Starting phenix.real_space_refine on Sat Mar 16 08:24:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0u_10359/03_2024/6t0u_10359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0u_10359/03_2024/6t0u_10359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0u_10359/03_2024/6t0u_10359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0u_10359/03_2024/6t0u_10359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0u_10359/03_2024/6t0u_10359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0u_10359/03_2024/6t0u_10359.pdb" } resolution = 3.12 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= 0.006 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 23 5.49 5 S 93 5.16 5 C 8863 2.51 5 N 2477 2.21 5 O 2720 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 ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" 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-5265/modules/chem_data/mon_lib" Total number of atoms: 14176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5741 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 704, 5733 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 25, 'TRANS': 678} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 704, 5733 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 25, 'TRANS': 678} Chain breaks: 2 bond proxies already assigned to first conformer: 5846 Chain: "B" Number of atoms: 5923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5923 Classifications: {'peptide': 740} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 711} Chain breaks: 1 Chain: "C" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2020 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain: "V" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 492 Classifications: {'RNA': 23} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 11, 'rna3p': 11} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 455 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 455 " occ=0.50 Time building chain proxies: 10.27, per 1000 atoms: 0.72 Number of scatterers: 14176 At special positions: 0 Unit cell: (96.39, 115.83, 117.45, 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 93 16.00 P 23 15.00 O 2720 8.00 N 2477 7.00 C 8863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 3.3 seconds 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 17 sheets defined 51.0% alpha, 13.0% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 4.057A pdb=" N ASN A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.637A pdb=" N TYR A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 removed outlier: 3.844A pdb=" N MET A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.561A 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 183 Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.618A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 346 removed outlier: 3.913A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.625A pdb=" N SER A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.619A 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: 3.714A pdb=" N GLU A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 4.041A pdb=" N GLU A 533 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 removed outlier: 3.549A pdb=" N GLU A 575 " --> pdb=" O LYS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 599 removed outlier: 4.168A pdb=" N LEU A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 removed outlier: 3.856A pdb=" N ASN A 609 " --> pdb=" O PRO A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 3.685A pdb=" N GLU A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 689 removed outlier: 3.560A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 689 " --> pdb=" O ILE A 685 " (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: 3.793A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (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: 3.520A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.537A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (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: 3.613A 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 274 through 289 removed outlier: 3.622A pdb=" N MET B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.540A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 326 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.646A 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 371 through 376 removed outlier: 4.083A pdb=" N SER B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.735A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 414 through 427 removed outlier: 4.230A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.643A pdb=" N LYS B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.616A 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 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.541A 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 613 through 616 removed outlier: 3.661A pdb=" N MET B 616 " --> pdb=" O TRP B 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.876A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.537A pdb=" N ILE B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 0 through 13 removed outlier: 3.612A pdb=" N ILE C 4 " --> pdb=" O GLY C 0 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.979A pdb=" N ILE C 31 " --> pdb=" O MET C 28 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS C 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 34 " --> pdb=" O ILE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.685A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.512A pdb=" N ILE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.830A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.519A pdb=" N HIS C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.743A pdb=" N GLN C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU C 161 " --> pdb=" O ARG C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.938A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.104A 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: 3.554A pdb=" N VAL C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 230' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.682A pdb=" N PHE A 53 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 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: 6.365A 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: 7.058A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 552 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 544 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 554 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP A 542 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 556 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N CYS A 536 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE A 322 " --> pdb=" O CYS A 536 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU A 538 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ALA A 320 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE A 540 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.378A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 373 removed outlier: 5.877A pdb=" N GLU A 372 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLN B 367 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.543A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (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 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 193 removed outlier: 3.778A pdb=" N LYS B 198 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.802A 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 492 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 135 removed outlier: 4.536A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.658A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1864 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: 4.50 Time building geometry restraints manager: 5.44 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: 3932 1.33 - 1.45: 2681 1.45 - 1.57: 7691 1.57 - 1.69: 44 1.69 - 1.81: 162 Bond restraints: 14510 Sorted by residual: bond pdb=" CA SER A 504 " pdb=" CB SER A 504 " ideal model delta sigma weight residual 1.531 1.488 0.043 3.12e-02 1.03e+03 1.88e+00 bond pdb=" CB VAL A 695 " pdb=" CG2 VAL A 695 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG1 ILE C 67 " pdb=" CD1 ILE C 67 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.51e+00 bond pdb=" C GLU A 604 " pdb=" N PRO A 605 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.28e-02 6.10e+03 1.47e+00 bond pdb=" CA ILE A 689 " pdb=" CB ILE A 689 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.35e+00 ... (remaining 14505 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.85: 414 105.85 - 112.93: 7673 112.93 - 120.01: 5251 120.01 - 127.10: 6129 127.10 - 134.18: 204 Bond angle restraints: 19671 Sorted by residual: angle pdb=" CA ARG B 734 " pdb=" C ARG B 734 " pdb=" N ILE B 735 " ideal model delta sigma weight residual 116.84 124.94 -8.10 1.71e+00 3.42e-01 2.24e+01 angle pdb=" C GLY B 733 " pdb=" N ARG B 734 " pdb=" CA ARG B 734 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" CA ARG B 734 " pdb=" C ARG B 734 " pdb=" O ARG B 734 " ideal model delta sigma weight residual 120.51 115.35 5.16 1.43e+00 4.89e-01 1.30e+01 angle pdb=" C HIS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 128.19 -6.65 1.91e+00 2.74e-01 1.21e+01 angle pdb=" N ILE A 302 " pdb=" CA ILE A 302 " pdb=" C ILE A 302 " ideal model delta sigma weight residual 108.95 105.69 3.26 9.80e-01 1.04e+00 1.11e+01 ... (remaining 19666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 7921 17.36 - 34.71: 679 34.71 - 52.07: 189 52.07 - 69.42: 57 69.42 - 86.78: 15 Dihedral angle restraints: 8861 sinusoidal: 3913 harmonic: 4948 Sorted by residual: dihedral pdb=" CA GLY B 733 " pdb=" C GLY B 733 " pdb=" N ARG B 734 " pdb=" CA ARG B 734 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ILE A 481 " pdb=" C ILE A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS B 152 " pdb=" C LYS B 152 " pdb=" N ASN B 153 " pdb=" CA ASN B 153 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 8858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1397 0.040 - 0.080: 589 0.080 - 0.120: 137 0.120 - 0.160: 30 0.160 - 0.200: 6 Chirality restraints: 2159 Sorted by residual: chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CB ILE B 484 " pdb=" CA ILE B 484 " pdb=" CG1 ILE B 484 " pdb=" CG2 ILE B 484 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 2156 not shown) Planarity restraints: 2449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.031 2.00e-02 2.50e+03 1.41e-02 5.48e+00 pdb=" N9 A V 7 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 27 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO A 28 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.029 2.00e-02 2.50e+03 1.32e-02 4.77e+00 pdb=" N9 A V 4 " 0.031 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.004 2.00e-02 2.50e+03 ... (remaining 2446 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3766 2.80 - 3.32: 11910 3.32 - 3.85: 24212 3.85 - 4.37: 29427 4.37 - 4.90: 50140 Nonbonded interactions: 119455 Sorted by model distance: nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.273 2.440 nonbonded pdb=" O ILE B 219 " pdb=" OG1 THR B 223 " model vdw 2.278 2.440 nonbonded pdb=" O ALA B 113 " pdb=" OG1 THR B 117 " model vdw 2.278 2.440 nonbonded pdb=" OE1 GLU A 588 " pdb=" OG1 THR B 543 " model vdw 2.287 2.440 nonbonded pdb=" O ALA B 659 " pdb=" OH TYR C 111 " model vdw 2.297 2.440 ... (remaining 119450 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: 2.190 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: 0.220 Set scattering table: 0.140 Process input model: 44.350 Find NCS groups from input model: 0.440 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 0.058 14510 Z= 0.353 Angle : 0.684 12.301 19671 Z= 0.391 Chirality : 0.046 0.200 2159 Planarity : 0.006 0.055 2449 Dihedral : 14.960 86.776 5661 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.25 % Allowed : 8.91 % Favored : 85.84 % 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: -3.41 (0.16), residues: 1686 helix: -2.10 (0.14), residues: 773 sheet: -1.77 (0.35), residues: 172 loop : -2.45 (0.18), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 49 HIS 0.006 0.001 HIS B 32 PHE 0.021 0.002 PHE B 505 TYR 0.017 0.002 TYR B 557 ARG 0.003 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 300 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.5435 (OUTLIER) cc_final: 0.5028 (mp) REVERT: A 97 MET cc_start: 0.7774 (tmm) cc_final: 0.7551 (ttp) REVERT: A 111 ASP cc_start: 0.7305 (t0) cc_final: 0.6711 (t0) REVERT: A 142 ASN cc_start: 0.6742 (OUTLIER) cc_final: 0.5927 (t0) REVERT: A 346 LYS cc_start: 0.8469 (tttt) cc_final: 0.8154 (mmtt) REVERT: A 397 LYS cc_start: 0.8407 (tttt) cc_final: 0.8113 (ttmt) REVERT: A 419 GLU cc_start: 0.7288 (tp30) cc_final: 0.7021 (mm-30) REVERT: A 606 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: B 191 ILE cc_start: 0.8342 (mt) cc_final: 0.7813 (pt) REVERT: B 205 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8238 (mp) REVERT: B 353 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7361 (ptm160) REVERT: B 368 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7868 (pt) REVERT: B 554 ASP cc_start: 0.8241 (t70) cc_final: 0.8024 (t0) REVERT: B 685 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7479 (t70) REVERT: B 687 ARG cc_start: 0.6709 (mtt180) cc_final: 0.6354 (ttp80) REVERT: B 706 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7465 (mmm-85) REVERT: B 742 GLU cc_start: 0.6890 (tp30) cc_final: 0.6347 (tt0) REVERT: C 8 MET cc_start: 0.6869 (tmt) cc_final: 0.6644 (tpt) REVERT: C 12 LYS cc_start: 0.7196 (mmtt) cc_final: 0.6982 (mtmt) REVERT: C 32 LYS cc_start: 0.7945 (tttt) cc_final: 0.7427 (tmtt) REVERT: C 134 LYS cc_start: 0.8272 (mttt) cc_final: 0.7743 (mmmt) REVERT: C 197 LYS cc_start: 0.6508 (mttt) cc_final: 0.6098 (mmtt) REVERT: C 213 ARG cc_start: 0.7021 (ttt90) cc_final: 0.6643 (ttp80) REVERT: C 215 THR cc_start: 0.7573 (p) cc_final: 0.7298 (p) REVERT: C 220 ILE cc_start: 0.8552 (mm) cc_final: 0.8251 (mm) outliers start: 79 outliers final: 28 residues processed: 362 average time/residue: 0.3079 time to fit residues: 153.6532 Evaluate side-chains 246 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 211 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 232 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.0030 chunk 155 optimal weight: 5.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN A 180 GLN A 217 GLN A 586 GLN A 665 GLN B 32 HIS B 158 ASN B 428 GLN B 628 ASN B 634 HIS B 679 GLN B 694 GLN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14510 Z= 0.142 Angle : 0.463 6.140 19671 Z= 0.249 Chirality : 0.039 0.179 2159 Planarity : 0.004 0.044 2449 Dihedral : 11.646 85.082 2258 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.46 % Allowed : 12.70 % Favored : 83.84 % 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: -1.43 (0.19), residues: 1686 helix: 0.04 (0.17), residues: 785 sheet: -1.28 (0.38), residues: 167 loop : -1.95 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 49 HIS 0.012 0.001 HIS A 41 PHE 0.014 0.001 PHE A 53 TYR 0.018 0.001 TYR B 557 ARG 0.004 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 232 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4921 (mp) REVERT: A 97 MET cc_start: 0.7880 (tmm) cc_final: 0.7509 (ttp) REVERT: A 111 ASP cc_start: 0.7541 (t0) cc_final: 0.6731 (t0) REVERT: A 142 ASN cc_start: 0.6562 (OUTLIER) cc_final: 0.5833 (t0) REVERT: A 346 LYS cc_start: 0.8445 (tttt) cc_final: 0.8149 (mmtt) REVERT: A 405 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7883 (mt-10) REVERT: A 606 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: B 191 ILE cc_start: 0.8075 (mt) cc_final: 0.7644 (pt) REVERT: B 353 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7153 (ptm160) REVERT: B 687 ARG cc_start: 0.6624 (mtt180) cc_final: 0.6306 (ttp-110) REVERT: C 8 MET cc_start: 0.6937 (tmt) cc_final: 0.6651 (tpt) REVERT: C 32 LYS cc_start: 0.7939 (tttt) cc_final: 0.7459 (tmtt) REVERT: C 134 LYS cc_start: 0.8172 (mttt) cc_final: 0.7765 (mmmt) REVERT: C 197 LYS cc_start: 0.6549 (mttt) cc_final: 0.6070 (mmtt) REVERT: C 213 ARG cc_start: 0.6914 (ttt90) cc_final: 0.6348 (ttp80) outliers start: 52 outliers final: 30 residues processed: 266 average time/residue: 0.2738 time to fit residues: 105.0307 Evaluate side-chains 230 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 155 optimal weight: 0.4980 chunk 168 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 GLN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14510 Z= 0.162 Angle : 0.464 9.244 19671 Z= 0.246 Chirality : 0.039 0.166 2159 Planarity : 0.003 0.039 2449 Dihedral : 11.249 84.453 2233 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.12 % Allowed : 14.36 % Favored : 82.51 % 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: -0.65 (0.19), residues: 1686 helix: 0.89 (0.18), residues: 786 sheet: -1.05 (0.38), residues: 169 loop : -1.76 (0.20), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 49 HIS 0.008 0.001 HIS A 41 PHE 0.020 0.001 PHE B 740 TYR 0.018 0.001 TYR B 557 ARG 0.005 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 215 time to evaluate : 1.663 Fit side-chains REVERT: A 55 ASP cc_start: 0.6589 (t0) cc_final: 0.6385 (t0) REVERT: A 72 LEU cc_start: 0.5253 (OUTLIER) cc_final: 0.4897 (mp) REVERT: A 97 MET cc_start: 0.7960 (tmm) cc_final: 0.7571 (ttp) REVERT: A 111 ASP cc_start: 0.7556 (t0) cc_final: 0.6782 (t0) REVERT: A 142 ASN cc_start: 0.6445 (OUTLIER) cc_final: 0.5752 (t0) REVERT: A 346 LYS cc_start: 0.8436 (tttt) cc_final: 0.8150 (mmtt) REVERT: A 351 LYS cc_start: 0.8705 (mttt) cc_final: 0.8391 (mtmt) REVERT: A 405 GLU cc_start: 0.8207 (mm-30) cc_final: 0.8005 (mt-10) REVERT: A 606 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: B 191 ILE cc_start: 0.8034 (mt) cc_final: 0.7653 (pt) REVERT: B 353 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7341 (ptm160) REVERT: B 429 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7028 (mtp180) REVERT: B 687 ARG cc_start: 0.6657 (mtt180) cc_final: 0.6381 (ttp-110) REVERT: C 8 MET cc_start: 0.7084 (tmt) cc_final: 0.6759 (tpt) REVERT: C 32 LYS cc_start: 0.7943 (tttt) cc_final: 0.7450 (tmtt) REVERT: C 134 LYS cc_start: 0.8164 (mttt) cc_final: 0.7749 (mmmt) REVERT: C 197 LYS cc_start: 0.6606 (mttt) cc_final: 0.6055 (mmtt) outliers start: 47 outliers final: 31 residues processed: 250 average time/residue: 0.2859 time to fit residues: 102.1797 Evaluate side-chains 237 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 GLN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14510 Z= 0.389 Angle : 0.563 7.426 19671 Z= 0.297 Chirality : 0.044 0.196 2159 Planarity : 0.004 0.041 2449 Dihedral : 11.423 88.891 2230 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.86 % Allowed : 15.29 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.56 (0.20), residues: 1686 helix: 1.00 (0.18), residues: 785 sheet: -1.00 (0.37), residues: 176 loop : -1.79 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 49 HIS 0.006 0.001 HIS A 41 PHE 0.021 0.002 PHE A 515 TYR 0.019 0.002 TYR B 555 ARG 0.005 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 55 ASP cc_start: 0.6674 (t0) cc_final: 0.6404 (t0) REVERT: A 72 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4974 (mt) REVERT: A 97 MET cc_start: 0.7994 (tmm) cc_final: 0.7621 (ttp) REVERT: A 142 ASN cc_start: 0.6492 (OUTLIER) cc_final: 0.5842 (t0) REVERT: A 346 LYS cc_start: 0.8468 (tttt) cc_final: 0.8159 (mmtt) REVERT: A 351 LYS cc_start: 0.8694 (mttt) cc_final: 0.8353 (mtmt) REVERT: B 112 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: B 191 ILE cc_start: 0.8056 (mt) cc_final: 0.7601 (pt) REVERT: B 246 MET cc_start: 0.8485 (tpt) cc_final: 0.8281 (tpt) REVERT: B 413 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7504 (t0) REVERT: B 429 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7062 (mtp180) REVERT: B 687 ARG cc_start: 0.6701 (mtt180) cc_final: 0.6416 (ttp-110) REVERT: C 32 LYS cc_start: 0.8025 (tttt) cc_final: 0.7531 (tmtt) REVERT: C 51 MET cc_start: 0.8735 (mmp) cc_final: 0.8532 (mmp) REVERT: C 134 LYS cc_start: 0.8138 (mttt) cc_final: 0.7716 (mmmt) REVERT: C 175 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5288 (mmp-170) REVERT: C 197 LYS cc_start: 0.6862 (mttt) cc_final: 0.6269 (mmtm) outliers start: 58 outliers final: 38 residues processed: 234 average time/residue: 0.2831 time to fit residues: 94.8404 Evaluate side-chains 228 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 353 ARG 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 413 ASN Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14510 Z= 0.140 Angle : 0.450 6.449 19671 Z= 0.239 Chirality : 0.039 0.178 2159 Planarity : 0.003 0.037 2449 Dihedral : 11.098 86.256 2229 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.59 % Allowed : 16.62 % Favored : 80.78 % 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: -0.10 (0.20), residues: 1686 helix: 1.43 (0.19), residues: 784 sheet: -0.72 (0.40), residues: 157 loop : -1.60 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 49 HIS 0.006 0.000 HIS A 41 PHE 0.022 0.001 PHE B 740 TYR 0.017 0.001 TYR B 557 ARG 0.005 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: A 55 ASP cc_start: 0.6630 (t0) cc_final: 0.6322 (t0) REVERT: A 72 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.5037 (mp) REVERT: A 97 MET cc_start: 0.8016 (tmm) cc_final: 0.7614 (ttp) REVERT: A 346 LYS cc_start: 0.8457 (tttt) cc_final: 0.8143 (mmtt) REVERT: A 351 LYS cc_start: 0.8654 (mttt) cc_final: 0.8341 (mtmt) REVERT: B 112 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: B 191 ILE cc_start: 0.8006 (mt) cc_final: 0.7623 (pt) REVERT: B 353 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7361 (ptm160) REVERT: B 429 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6989 (mtp180) REVERT: B 687 ARG cc_start: 0.6559 (mtt180) cc_final: 0.6272 (ttp-110) REVERT: C 32 LYS cc_start: 0.7932 (tttt) cc_final: 0.7468 (tmtt) REVERT: C 197 LYS cc_start: 0.6773 (mttt) cc_final: 0.6203 (mmtt) outliers start: 39 outliers final: 32 residues processed: 227 average time/residue: 0.2810 time to fit residues: 91.1883 Evaluate side-chains 222 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.5980 chunk 148 optimal weight: 0.0670 chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14510 Z= 0.130 Angle : 0.438 6.656 19671 Z= 0.233 Chirality : 0.038 0.157 2159 Planarity : 0.003 0.037 2449 Dihedral : 10.953 84.888 2226 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.73 % Allowed : 16.49 % Favored : 80.78 % 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: 0.06 (0.20), residues: 1686 helix: 1.56 (0.19), residues: 790 sheet: -0.70 (0.41), residues: 155 loop : -1.53 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 49 HIS 0.005 0.000 HIS A 41 PHE 0.024 0.001 PHE B 740 TYR 0.017 0.001 TYR B 557 ARG 0.005 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 55 ASP cc_start: 0.6638 (t0) cc_final: 0.6379 (t0) REVERT: A 72 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5134 (mp) REVERT: A 97 MET cc_start: 0.8029 (tmm) cc_final: 0.7585 (ttp) REVERT: A 346 LYS cc_start: 0.8454 (tttt) cc_final: 0.8174 (mttm) REVERT: B 112 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6944 (m-30) REVERT: B 191 ILE cc_start: 0.7950 (mt) cc_final: 0.7647 (pt) REVERT: B 429 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6996 (mtp180) REVERT: C 32 LYS cc_start: 0.7925 (tttt) cc_final: 0.7454 (tmtt) REVERT: C 134 LYS cc_start: 0.8137 (mttt) cc_final: 0.7750 (mmmt) REVERT: C 197 LYS cc_start: 0.6741 (mttt) cc_final: 0.6168 (mmtt) outliers start: 41 outliers final: 32 residues processed: 222 average time/residue: 0.2777 time to fit residues: 89.1248 Evaluate side-chains 216 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 120 optimal weight: 0.0670 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 103 optimal weight: 0.0070 chunk 100 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14510 Z= 0.194 Angle : 0.464 6.549 19671 Z= 0.245 Chirality : 0.039 0.149 2159 Planarity : 0.003 0.037 2449 Dihedral : 10.873 85.834 2220 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.79 % Allowed : 16.82 % Favored : 80.39 % 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: 0.12 (0.20), residues: 1686 helix: 1.61 (0.19), residues: 789 sheet: -0.65 (0.41), residues: 162 loop : -1.50 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 49 HIS 0.005 0.001 HIS A 41 PHE 0.020 0.001 PHE B 740 TYR 0.018 0.001 TYR B 557 ARG 0.006 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 55 ASP cc_start: 0.6663 (t0) cc_final: 0.6418 (t0) REVERT: A 72 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.5134 (mp) REVERT: A 97 MET cc_start: 0.8032 (tmm) cc_final: 0.7716 (ttp) REVERT: A 346 LYS cc_start: 0.8452 (tttt) cc_final: 0.8171 (mttm) REVERT: B 112 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6951 (m-30) REVERT: B 191 ILE cc_start: 0.7963 (mt) cc_final: 0.7637 (pt) REVERT: B 429 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7016 (mtp180) REVERT: B 687 ARG cc_start: 0.6584 (mtt180) cc_final: 0.6299 (ttp-110) REVERT: C 32 LYS cc_start: 0.7967 (tttt) cc_final: 0.7490 (tmtt) REVERT: C 134 LYS cc_start: 0.8142 (mttt) cc_final: 0.7743 (mmmt) REVERT: C 197 LYS cc_start: 0.6734 (mttt) cc_final: 0.6163 (mmtt) outliers start: 42 outliers final: 35 residues processed: 219 average time/residue: 0.2880 time to fit residues: 90.6613 Evaluate side-chains 224 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN B 394 HIS B 628 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14510 Z= 0.127 Angle : 0.431 6.835 19671 Z= 0.229 Chirality : 0.038 0.148 2159 Planarity : 0.003 0.036 2449 Dihedral : 10.711 84.013 2219 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.79 % Allowed : 16.89 % Favored : 80.32 % 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: 0.38 (0.21), residues: 1686 helix: 1.82 (0.19), residues: 783 sheet: -0.57 (0.41), residues: 167 loop : -1.33 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 49 HIS 0.005 0.000 HIS A 41 PHE 0.020 0.001 PHE B 740 TYR 0.015 0.001 TYR B 557 ARG 0.011 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 196 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5150 (mp) REVERT: A 97 MET cc_start: 0.8017 (tmm) cc_final: 0.7657 (ttp) REVERT: A 346 LYS cc_start: 0.8447 (tttt) cc_final: 0.8165 (mttm) REVERT: B 27 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8627 (p0) REVERT: B 112 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: B 191 ILE cc_start: 0.7920 (mt) cc_final: 0.7673 (pt) REVERT: B 429 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7060 (mtp180) REVERT: C 32 LYS cc_start: 0.7915 (tttt) cc_final: 0.7450 (tmtt) REVERT: C 55 TYR cc_start: 0.8005 (m-80) cc_final: 0.7296 (m-80) REVERT: C 134 LYS cc_start: 0.8137 (mttt) cc_final: 0.7753 (mmmt) REVERT: C 197 LYS cc_start: 0.6720 (mttt) cc_final: 0.6210 (mmtt) outliers start: 42 outliers final: 34 residues processed: 227 average time/residue: 0.2889 time to fit residues: 94.3126 Evaluate side-chains 226 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN B 363 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14510 Z= 0.284 Angle : 0.510 6.735 19671 Z= 0.268 Chirality : 0.041 0.144 2159 Planarity : 0.004 0.038 2449 Dihedral : 10.896 87.038 2215 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.99 % Allowed : 16.95 % Favored : 80.05 % 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: 0.15 (0.20), residues: 1686 helix: 1.61 (0.19), residues: 789 sheet: -0.55 (0.39), residues: 174 loop : -1.49 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 49 HIS 0.008 0.001 HIS B 363 PHE 0.025 0.001 PHE B 740 TYR 0.020 0.001 TYR B 557 ARG 0.008 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.743 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5082 (mp) REVERT: A 97 MET cc_start: 0.8037 (tmm) cc_final: 0.7696 (ttp) REVERT: A 346 LYS cc_start: 0.8457 (tttt) cc_final: 0.8159 (mttm) REVERT: B 27 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8687 (p0) REVERT: B 112 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: B 191 ILE cc_start: 0.7988 (mt) cc_final: 0.7638 (pt) REVERT: B 429 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7043 (mtp180) REVERT: B 687 ARG cc_start: 0.6644 (mtt180) cc_final: 0.6344 (ttp-110) REVERT: B 697 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7373 (tm-30) REVERT: C 32 LYS cc_start: 0.8011 (tttt) cc_final: 0.7516 (tmtt) REVERT: C 134 LYS cc_start: 0.8152 (mttt) cc_final: 0.7733 (mmmt) REVERT: C 197 LYS cc_start: 0.6848 (mttt) cc_final: 0.6315 (mmtt) outliers start: 45 outliers final: 35 residues processed: 215 average time/residue: 0.3120 time to fit residues: 96.2049 Evaluate side-chains 220 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 135 optimal weight: 0.0270 chunk 14 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14510 Z= 0.151 Angle : 0.453 7.023 19671 Z= 0.239 Chirality : 0.039 0.137 2159 Planarity : 0.003 0.036 2449 Dihedral : 10.772 85.820 2215 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.59 % Allowed : 17.42 % Favored : 79.99 % 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: 0.33 (0.20), residues: 1686 helix: 1.77 (0.19), residues: 788 sheet: -0.47 (0.41), residues: 167 loop : -1.40 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 49 HIS 0.005 0.001 HIS A 41 PHE 0.027 0.001 PHE B 740 TYR 0.017 0.001 TYR B 557 ARG 0.008 0.000 ARG B 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8021 (tmm) cc_final: 0.7652 (ttp) REVERT: A 346 LYS cc_start: 0.8445 (tttt) cc_final: 0.8156 (mttm) REVERT: A 508 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7538 (m110) REVERT: B 27 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8655 (p0) REVERT: B 112 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: B 191 ILE cc_start: 0.7945 (mt) cc_final: 0.7677 (pt) REVERT: B 429 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6986 (mtp180) REVERT: C 32 LYS cc_start: 0.7975 (tttt) cc_final: 0.7487 (tmtt) REVERT: C 134 LYS cc_start: 0.8144 (mttt) cc_final: 0.7762 (mmmt) REVERT: C 197 LYS cc_start: 0.6819 (mttt) cc_final: 0.6284 (mmtt) outliers start: 39 outliers final: 34 residues processed: 216 average time/residue: 0.2823 time to fit residues: 87.0796 Evaluate side-chains 224 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.0040 chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.118695 restraints weight = 31604.796| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.97 r_work: 0.3092 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14510 Z= 0.141 Angle : 0.448 6.671 19671 Z= 0.237 Chirality : 0.038 0.138 2159 Planarity : 0.003 0.039 2449 Dihedral : 10.698 85.075 2213 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.46 % Allowed : 17.75 % Favored : 79.79 % 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: 0.53 (0.21), residues: 1686 helix: 1.93 (0.19), residues: 776 sheet: -0.43 (0.41), residues: 167 loop : -1.22 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 49 HIS 0.005 0.000 HIS A 41 PHE 0.027 0.001 PHE B 740 TYR 0.016 0.001 TYR B 557 ARG 0.010 0.000 ARG A 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.87 seconds wall clock time: 62 minutes 37.79 seconds (3757.79 seconds total)