVERT: E 483 ASN cc_start: 0.8271 (t0) cc_final: 0.7989 (t0) REVERT: E 581 MET cc_start: 0.8569 (tpt) cc_final: 0.8227 (tpp) REVERT: E 659 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8038 (mtp180) REVERT: K 217 TYR cc_start: 0.7638 (t80) cc_final: 0.7328 (t80) REVERT: K 247 GLN cc_start: 0.8784 (mp10) cc_final: 0.8480 (mm-40) REVERT: K 300 MET cc_start: 0.6230 (mtp) cc_final: 0.5774 (mtp) REVERT: K 415 MET cc_start: 0.7606 (mmt) cc_final: 0.7193 (mmt) REVERT: K 459 MET cc_start: 0.7808 (mmt) cc_final: 0.7262 (mmt) REVERT: K 556 TYR cc_start: 0.8285 (t80) cc_final: 0.7942 (t80) REVERT: K 572 MET cc_start: 0.8203 (mmm) cc_final: 0.7588 (tpp) REVERT: K 602 ASN cc_start: 0.7807 (m110) cc_final: 0.7425 (m110) REVERT: Q 163 ASN cc_start: 0.7774 (t0) cc_final: 0.7317 (t0) REVERT: Q 166 MET cc_start: 0.3720 (mtt) cc_final: 0.3200 (mmt) REVERT: Q 218 ARG cc_start: 0.9082 (tpp-160) cc_final: 0.8785 (tpp80) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2208 time to fit residues: 49.2956 Evaluate side-chains 129 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 HIS E 648 ASN E 693 ASN ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 247 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10668 Z= 0.250 Angle : 0.638 8.710 14523 Z= 0.328 Chirality : 0.044 0.200 1625 Planarity : 0.004 0.051 1767 Dihedral : 14.305 177.453 1738 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % 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: -1.95 (0.24), residues: 1226 helix: 0.20 (0.23), residues: 545 sheet: -3.43 (0.47), residues: 93 loop : -2.45 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 131 HIS 0.004 0.001 HIS Q 235 PHE 0.023 0.002 PHE E 604 TYR 0.018 0.002 TYR E 229 ARG 0.002 0.000 ARG E 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 477 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8202 (ptpp) REVERT: E 581 MET cc_start: 0.8525 (tpt) cc_final: 0.8210 (tpp) REVERT: E 659 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8166 (ttm110) REVERT: K 111 MET cc_start: 0.8114 (mtm) cc_final: 0.7808 (ptp) REVERT: K 217 TYR cc_start: 0.7531 (t80) cc_final: 0.7145 (t80) REVERT: K 247 GLN cc_start: 0.8818 (mp10) cc_final: 0.8483 (mm-40) REVERT: K 300 MET cc_start: 0.6263 (mtp) cc_final: 0.5794 (mtp) REVERT: K 415 MET cc_start: 0.7574 (mmt) cc_final: 0.7230 (mmt) REVERT: K 459 MET cc_start: 0.7859 (mmt) cc_final: 0.7347 (mmt) REVERT: K 556 TYR cc_start: 0.8340 (t80) cc_final: 0.7978 (t80) REVERT: K 572 MET cc_start: 0.8250 (mmm) cc_final: 0.7740 (tpp) REVERT: Q 163 ASN cc_start: 0.7672 (t0) cc_final: 0.7170 (t0) REVERT: Q 166 MET cc_start: 0.3546 (mtt) cc_final: 0.3050 (mmt) REVERT: Q 211 ARG cc_start: 0.7121 (tpt90) cc_final: 0.6783 (tpm170) REVERT: Q 217 ARG cc_start: 0.6890 (mtp85) cc_final: 0.6664 (mtp85) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.2272 time to fit residues: 48.8288 Evaluate side-chains 125 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 105 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10668 Z= 0.168 Angle : 0.593 8.974 14523 Z= 0.302 Chirality : 0.042 0.182 1625 Planarity : 0.004 0.050 1767 Dihedral : 14.207 176.919 1738 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -1.70 (0.24), residues: 1226 helix: 0.42 (0.23), residues: 548 sheet: -3.29 (0.49), residues: 91 loop : -2.34 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 131 HIS 0.004 0.001 HIS E 506 PHE 0.022 0.001 PHE E 604 TYR 0.014 0.001 TYR E 361 ARG 0.003 0.000 ARG K 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 326 MET cc_start: 0.6357 (tmm) cc_final: 0.6046 (tmm) REVERT: E 483 ASN cc_start: 0.8270 (t0) cc_final: 0.7920 (t0) REVERT: E 581 MET cc_start: 0.8428 (tpt) cc_final: 0.8205 (tpp) REVERT: E 659 ARG cc_start: 0.8467 (ttm110) cc_final: 0.8039 (mtp180) REVERT: K 217 TYR cc_start: 0.7577 (t80) cc_final: 0.7233 (t80) REVERT: K 247 GLN cc_start: 0.8767 (mp10) cc_final: 0.8431 (mm-40) REVERT: K 300 MET cc_start: 0.6340 (mtp) cc_final: 0.6046 (mtp) REVERT: K 309 TRP cc_start: 0.8226 (t-100) cc_final: 0.7932 (t-100) REVERT: K 310 ASN cc_start: 0.8470 (m110) cc_final: 0.8167 (p0) REVERT: K 415 MET cc_start: 0.7622 (mmt) cc_final: 0.7147 (mmt) REVERT: K 459 MET cc_start: 0.7857 (mmt) cc_final: 0.7589 (mmp) REVERT: K 556 TYR cc_start: 0.8264 (t80) cc_final: 0.8002 (t80) REVERT: K 572 MET cc_start: 0.8195 (mmm) cc_final: 0.7598 (tpp) REVERT: K 602 ASN cc_start: 0.7678 (m110) cc_final: 0.7392 (m110) REVERT: Q 163 ASN cc_start: 0.7649 (t0) cc_final: 0.7174 (t0) REVERT: Q 166 MET cc_start: 0.3574 (mtt) cc_final: 0.3279 (mmt) REVERT: Q 208 MET cc_start: 0.3218 (tpt) cc_final: 0.2730 (tpt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2150 time to fit residues: 50.4463 Evaluate side-chains 132 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 0.1980 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 ASN E 693 ASN ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10668 Z= 0.185 Angle : 0.597 8.577 14523 Z= 0.305 Chirality : 0.042 0.183 1625 Planarity : 0.004 0.051 1767 Dihedral : 14.157 176.916 1738 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.35 % 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: -1.68 (0.24), residues: 1226 helix: 0.45 (0.23), residues: 549 sheet: -3.20 (0.49), residues: 91 loop : -2.36 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 131 HIS 0.003 0.001 HIS E 643 PHE 0.023 0.001 PHE E 604 TYR 0.022 0.002 TYR K 482 ARG 0.003 0.000 ARG Q 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 483 ASN cc_start: 0.8286 (t0) cc_final: 0.7916 (t0) REVERT: E 581 MET cc_start: 0.8426 (tpt) cc_final: 0.8159 (tpp) REVERT: E 659 ARG cc_start: 0.8478 (ttm110) cc_final: 0.8042 (mtp180) REVERT: K 217 TYR cc_start: 0.7576 (t80) cc_final: 0.7233 (t80) REVERT: K 247 GLN cc_start: 0.8779 (mp10) cc_final: 0.8440 (mm-40) REVERT: K 300 MET cc_start: 0.6586 (mtp) cc_final: 0.6341 (mtp) REVERT: K 309 TRP cc_start: 0.8229 (t-100) cc_final: 0.7959 (t-100) REVERT: K 310 ASN cc_start: 0.8484 (m110) cc_final: 0.8159 (p0) REVERT: K 415 MET cc_start: 0.7630 (mmt) cc_final: 0.7199 (mmt) REVERT: K 459 MET cc_start: 0.7845 (mmt) cc_final: 0.7626 (mmp) REVERT: K 556 TYR cc_start: 0.8280 (t80) cc_final: 0.8017 (t80) REVERT: K 572 MET cc_start: 0.8209 (mmm) cc_final: 0.7608 (tpp) REVERT: K 602 ASN cc_start: 0.7779 (m110) cc_final: 0.7470 (m110) REVERT: Q 163 ASN cc_start: 0.7686 (t0) cc_final: 0.7277 (t0) REVERT: Q 166 MET cc_start: 0.3639 (mtt) cc_final: 0.3071 (mmt) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2215 time to fit residues: 50.0724 Evaluate side-chains 130 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 105 optimal weight: 10.0000 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 693 ASN ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10668 Z= 0.154 Angle : 0.607 9.848 14523 Z= 0.305 Chirality : 0.042 0.182 1625 Planarity : 0.004 0.051 1767 Dihedral : 14.119 176.857 1738 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -1.57 (0.24), residues: 1226 helix: 0.57 (0.23), residues: 543 sheet: -3.19 (0.52), residues: 83 loop : -2.32 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 131 HIS 0.004 0.001 HIS E 506 PHE 0.022 0.001 PHE E 604 TYR 0.022 0.001 TYR K 482 ARG 0.003 0.000 ARG Q 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 326 MET cc_start: 0.6331 (tmm) cc_final: 0.6106 (tmm) REVERT: E 483 ASN cc_start: 0.8232 (t0) cc_final: 0.7878 (t0) REVERT: E 581 MET cc_start: 0.8366 (tpt) cc_final: 0.8088 (tpp) REVERT: E 599 MET cc_start: 0.4984 (mpp) cc_final: 0.4747 (mpp) REVERT: E 659 ARG cc_start: 0.8422 (ttm110) cc_final: 0.7999 (mtp180) REVERT: K 217 TYR cc_start: 0.7536 (t80) cc_final: 0.7170 (t80) REVERT: K 247 GLN cc_start: 0.8754 (mp10) cc_final: 0.8421 (mm-40) REVERT: K 300 MET cc_start: 0.6453 (mtp) cc_final: 0.6074 (mtp) REVERT: K 309 TRP cc_start: 0.8222 (t-100) cc_final: 0.7904 (t-100) REVERT: K 310 ASN cc_start: 0.8394 (m110) cc_final: 0.8129 (p0) REVERT: K 415 MET cc_start: 0.7635 (mmt) cc_final: 0.7158 (mmt) REVERT: K 459 MET cc_start: 0.7794 (mmt) cc_final: 0.7509 (mmp) REVERT: K 556 TYR cc_start: 0.8241 (t80) cc_final: 0.8010 (t80) REVERT: K 572 MET cc_start: 0.8128 (mmm) cc_final: 0.7496 (tpp) REVERT: K 602 ASN cc_start: 0.7727 (m110) cc_final: 0.7335 (m110) REVERT: Q 163 ASN cc_start: 0.7509 (t0) cc_final: 0.7111 (t0) REVERT: Q 166 MET cc_start: 0.3601 (mtt) cc_final: 0.3054 (mmt) REVERT: Q 211 ARG cc_start: 0.7121 (tpt90) cc_final: 0.6867 (tpm170) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2171 time to fit residues: 50.3011 Evaluate side-chains 135 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.0060 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN E 693 ASN ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.123081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.101168 restraints weight = 27318.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102012 restraints weight = 22603.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.102683 restraints weight = 20145.631| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10668 Z= 0.151 Angle : 0.578 9.762 14523 Z= 0.293 Chirality : 0.041 0.182 1625 Planarity : 0.004 0.051 1767 Dihedral : 14.046 176.916 1738 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1226 helix: 0.65 (0.23), residues: 544 sheet: -3.09 (0.50), residues: 91 loop : -2.24 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 131 HIS 0.004 0.001 HIS E 506 PHE 0.022 0.001 PHE E 604 TYR 0.011 0.001 TYR E 597 ARG 0.003 0.000 ARG Q 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.18 seconds wall clock time: 38 minutes 25.02 seconds (2305.02 seconds total)