Starting phenix.real_space_refine on Tue Feb 20 10:51:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhc_12323/02_2024/7nhc_12323.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhc_12323/02_2024/7nhc_12323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhc_12323/02_2024/7nhc_12323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhc_12323/02_2024/7nhc_12323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhc_12323/02_2024/7nhc_12323.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhc_12323/02_2024/7nhc_12323.pdb" } resolution = 2.87 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= 0.002 sd= 0.042 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 23 5.49 5 S 100 5.16 5 C 8764 2.51 5 N 2440 2.21 5 O 2705 1.98 5 H 13727 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 27": "OD1" <-> "OD2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 697": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27759 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 11436 Classifications: {'peptide': 717} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 686} Chain breaks: 2 Chain: "C" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 4053 Classifications: {'peptide': 247} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 12.20, per 1000 atoms: 0.44 Number of scatterers: 27759 At special positions: 0 Unit cell: (100.65, 102.3, 146.025, 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 100 16.00 P 23 15.00 O 2705 8.00 N 2440 7.00 C 8764 6.00 H 13727 1.00 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: 22.38 Conformation dependent library (CDL) restraints added in 3.0 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3174 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 15 sheets defined 53.3% alpha, 13.0% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 12.12 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.517A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.826A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.564A pdb=" N PHE A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.729A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.722A pdb=" N GLN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.617A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 404 through 415 removed outlier: 4.549A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.727A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.936A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 603 removed outlier: 3.763A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.672A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.602A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.747A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.570A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.730A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 290 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.599A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.731A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.002A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.652A pdb=" N MET B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.557A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 672 through 677 removed outlier: 4.030A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 700 Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.085A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.550A pdb=" N GLU C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.009A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.768A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.741A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.608A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.660A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.815A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.540A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 324 removed outlier: 10.261A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.205A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.604A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 184 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.811A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.477A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 6.040A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 701 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 10.96 Time building geometry restraints manager: 23.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13700 1.03 - 1.23: 31 1.23 - 1.42: 6011 1.42 - 1.62: 8176 1.62 - 1.81: 173 Bond restraints: 28091 Sorted by residual: bond pdb=" CG ARG A 185 " pdb=" CD ARG A 185 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.82e+00 bond pdb=" CA PHE B 412 " pdb=" CB PHE B 412 " ideal model delta sigma weight residual 1.527 1.550 -0.023 1.39e-02 5.18e+03 2.82e+00 bond pdb=" C GLU A 181 " pdb=" O GLU A 181 " ideal model delta sigma weight residual 1.237 1.253 -0.017 1.16e-02 7.43e+03 2.09e+00 bond pdb=" C PRO A 265 " pdb=" N ARG A 266 " ideal model delta sigma weight residual 1.333 1.312 0.021 1.59e-02 3.96e+03 1.68e+00 bond pdb=" CA GLU A 181 " pdb=" C GLU A 181 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.22e+00 ... (remaining 28086 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.58: 555 106.58 - 113.43: 32964 113.43 - 120.29: 9292 120.29 - 127.14: 7721 127.14 - 133.99: 208 Bond angle restraints: 50740 Sorted by residual: angle pdb=" CA GLU A 181 " pdb=" CB GLU A 181 " pdb=" CG GLU A 181 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 angle pdb=" N GLU A 181 " pdb=" CA GLU A 181 " pdb=" CB GLU A 181 " ideal model delta sigma weight residual 110.07 104.71 5.36 1.45e+00 4.76e-01 1.37e+01 angle pdb=" C GLU A 181 " pdb=" CA GLU A 181 " pdb=" CB GLU A 181 " ideal model delta sigma weight residual 110.90 116.14 -5.24 1.58e+00 4.01e-01 1.10e+01 angle pdb=" C HIS A 326 " pdb=" N GLU A 327 " pdb=" CA GLU A 327 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.13e+00 angle pdb=" CA GLY B 513 " pdb=" C GLY B 513 " pdb=" N VAL B 514 " ideal model delta sigma weight residual 114.65 117.31 -2.66 9.20e-01 1.18e+00 8.35e+00 ... (remaining 50735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12027 17.87 - 35.73: 864 35.73 - 53.60: 216 53.60 - 71.47: 72 71.47 - 89.33: 24 Dihedral angle restraints: 13203 sinusoidal: 7482 harmonic: 5721 Sorted by residual: dihedral pdb=" CA LYS B 736 " pdb=" C LYS B 736 " pdb=" N LYS B 737 " pdb=" CA LYS B 737 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY A 58 " pdb=" C GLY A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA CYS C 196 " pdb=" C CYS C 196 " pdb=" N LYS C 197 " pdb=" CA LYS C 197 " ideal model delta harmonic sigma weight residual 180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 13200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1377 0.030 - 0.059: 545 0.059 - 0.089: 130 0.089 - 0.118: 70 0.118 - 0.148: 19 Chirality restraints: 2141 Sorted by residual: chirality pdb=" C1' A D 4 " pdb=" O4' A D 4 " pdb=" C2' A D 4 " pdb=" N9 A D 4 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE B 667 " pdb=" N ILE B 667 " pdb=" C ILE B 667 " pdb=" CB ILE B 667 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE B 302 " pdb=" N ILE B 302 " pdb=" C ILE B 302 " pdb=" CB ILE B 302 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2138 not shown) Planarity restraints: 4048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 496 " -0.327 9.50e-02 1.11e+02 1.09e-01 1.40e+01 pdb=" NE ARG A 496 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 496 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 496 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 496 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 496 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 496 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG A 496 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG A 496 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 4 " -0.029 2.00e-02 2.50e+03 1.18e-02 4.52e+00 pdb=" N9 A D 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A D 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A D 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A D 4 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A D 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A D 4 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A D 4 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 181 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C GLU A 181 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU A 181 " 0.012 2.00e-02 2.50e+03 pdb=" N MET A 182 " 0.011 2.00e-02 2.50e+03 ... (remaining 4045 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1241 2.18 - 2.79: 56358 2.79 - 3.39: 79443 3.39 - 4.00: 105464 4.00 - 4.60: 164712 Nonbonded interactions: 407218 Sorted by model distance: nonbonded pdb=" O TRP A 699 " pdb="HD21 ASN A 703 " model vdw 1.579 1.850 nonbonded pdb=" O GLY A 152 " pdb=" HZ2 LYS A 172 " model vdw 1.580 1.850 nonbonded pdb=" OP2 G D 5 " pdb=" H22 G D 5 " model vdw 1.588 1.850 nonbonded pdb=" O LYS C 190 " pdb="HE21 GLN C 194 " model vdw 1.588 1.850 nonbonded pdb=" OD2 ASP B 593 " pdb=" HH TYR B 620 " model vdw 1.591 1.850 ... (remaining 407213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.390 Extract box with map and model: 5.120 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 96.420 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.002 0.059 14364 Z= 0.152 Angle : 0.512 9.121 19477 Z= 0.287 Chirality : 0.037 0.148 2141 Planarity : 0.005 0.146 2426 Dihedral : 14.218 89.335 5642 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.17 (0.20), residues: 1670 helix: 1.03 (0.19), residues: 790 sheet: -0.50 (0.42), residues: 144 loop : -0.72 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 188 HIS 0.004 0.001 HIS A 146 PHE 0.015 0.001 PHE A 176 TYR 0.013 0.001 TYR A 130 ARG 0.012 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.7596 (t0) cc_final: 0.7320 (t0) REVERT: A 423 ILE cc_start: 0.7375 (tp) cc_final: 0.7149 (tp) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 2.9814 time to fit residues: 992.7316 Evaluate side-chains 222 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 0.0270 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN B 137 GLN C 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14364 Z= 0.247 Angle : 0.535 6.626 19477 Z= 0.287 Chirality : 0.039 0.176 2141 Planarity : 0.005 0.087 2426 Dihedral : 10.094 74.006 2186 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.40 % Allowed : 10.84 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1670 helix: 1.10 (0.18), residues: 796 sheet: -0.44 (0.41), residues: 153 loop : -0.77 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 98 HIS 0.003 0.001 HIS A 52 PHE 0.016 0.001 PHE A 176 TYR 0.011 0.001 TYR C 115 ARG 0.011 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 228 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5891 (tpp) REVERT: A 147 ILE cc_start: 0.8408 (mm) cc_final: 0.8176 (mp) REVERT: A 610 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6819 (mt-10) REVERT: B 172 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6996 (mm-30) outliers start: 21 outliers final: 8 residues processed: 235 average time/residue: 2.7434 time to fit residues: 709.5661 Evaluate side-chains 227 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 408 GLN B 115 GLN B 314 ASN B 671 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14364 Z= 0.209 Angle : 0.510 6.312 19477 Z= 0.271 Chirality : 0.038 0.174 2141 Planarity : 0.004 0.050 2426 Dihedral : 10.058 74.066 2186 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.81 % Allowed : 12.31 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1670 helix: 1.27 (0.18), residues: 798 sheet: -0.28 (0.41), residues: 153 loop : -0.72 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.004 0.001 HIS A 146 PHE 0.019 0.001 PHE A 176 TYR 0.013 0.001 TYR A 131 ARG 0.014 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.8543 (mm) cc_final: 0.8329 (mp) REVERT: A 561 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7522 (ttt) REVERT: A 610 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: B 172 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: B 628 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8278 (mp) REVERT: C 1 MET cc_start: 0.6302 (tpt) cc_final: 0.5624 (tpt) outliers start: 27 outliers final: 10 residues processed: 235 average time/residue: 2.6486 time to fit residues: 685.7451 Evaluate side-chains 229 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 215 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 78 optimal weight: 0.0010 chunk 16 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14364 Z= 0.220 Angle : 0.512 5.761 19477 Z= 0.272 Chirality : 0.038 0.176 2141 Planarity : 0.004 0.052 2426 Dihedral : 10.048 73.762 2186 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.27 % Allowed : 13.24 % Favored : 84.48 % 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: 0.41 (0.20), residues: 1670 helix: 1.33 (0.18), residues: 805 sheet: -0.26 (0.41), residues: 153 loop : -0.81 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.003 0.001 HIS A 146 PHE 0.017 0.001 PHE A 176 TYR 0.011 0.001 TYR A 131 ARG 0.010 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 224 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.5905 (tpp) REVERT: A 147 ILE cc_start: 0.8478 (mm) cc_final: 0.8227 (mp) REVERT: A 610 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: A 670 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: B 1 MET cc_start: 0.7612 (ttp) cc_final: 0.7336 (ttm) REVERT: B 172 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: B 398 ASP cc_start: 0.7183 (t0) cc_final: 0.6983 (t0) REVERT: B 480 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7953 (mtpm) REVERT: B 628 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 674 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6769 (mm) outliers start: 34 outliers final: 13 residues processed: 238 average time/residue: 2.7496 time to fit residues: 720.6139 Evaluate side-chains 240 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14364 Z= 0.290 Angle : 0.540 5.547 19477 Z= 0.287 Chirality : 0.040 0.194 2141 Planarity : 0.004 0.060 2426 Dihedral : 10.178 73.984 2186 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.94 % Allowed : 14.31 % Favored : 83.75 % 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: 0.29 (0.20), residues: 1670 helix: 1.22 (0.18), residues: 805 sheet: -0.31 (0.41), residues: 153 loop : -0.86 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.005 0.001 HIS A 452 PHE 0.018 0.001 PHE A 176 TYR 0.011 0.002 TYR A 540 ARG 0.009 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: A 561 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7707 (ttt) REVERT: A 610 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: B 1 MET cc_start: 0.7630 (ttp) cc_final: 0.7375 (ttm) REVERT: B 172 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7028 (mm-30) REVERT: B 398 ASP cc_start: 0.7255 (t0) cc_final: 0.7050 (t0) REVERT: B 480 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7934 (mtpm) REVERT: B 628 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8300 (mp) REVERT: B 674 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6779 (mm) REVERT: C 3 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6330 (ptp-170) outliers start: 29 outliers final: 10 residues processed: 242 average time/residue: 2.6930 time to fit residues: 719.0508 Evaluate side-chains 232 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 670 GLN B 314 ASN B 533 ASN C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14364 Z= 0.209 Angle : 0.508 6.065 19477 Z= 0.269 Chirality : 0.038 0.184 2141 Planarity : 0.004 0.052 2426 Dihedral : 10.075 73.773 2186 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.87 % Allowed : 14.85 % Favored : 83.28 % 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: 0.45 (0.20), residues: 1670 helix: 1.40 (0.18), residues: 800 sheet: -0.29 (0.41), residues: 153 loop : -0.80 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.004 0.001 HIS A 146 PHE 0.015 0.001 PHE A 176 TYR 0.015 0.001 TYR A 131 ARG 0.007 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5940 (tpp) REVERT: A 252 GLU cc_start: 0.7344 (mp0) cc_final: 0.7142 (mm-30) REVERT: A 561 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7617 (ttt) REVERT: A 610 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6906 (mt-10) REVERT: B 1 MET cc_start: 0.7578 (ttp) cc_final: 0.7309 (ttm) REVERT: B 172 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7052 (mm-30) REVERT: B 480 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7983 (mtpm) REVERT: B 628 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 674 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6809 (mm) REVERT: C 1 MET cc_start: 0.6231 (tpt) cc_final: 0.5889 (tpt) REVERT: C 3 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6279 (ptp-170) outliers start: 28 outliers final: 11 residues processed: 233 average time/residue: 2.6471 time to fit residues: 681.4060 Evaluate side-chains 230 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 211 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14364 Z= 0.258 Angle : 0.531 6.135 19477 Z= 0.281 Chirality : 0.039 0.188 2141 Planarity : 0.004 0.046 2426 Dihedral : 10.131 73.856 2186 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.01 % Allowed : 15.25 % Favored : 82.74 % 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: 0.38 (0.20), residues: 1670 helix: 1.33 (0.18), residues: 800 sheet: -0.27 (0.41), residues: 153 loop : -0.85 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.004 0.001 HIS A 452 PHE 0.014 0.001 PHE A 176 TYR 0.017 0.001 TYR A 131 ARG 0.006 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 218 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.5982 (tpp) REVERT: A 252 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: A 561 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7627 (ttt) REVERT: A 607 MET cc_start: 0.7717 (mmm) cc_final: 0.7080 (tpp) REVERT: A 610 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: B 1 MET cc_start: 0.7575 (ttp) cc_final: 0.7345 (ttm) REVERT: B 172 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: B 480 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7943 (mtpm) REVERT: B 628 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 674 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6884 (mm) REVERT: C 1 MET cc_start: 0.6240 (tpt) cc_final: 0.5894 (tpt) REVERT: C 3 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6268 (ptp-170) outliers start: 30 outliers final: 13 residues processed: 232 average time/residue: 2.5651 time to fit residues: 659.2716 Evaluate side-chains 233 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14364 Z= 0.156 Angle : 0.492 6.237 19477 Z= 0.259 Chirality : 0.037 0.172 2141 Planarity : 0.004 0.047 2426 Dihedral : 9.974 73.652 2186 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.34 % Allowed : 16.32 % Favored : 82.34 % 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: 0.61 (0.20), residues: 1670 helix: 1.58 (0.18), residues: 801 sheet: -0.19 (0.40), residues: 160 loop : -0.80 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.002 0.001 HIS A 326 PHE 0.013 0.001 PHE A 176 TYR 0.014 0.001 TYR A 131 ARG 0.007 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 217 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.5736 (tpp) REVERT: A 607 MET cc_start: 0.7638 (mmm) cc_final: 0.7092 (tpp) REVERT: A 610 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: B 172 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: B 480 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7956 (mtpm) REVERT: B 674 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.6810 (mm) REVERT: C 1 MET cc_start: 0.6227 (tpt) cc_final: 0.5869 (tpt) REVERT: C 3 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.6225 (ptp-170) outliers start: 20 outliers final: 10 residues processed: 226 average time/residue: 2.7232 time to fit residues: 682.5573 Evaluate side-chains 228 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14364 Z= 0.323 Angle : 0.558 6.124 19477 Z= 0.295 Chirality : 0.041 0.196 2141 Planarity : 0.004 0.041 2426 Dihedral : 10.186 73.902 2186 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.54 % Allowed : 16.52 % Favored : 81.94 % 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: 0.33 (0.20), residues: 1670 helix: 1.29 (0.18), residues: 806 sheet: -0.36 (0.39), residues: 165 loop : -0.87 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.006 0.001 HIS A 452 PHE 0.015 0.001 PHE A 520 TYR 0.020 0.002 TYR A 131 ARG 0.005 0.001 ARG C 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7613 (ttt) REVERT: A 607 MET cc_start: 0.7790 (mmm) cc_final: 0.7266 (tpp) REVERT: A 610 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: B 172 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7118 (mm-30) REVERT: B 480 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8017 (mtpm) REVERT: B 674 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.6948 (mm) outliers start: 23 outliers final: 11 residues processed: 227 average time/residue: 2.6717 time to fit residues: 669.4721 Evaluate side-chains 229 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14364 Z= 0.167 Angle : 0.502 6.568 19477 Z= 0.264 Chirality : 0.037 0.176 2141 Planarity : 0.004 0.045 2426 Dihedral : 10.023 73.660 2186 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.07 % Allowed : 16.92 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1670 helix: 1.54 (0.18), residues: 801 sheet: -0.29 (0.40), residues: 165 loop : -0.80 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 438 HIS 0.004 0.001 HIS A 144 PHE 0.012 0.001 PHE A 176 TYR 0.010 0.001 TYR A 131 ARG 0.008 0.000 ARG A 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 216 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.7752 (mmm) cc_final: 0.7245 (tpp) REVERT: A 610 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: B 172 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: B 480 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8020 (mtpm) REVERT: B 674 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.6885 (mm) REVERT: C 3 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6213 (ptp-170) outliers start: 16 outliers final: 9 residues processed: 225 average time/residue: 2.7497 time to fit residues: 688.0002 Evaluate side-chains 228 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 214 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.156753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127503 restraints weight = 43400.587| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.49 r_work: 0.3178 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14364 Z= 0.249 Angle : 0.529 6.405 19477 Z= 0.278 Chirality : 0.039 0.186 2141 Planarity : 0.004 0.039 2426 Dihedral : 10.091 73.820 2186 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.40 % Allowed : 16.52 % Favored : 82.07 % 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: 0.49 (0.20), residues: 1670 helix: 1.45 (0.18), residues: 800 sheet: -0.27 (0.40), residues: 165 loop : -0.82 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.004 0.001 HIS A 452 PHE 0.013 0.001 PHE A 520 TYR 0.013 0.001 TYR A 131 ARG 0.008 0.000 ARG A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11387.71 seconds wall clock time: 200 minutes 9.69 seconds (12009.69 seconds total)