Starting phenix.real_space_refine on Mon Apr 8 18:06:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/04_2024/6t0r_10357.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/04_2024/6t0r_10357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/04_2024/6t0r_10357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/04_2024/6t0r_10357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/04_2024/6t0r_10357.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0r_10357/04_2024/6t0r_10357.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 20 5.49 5 S 92 5.16 5 C 8826 2.51 5 N 2460 2.21 5 O 2722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14120 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 701, 5716 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 701, 5716 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 2 bond proxies already assigned to first conformer: 5828 Chain: "B" Number of atoms: 5919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5919 Classifications: {'peptide': 739} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 710} Chain breaks: 1 Chain: "C" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2016 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "V" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 430 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 10, 'rna3p': 9} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 10.80, per 1000 atoms: 0.76 Number of scatterers: 14120 At special positions: 0 Unit cell: (94.2732, 118.654, 117.841, 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 92 16.00 P 20 15.00 O 2722 8.00 N 2460 7.00 C 8826 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: 5.50 Conformation dependent library (CDL) restraints added in 3.5 seconds 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3194 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 17 sheets defined 50.3% alpha, 12.5% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.648A pdb=" N ARG A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.657A pdb=" N TYR A 130 " --> pdb=" O LYS 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 185 Processing helix chain 'A' and resid 188 through 193 removed outlier: 4.046A pdb=" N ARG A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 193' Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.602A pdb=" N ALA A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.627A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 399 through 410 removed outlier: 4.548A pdb=" N GLN A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 removed outlier: 3.533A pdb=" N GLU A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 577 through 599 removed outlier: 4.053A pdb=" N VAL A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 4.505A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 688 removed outlier: 4.072A pdb=" N CYS A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.964A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (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 115 removed outlier: 3.623A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.786A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.524A pdb=" N PHE B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.975A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.682A pdb=" N ASN B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.729A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.559A pdb=" N TYR B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 3.611A 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 427 removed outlier: 3.577A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.502A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 582 removed outlier: 3.514A pdb=" N GLU B 582 " --> pdb=" O ARG B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.547A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.839A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.642A pdb=" N TYR C 34 " --> pdb=" O ILE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.735A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.654A pdb=" N ILE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.891A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.560A pdb=" N ARG C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 167 removed outlier: 4.145A pdb=" N GLN C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU C 161 " --> pdb=" O ARG C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.893A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.711A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.820A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.564A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.057A pdb=" N PHE A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.466A pdb=" N LYS A 274 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.235A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.403A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A 475 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.349A pdb=" N GLN B 367 " --> pdb=" O MET A 374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.338A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 2 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.513A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 192 removed outlier: 7.877A pdb=" N ASN B 678 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B 203 " --> pdb=" O ASN B 678 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.969A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 57 through 59 Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 133 removed outlier: 4.550A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.362A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 5.97 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: 3789 1.33 - 1.45: 2601 1.45 - 1.57: 7829 1.57 - 1.69: 38 1.69 - 1.81: 160 Bond restraints: 14417 Sorted by residual: bond pdb=" C GLU A 604 " pdb=" N PRO A 605 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.35e+00 bond pdb=" CB VAL A 631 " pdb=" CG2 VAL A 631 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CG1 ILE C 67 " pdb=" CD1 ILE C 67 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.31e+00 bond pdb=" CA SER A 504 " pdb=" CB SER A 504 " ideal model delta sigma weight residual 1.539 1.485 0.055 4.88e-02 4.20e+02 1.26e+00 bond pdb=" CG1 ILE B 389 " pdb=" CD1 ILE B 389 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.25e+00 ... (remaining 14412 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.31: 479 106.31 - 113.26: 7741 113.26 - 120.22: 5389 120.22 - 127.17: 5730 127.17 - 134.12: 192 Bond angle restraints: 19531 Sorted by residual: angle pdb=" N ILE A 79 " pdb=" CA ILE A 79 " pdb=" C ILE A 79 " ideal model delta sigma weight residual 113.42 108.10 5.32 1.17e+00 7.31e-01 2.07e+01 angle pdb=" C HIS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.36e+00 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 112.66 -4.46 1.50e+00 4.44e-01 8.86e+00 angle pdb=" CA TYR B 557 " pdb=" CB TYR B 557 " pdb=" CG TYR B 557 " ideal model delta sigma weight residual 113.90 108.59 5.31 1.80e+00 3.09e-01 8.72e+00 angle pdb=" CA SER B 404 " pdb=" C SER B 404 " pdb=" N PRO B 405 " ideal model delta sigma weight residual 118.44 122.89 -4.45 1.59e+00 3.96e-01 7.82e+00 ... (remaining 19526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7978 17.81 - 35.62: 602 35.62 - 53.43: 154 53.43 - 71.24: 57 71.24 - 89.05: 14 Dihedral angle restraints: 8805 sinusoidal: 3868 harmonic: 4937 Sorted by residual: dihedral pdb=" CA THR B 223 " pdb=" C THR B 223 " pdb=" N LEU B 224 " pdb=" CA LEU B 224 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASN A 8 " pdb=" C ASN A 8 " pdb=" N PHE A 9 " pdb=" CA PHE A 9 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU A 219 " pdb=" C LEU A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta harmonic sigma weight residual 180.00 161.02 18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 8802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1485 0.043 - 0.086: 518 0.086 - 0.129: 122 0.129 - 0.172: 13 0.172 - 0.215: 3 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CB ILE B 368 " pdb=" CA ILE B 368 " pdb=" CG1 ILE B 368 " pdb=" CG2 ILE B 368 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CB VAL A 445 " pdb=" CA VAL A 445 " pdb=" CG1 VAL A 445 " pdb=" CG2 VAL A 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 2138 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 620 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.031 2.00e-02 2.50e+03 1.47e-02 5.93e+00 pdb=" N9 A V 7 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A V 7 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A V 7 " -0.000 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 111 " 0.039 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO C 112 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.033 5.00e-02 4.00e+02 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3824 2.80 - 3.33: 11808 3.33 - 3.85: 24720 3.85 - 4.38: 29485 4.38 - 4.90: 49848 Nonbonded interactions: 119685 Sorted by model distance: nonbonded pdb=" O THR C 224 " pdb=" OG1 THR C 224 " model vdw 2.279 2.440 nonbonded pdb=" OE1 GLU A 588 " pdb=" OG1 THR B 543 " model vdw 2.290 2.440 nonbonded pdb=" OD2 ASP B 593 " pdb=" OH TYR B 620 " model vdw 2.294 2.440 nonbonded pdb=" O ASN A 3 " pdb=" OG1 THR A 7 " model vdw 2.294 2.440 nonbonded pdb=" O ALA B 113 " pdb=" OG1 THR B 117 " model vdw 2.295 2.440 ... (remaining 119680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.240 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 47.630 Find NCS groups from input model: 0.490 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: 0.000 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.005 0.056 14417 Z= 0.303 Angle : 0.662 8.137 19531 Z= 0.389 Chirality : 0.045 0.215 2141 Planarity : 0.006 0.064 2439 Dihedral : 14.591 89.049 5611 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.99 % Allowed : 7.52 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -2.98 (0.16), residues: 1679 helix: -1.80 (0.14), residues: 764 sheet: -1.82 (0.34), residues: 189 loop : -2.07 (0.19), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 438 HIS 0.005 0.001 HIS B 32 PHE 0.020 0.002 PHE A 515 TYR 0.025 0.002 TYR B 557 ARG 0.005 0.001 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 294 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8261 (m-40) cc_final: 0.7870 (m110) REVERT: A 97 MET cc_start: 0.6944 (tmm) cc_final: 0.6681 (ttt) REVERT: A 202 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.4990 (mp0) REVERT: A 272 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 419 GLU cc_start: 0.7832 (tp30) cc_final: 0.7630 (tp30) REVERT: A 616 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 669 LYS cc_start: 0.7388 (tttt) cc_final: 0.7121 (tptm) REVERT: B 672 ARG cc_start: 0.7656 (mtm180) cc_final: 0.7050 (mtt-85) REVERT: B 709 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7887 (mm) REVERT: C 15 ARG cc_start: 0.8121 (tpt90) cc_final: 0.7891 (tmt170) REVERT: C 49 TRP cc_start: 0.8041 (p-90) cc_final: 0.7549 (p90) REVERT: C 51 MET cc_start: 0.8623 (mmm) cc_final: 0.8256 (mmt) REVERT: C 82 LYS cc_start: 0.4296 (OUTLIER) cc_final: 0.3441 (mmtt) outliers start: 75 outliers final: 20 residues processed: 349 average time/residue: 1.5014 time to fit residues: 566.4868 Evaluate side-chains 235 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 210 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 124 GLN B 314 ASN B 452 ASN B 690 GLN C 87 ASN C 182 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14417 Z= 0.202 Angle : 0.507 6.619 19531 Z= 0.272 Chirality : 0.040 0.200 2141 Planarity : 0.004 0.046 2439 Dihedral : 11.058 75.744 2200 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.19 % Allowed : 15.70 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.03 (0.19), residues: 1679 helix: 0.36 (0.18), residues: 772 sheet: -1.29 (0.38), residues: 171 loop : -1.64 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.001 PHE A 702 TYR 0.024 0.001 TYR B 557 ARG 0.009 0.001 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 213 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7037 (tmm) cc_final: 0.6577 (ttt) REVERT: A 155 MET cc_start: 0.4800 (mmm) cc_final: 0.4306 (mmm) REVERT: A 202 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.4986 (mp0) REVERT: A 272 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: A 286 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: A 293 LEU cc_start: 0.8190 (tt) cc_final: 0.7976 (tm) REVERT: A 612 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8406 (m110) REVERT: A 616 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8371 (pp) REVERT: B 268 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: B 384 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: B 414 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7399 (mpp) REVERT: B 481 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8231 (mttm) REVERT: B 672 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7028 (mtt90) REVERT: B 683 LEU cc_start: 0.7711 (mm) cc_final: 0.7437 (mt) REVERT: B 687 ARG cc_start: 0.6972 (ttt180) cc_final: 0.6728 (ptp90) REVERT: C 28 MET cc_start: 0.8399 (ptm) cc_final: 0.8020 (ttp) REVERT: C 51 MET cc_start: 0.8759 (mmm) cc_final: 0.8325 (mmt) REVERT: C 82 LYS cc_start: 0.4276 (OUTLIER) cc_final: 0.3990 (mtmm) REVERT: C 83 ASP cc_start: 0.4329 (OUTLIER) cc_final: 0.3678 (t70) REVERT: C 198 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6945 (mp) REVERT: C 201 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7477 (mm) outliers start: 63 outliers final: 26 residues processed: 250 average time/residue: 1.4890 time to fit residues: 404.2863 Evaluate side-chains 231 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 128 optimal weight: 0.0770 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS B 116 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 452 ASN B 690 GLN C 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14417 Z= 0.260 Angle : 0.529 7.300 19531 Z= 0.282 Chirality : 0.041 0.162 2141 Planarity : 0.004 0.044 2439 Dihedral : 10.941 76.121 2189 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.79 % Allowed : 16.97 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.36 (0.20), residues: 1679 helix: 1.01 (0.18), residues: 779 sheet: -1.15 (0.38), residues: 170 loop : -1.38 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 49 HIS 0.004 0.001 HIS A 360 PHE 0.017 0.002 PHE A 702 TYR 0.025 0.002 TYR B 557 ARG 0.011 0.001 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 195 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7071 (tmm) cc_final: 0.6654 (ttt) REVERT: A 272 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: A 293 LEU cc_start: 0.8260 (tt) cc_final: 0.8047 (tm) REVERT: A 304 MET cc_start: 0.8096 (mmm) cc_final: 0.7858 (tpt) REVERT: A 616 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8413 (pp) REVERT: B 268 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: B 287 LYS cc_start: 0.7395 (pptt) cc_final: 0.6926 (ptpt) REVERT: B 362 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7191 (mtm) REVERT: B 384 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6721 (m-30) REVERT: B 414 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7503 (mpp) REVERT: B 514 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8406 (m) REVERT: B 672 ARG cc_start: 0.7572 (mtm180) cc_final: 0.6899 (mtt-85) REVERT: B 683 LEU cc_start: 0.7768 (mm) cc_final: 0.7415 (mt) REVERT: B 742 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: C 51 MET cc_start: 0.8846 (mmm) cc_final: 0.8407 (mmt) REVERT: C 82 LYS cc_start: 0.4334 (OUTLIER) cc_final: 0.3995 (mtmt) REVERT: C 201 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7504 (tt) outliers start: 72 outliers final: 37 residues processed: 242 average time/residue: 1.4433 time to fit residues: 380.6199 Evaluate side-chains 238 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 690 GLN C 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14417 Z= 0.242 Angle : 0.514 7.940 19531 Z= 0.273 Chirality : 0.040 0.159 2141 Planarity : 0.004 0.042 2439 Dihedral : 10.750 76.221 2184 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.39 % Allowed : 16.37 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.02 (0.20), residues: 1679 helix: 1.39 (0.19), residues: 773 sheet: -1.03 (0.38), residues: 170 loop : -1.22 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.016 0.001 PHE A 702 TYR 0.023 0.002 TYR B 557 ARG 0.004 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 197 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7058 (tmm) cc_final: 0.6587 (ttt) REVERT: A 272 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 616 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8422 (pp) REVERT: B 268 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: B 287 LYS cc_start: 0.7403 (pptt) cc_final: 0.6969 (ptpt) REVERT: B 362 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7181 (mtm) REVERT: B 384 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6649 (m-30) REVERT: B 514 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8368 (m) REVERT: B 672 ARG cc_start: 0.7573 (mtm180) cc_final: 0.6890 (mtt-85) REVERT: B 683 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7308 (mt) REVERT: B 742 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: C 15 ARG cc_start: 0.8192 (tpt90) cc_final: 0.7908 (tmt170) REVERT: C 51 MET cc_start: 0.8860 (mmm) cc_final: 0.8448 (mmt) REVERT: C 82 LYS cc_start: 0.4416 (OUTLIER) cc_final: 0.4048 (mtmm) REVERT: C 191 GLU cc_start: 0.6819 (tt0) cc_final: 0.6411 (mt-10) REVERT: C 201 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7543 (tt) REVERT: C 214 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6352 (mtm180) outliers start: 81 outliers final: 40 residues processed: 249 average time/residue: 1.4086 time to fit residues: 382.2662 Evaluate side-chains 238 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 187 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.1980 chunk 147 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS A 354 ASN A 585 GLN B 127 GLN B 158 ASN B 314 ASN B 452 ASN B 690 GLN C 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14417 Z= 0.146 Angle : 0.457 6.756 19531 Z= 0.243 Chirality : 0.038 0.146 2141 Planarity : 0.003 0.041 2439 Dihedral : 10.252 74.748 2177 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.86 % Allowed : 18.50 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.47 (0.21), residues: 1679 helix: 1.79 (0.19), residues: 766 sheet: -0.72 (0.38), residues: 177 loop : -1.04 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 49 HIS 0.002 0.000 HIS A 360 PHE 0.014 0.001 PHE A 46 TYR 0.019 0.001 TYR B 557 ARG 0.005 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 204 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7099 (tmm) cc_final: 0.6603 (ttt) REVERT: A 455 MET cc_start: 0.7904 (ttt) cc_final: 0.7447 (mmm) REVERT: A 568 ILE cc_start: 0.9083 (tp) cc_final: 0.8834 (pt) REVERT: A 616 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8324 (pp) REVERT: B 287 LYS cc_start: 0.7266 (pptt) cc_final: 0.6962 (ptpt) REVERT: B 384 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: B 672 ARG cc_start: 0.7548 (mtm180) cc_final: 0.6896 (mtt-85) REVERT: B 683 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7368 (mt) REVERT: B 707 ARG cc_start: 0.7867 (ttt90) cc_final: 0.7624 (ttt90) REVERT: B 725 ASP cc_start: 0.6635 (t0) cc_final: 0.6269 (m-30) REVERT: B 739 ASP cc_start: 0.6119 (OUTLIER) cc_final: 0.5820 (m-30) REVERT: B 742 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: C 40 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: C 51 MET cc_start: 0.8855 (mmm) cc_final: 0.8408 (mmt) REVERT: C 82 LYS cc_start: 0.4505 (OUTLIER) cc_final: 0.4103 (mtmt) REVERT: C 83 ASP cc_start: 0.4215 (OUTLIER) cc_final: 0.3615 (t70) REVERT: C 191 GLU cc_start: 0.6825 (tt0) cc_final: 0.6410 (mt-10) REVERT: C 214 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6338 (mtm180) outliers start: 58 outliers final: 25 residues processed: 247 average time/residue: 1.3582 time to fit residues: 367.2920 Evaluate side-chains 226 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 313 GLN B 314 ASN B 452 ASN B 690 GLN C 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14417 Z= 0.291 Angle : 0.537 8.967 19531 Z= 0.284 Chirality : 0.041 0.167 2141 Planarity : 0.004 0.043 2439 Dihedral : 10.306 76.748 2168 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.59 % Allowed : 18.30 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.32 (0.20), residues: 1679 helix: 1.57 (0.19), residues: 778 sheet: -0.76 (0.39), residues: 170 loop : -1.05 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 49 HIS 0.004 0.001 HIS A 360 PHE 0.021 0.002 PHE C 168 TYR 0.024 0.002 TYR B 557 ARG 0.006 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 195 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7085 (tmm) cc_final: 0.6626 (ttt) REVERT: A 616 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8428 (pp) REVERT: B 118 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7348 (mmt180) REVERT: B 287 LYS cc_start: 0.7397 (pptt) cc_final: 0.7031 (ptpt) REVERT: B 384 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6649 (m-30) REVERT: B 414 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7525 (mpp) REVERT: B 672 ARG cc_start: 0.7542 (mtm180) cc_final: 0.6871 (mtt-85) REVERT: B 683 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7397 (mt) REVERT: B 739 ASP cc_start: 0.6066 (OUTLIER) cc_final: 0.5768 (m-30) REVERT: C 40 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6716 (tt0) REVERT: C 51 MET cc_start: 0.8866 (mmm) cc_final: 0.8457 (mmt) REVERT: C 82 LYS cc_start: 0.4589 (OUTLIER) cc_final: 0.3545 (ptmm) REVERT: C 191 GLU cc_start: 0.6799 (tt0) cc_final: 0.6386 (mt-10) REVERT: C 214 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6419 (mtm180) outliers start: 69 outliers final: 39 residues processed: 241 average time/residue: 1.3766 time to fit residues: 366.2047 Evaluate side-chains 236 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 188 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 93 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 127 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 314 ASN B 597 ASN B 690 GLN C 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 0.053 14417 Z= 0.250 Angle : 0.510 7.414 19531 Z= 0.271 Chirality : 0.040 0.161 2141 Planarity : 0.004 0.042 2439 Dihedral : 10.272 76.540 2168 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.66 % Allowed : 19.23 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1679 helix: 1.64 (0.19), residues: 775 sheet: -0.72 (0.39), residues: 170 loop : -0.96 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 49 HIS 0.004 0.001 HIS A 360 PHE 0.016 0.001 PHE A 702 TYR 0.023 0.002 TYR B 557 ARG 0.004 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5276 (ptm) cc_final: 0.5035 (ppp) REVERT: A 83 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: A 97 MET cc_start: 0.7099 (tmm) cc_final: 0.6613 (ttt) REVERT: A 616 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8431 (pp) REVERT: B 118 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7282 (mmt180) REVERT: B 287 LYS cc_start: 0.7377 (pptt) cc_final: 0.7031 (ptpt) REVERT: B 362 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7195 (mtm) REVERT: B 384 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: B 672 ARG cc_start: 0.7526 (mtm180) cc_final: 0.6859 (mtt-85) REVERT: B 683 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7379 (mt) REVERT: B 739 ASP cc_start: 0.6101 (OUTLIER) cc_final: 0.5777 (m-30) REVERT: C 40 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6698 (tt0) REVERT: C 51 MET cc_start: 0.8850 (mmm) cc_final: 0.8386 (mmt) REVERT: C 82 LYS cc_start: 0.4514 (OUTLIER) cc_final: 0.3473 (ptmm) REVERT: C 191 GLU cc_start: 0.6810 (tt0) cc_final: 0.6357 (mt-10) REVERT: C 214 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6443 (mtm180) outliers start: 55 outliers final: 39 residues processed: 231 average time/residue: 1.3469 time to fit residues: 341.0578 Evaluate side-chains 239 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 190 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 313 GLN B 690 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14417 Z= 0.158 Angle : 0.470 7.611 19531 Z= 0.250 Chirality : 0.038 0.147 2141 Planarity : 0.003 0.041 2439 Dihedral : 10.109 75.300 2168 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.19 % Allowed : 19.89 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.62 (0.21), residues: 1679 helix: 1.86 (0.19), residues: 768 sheet: -0.68 (0.38), residues: 177 loop : -0.86 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 49 HIS 0.002 0.001 HIS B 32 PHE 0.011 0.001 PHE A 702 TYR 0.020 0.001 TYR B 557 ARG 0.005 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5380 (ptm) cc_final: 0.5114 (ppp) REVERT: A 83 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: A 97 MET cc_start: 0.7109 (tmm) cc_final: 0.6566 (ttt) REVERT: A 455 MET cc_start: 0.7928 (ttt) cc_final: 0.7482 (mmm) REVERT: A 611 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6854 (tp30) REVERT: A 616 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8323 (pp) REVERT: B 118 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7266 (mmt180) REVERT: B 287 LYS cc_start: 0.7242 (pptt) cc_final: 0.6979 (ptpt) REVERT: B 384 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: B 431 ILE cc_start: 0.7082 (mt) cc_final: 0.6735 (mm) REVERT: B 672 ARG cc_start: 0.7519 (mtm180) cc_final: 0.6869 (mtt-85) REVERT: B 683 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7382 (mt) REVERT: B 725 ASP cc_start: 0.6595 (t0) cc_final: 0.6207 (m-30) REVERT: B 739 ASP cc_start: 0.6097 (OUTLIER) cc_final: 0.5786 (m-30) REVERT: C 40 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: C 51 MET cc_start: 0.8875 (mmm) cc_final: 0.8411 (mmt) REVERT: C 82 LYS cc_start: 0.4562 (OUTLIER) cc_final: 0.4210 (mtmm) REVERT: C 214 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6434 (mtm180) outliers start: 48 outliers final: 30 residues processed: 232 average time/residue: 1.3211 time to fit residues: 336.3373 Evaluate side-chains 232 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 452 ASN B 690 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14417 Z= 0.147 Angle : 0.460 7.742 19531 Z= 0.244 Chirality : 0.038 0.142 2141 Planarity : 0.003 0.041 2439 Dihedral : 9.986 74.891 2168 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.79 % Allowed : 20.69 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.76 (0.21), residues: 1679 helix: 1.94 (0.19), residues: 772 sheet: -0.58 (0.39), residues: 172 loop : -0.78 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 49 HIS 0.003 0.001 HIS B 32 PHE 0.011 0.001 PHE B 412 TYR 0.019 0.001 TYR B 557 ARG 0.005 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 198 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5270 (ptm) cc_final: 0.4994 (ppp) REVERT: A 83 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: A 97 MET cc_start: 0.7018 (tmm) cc_final: 0.6549 (ttt) REVERT: A 455 MET cc_start: 0.7924 (ttt) cc_final: 0.7473 (mmm) REVERT: A 611 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6788 (tp30) REVERT: A 616 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8317 (tp) REVERT: B 118 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7226 (mmt180) REVERT: B 287 LYS cc_start: 0.7187 (pptt) cc_final: 0.6985 (ptpt) REVERT: B 384 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6608 (m-30) REVERT: B 431 ILE cc_start: 0.7056 (mt) cc_final: 0.6763 (mm) REVERT: B 672 ARG cc_start: 0.7529 (mtm180) cc_final: 0.6848 (mtt-85) REVERT: B 683 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7369 (mt) REVERT: B 725 ASP cc_start: 0.6604 (t0) cc_final: 0.6225 (m-30) REVERT: B 739 ASP cc_start: 0.6068 (OUTLIER) cc_final: 0.5819 (m-30) REVERT: C 40 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: C 51 MET cc_start: 0.8841 (mmm) cc_final: 0.8389 (mmt) REVERT: C 82 LYS cc_start: 0.4546 (OUTLIER) cc_final: 0.4186 (mtmm) REVERT: C 83 ASP cc_start: 0.4222 (OUTLIER) cc_final: 0.3592 (t70) REVERT: C 213 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6580 (ttm170) REVERT: C 214 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6411 (mtm180) outliers start: 42 outliers final: 27 residues processed: 233 average time/residue: 1.2975 time to fit residues: 332.8460 Evaluate side-chains 231 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 214 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 313 GLN B 452 ASN B 690 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14417 Z= 0.229 Angle : 0.502 7.846 19531 Z= 0.266 Chirality : 0.040 0.155 2141 Planarity : 0.004 0.042 2439 Dihedral : 10.068 76.100 2165 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.73 % Allowed : 20.89 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.21), residues: 1679 helix: 1.76 (0.19), residues: 782 sheet: -0.67 (0.39), residues: 170 loop : -0.89 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.014 0.001 PHE A 702 TYR 0.023 0.001 TYR B 557 ARG 0.004 0.000 ARG A 578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5265 (ptm) cc_final: 0.4959 (ppp) REVERT: A 83 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: A 97 MET cc_start: 0.7096 (tmm) cc_final: 0.6590 (ttt) REVERT: A 616 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8407 (pp) REVERT: B 118 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7187 (mmt180) REVERT: B 287 LYS cc_start: 0.7250 (pptt) cc_final: 0.6984 (ptpt) REVERT: B 384 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: B 672 ARG cc_start: 0.7526 (mtm180) cc_final: 0.6879 (mtt-85) REVERT: B 683 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7409 (mt) REVERT: B 725 ASP cc_start: 0.6623 (t0) cc_final: 0.6233 (m-30) REVERT: B 739 ASP cc_start: 0.6168 (OUTLIER) cc_final: 0.5898 (m-30) REVERT: C 40 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6603 (tt0) REVERT: C 51 MET cc_start: 0.8826 (mmm) cc_final: 0.8414 (mmt) REVERT: C 82 LYS cc_start: 0.4520 (OUTLIER) cc_final: 0.4166 (mtmm) REVERT: C 191 GLU cc_start: 0.6823 (tt0) cc_final: 0.6368 (mt-10) REVERT: C 214 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6479 (mtm180) outliers start: 41 outliers final: 32 residues processed: 225 average time/residue: 1.3082 time to fit residues: 323.3617 Evaluate side-chains 229 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 135 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 690 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.161305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130272 restraints weight = 19094.851| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.67 r_work: 0.3285 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14417 Z= 0.144 Angle : 0.457 8.704 19531 Z= 0.242 Chirality : 0.038 0.136 2141 Planarity : 0.003 0.041 2439 Dihedral : 9.905 74.599 2165 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.46 % Allowed : 21.09 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.76 (0.21), residues: 1679 helix: 1.91 (0.19), residues: 779 sheet: -0.54 (0.39), residues: 172 loop : -0.79 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 49 HIS 0.003 0.000 HIS B 32 PHE 0.013 0.001 PHE C 168 TYR 0.019 0.001 TYR B 557 ARG 0.004 0.000 ARG B 707 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6105.28 seconds wall clock time: 113 minutes 35.93 seconds (6815.93 seconds total)