Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 08:43:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/04_2023/6t0s_10358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/04_2023/6t0s_10358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/04_2023/6t0s_10358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/04_2023/6t0s_10358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/04_2023/6t0s_10358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/04_2023/6t0s_10358.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 6 Type Number sf(0) Gaussians P 43 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 9083 2.51 5 N 2553 2.21 5 O 2878 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 "A ARG 610": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B TYR 497": "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 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 708, 5769 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 25, 'TRANS': 682} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 708, 5769 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 25, 'TRANS': 682} Chain breaks: 2 bond proxies already assigned to first conformer: 5879 Chain: "B" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5947 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 714} Chain breaks: 1 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 690 Classifications: {'RNA': 33} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 12} Link IDs: {'rna2p': 12, 'rna3p': 20} Chain breaks: 2 Chain: "M" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 491 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 491 " occ=0.50 Time building chain proxies: 10.85, per 1000 atoms: 0.74 Number of scatterers: 14651 At special positions: 0 Unit cell: (97.2, 119.07, 117.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 43 15.00 Mg 2 11.99 O 2878 8.00 N 2553 7.00 C 9083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 3.0 seconds 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 17 sheets defined 50.7% alpha, 13.8% beta 11 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.560A pdb=" N PHE A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 96 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.523A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.628A pdb=" N ALA A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 346 removed outlier: 3.801A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 399 through 409 removed outlier: 4.522A pdb=" N GLN A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 Processing helix chain 'A' and resid 528 through 533 removed outlier: 4.175A pdb=" N GLU A 533 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 578 through 598 removed outlier: 3.780A pdb=" N GLN A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 4.269A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 692 through 713 Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.580A pdb=" N ILE B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.616A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 4.064A pdb=" N THR B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.618A pdb=" N GLY B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 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 247 through 266 removed outlier: 4.650A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.744A 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 369 through 373 removed outlier: 3.731A pdb=" N LEU B 373 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.700A 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 412 through 427 removed outlier: 3.533A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.740A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 removed outlier: 3.557A pdb=" N LEU B 509 " --> pdb=" O SER B 506 " (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 583 removed outlier: 3.738A pdb=" N ILE B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 removed outlier: 3.631A 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 697 removed outlier: 3.703A pdb=" N GLU B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 0 through 13 removed outlier: 3.504A pdb=" N ILE C 4 " --> pdb=" O GLY C 0 " (cutoff:3.500A) removed outlier: 3.999A 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 24 through 33 removed outlier: 4.288A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.670A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.922A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 4.041A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 removed outlier: 4.151A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.732A 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: 3.993A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.617A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.852A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.657A pdb=" N GLY A 121 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.282A 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: 6.803A pdb=" N AARG A 491 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP A 486 " --> pdb=" O AARG A 491 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 475 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.508A pdb=" N LYS A 318 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N MET A 543 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA A 320 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N GLY A 541 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 322 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU A 539 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 556 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 542 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 554 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 544 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE A 552 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N AARG A 491 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP A 486 " --> pdb=" O AARG A 491 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 374 removed outlier: 5.952A pdb=" N GLU A 372 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLN B 367 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N MET A 374 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 623 through 626 removed outlier: 6.593A 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 127 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 187 Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 192 Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.920A pdb=" N THR B 226 " --> 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: 4.628A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.259A 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: 6.264A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4111 1.34 - 1.45: 2727 1.45 - 1.57: 7949 1.57 - 1.69: 82 1.69 - 1.81: 160 Bond restraints: 15029 Sorted by residual: bond pdb=" N THR C 176 " pdb=" CA THR C 176 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.43e+00 bond pdb=" N LEU C 177 " pdb=" CA LEU C 177 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.25e-02 6.40e+03 5.62e+00 bond pdb=" N ARG C 175 " pdb=" CA ARG C 175 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.20e-02 6.94e+03 5.05e+00 bond pdb=" N GLY C 173 " pdb=" CA GLY C 173 " ideal model delta sigma weight residual 1.449 1.476 -0.027 1.68e-02 3.54e+03 2.50e+00 bond pdb=" N ALA C 174 " pdb=" CA ALA C 174 " ideal model delta sigma weight residual 1.464 1.482 -0.018 1.20e-02 6.94e+03 2.18e+00 ... (remaining 15024 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.17: 573 106.17 - 113.18: 8074 113.18 - 120.19: 5666 120.19 - 127.20: 5921 127.20 - 134.22: 228 Bond angle restraints: 20462 Sorted by residual: angle pdb=" CA GLY C 173 " pdb=" C GLY C 173 " pdb=" O GLY C 173 " ideal model delta sigma weight residual 122.01 118.21 3.80 1.19e+00 7.06e-01 1.02e+01 angle pdb=" N LEU B 509 " pdb=" CA LEU B 509 " pdb=" C LEU B 509 " ideal model delta sigma weight residual 109.81 116.19 -6.38 2.21e+00 2.05e-01 8.32e+00 angle pdb=" CA LEU B 509 " pdb=" C LEU B 509 " pdb=" N PRO B 510 " ideal model delta sigma weight residual 118.44 122.74 -4.30 1.59e+00 3.96e-01 7.31e+00 angle pdb=" CA TRP C 49 " pdb=" CB TRP C 49 " pdb=" CG TRP C 49 " ideal model delta sigma weight residual 113.60 118.68 -5.08 1.90e+00 2.77e-01 7.16e+00 angle pdb=" N ALA B 340 " pdb=" CA ALA B 340 " pdb=" C ALA B 340 " ideal model delta sigma weight residual 109.81 115.55 -5.74 2.21e+00 2.05e-01 6.75e+00 ... (remaining 20457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 8232 16.88 - 33.76: 633 33.76 - 50.65: 153 50.65 - 67.53: 38 67.53 - 84.41: 10 Dihedral angle restraints: 9066 sinusoidal: 4097 harmonic: 4969 Sorted by residual: dihedral pdb=" O4' C V 40 " pdb=" C1' C V 40 " pdb=" N1 C V 40 " pdb=" C2 C V 40 " ideal model delta sinusoidal sigma weight residual -128.00 -70.50 -57.50 1 1.70e+01 3.46e-03 1.54e+01 dihedral pdb=" CA LEU A 219 " pdb=" C LEU A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A 583 " pdb=" C SER A 583 " pdb=" N LEU A 584 " pdb=" CA LEU A 584 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 9063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1415 0.033 - 0.066: 611 0.066 - 0.099: 160 0.099 - 0.131: 71 0.131 - 0.164: 13 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CA LEU C 177 " pdb=" N LEU C 177 " pdb=" C LEU C 177 " pdb=" CB LEU C 177 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.52e-01 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 2.49 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 2267 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 137 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO B 138 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 219 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A 220 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO A 620 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.031 5.00e-02 4.00e+02 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 323 2.67 - 3.23: 12366 3.23 - 3.78: 23941 3.78 - 4.34: 33660 4.34 - 4.90: 54129 Nonbonded interactions: 124419 Sorted by model distance: nonbonded pdb=" OD1 ASP B 446 " pdb="MG MG B 802 " model vdw 2.109 2.170 nonbonded pdb=" O ARG C 175 " pdb=" NH1 ARG C 175 " model vdw 2.211 2.520 nonbonded pdb=" O ALA B 113 " pdb=" OG1 THR B 117 " model vdw 2.266 2.440 nonbonded pdb=" O ILE B 219 " pdb=" OG1 THR B 223 " model vdw 2.285 2.440 nonbonded pdb=" O SER B 524 " pdb=" OG1 THR B 528 " model vdw 2.298 2.440 ... (remaining 124414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 7.820 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 47.270 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.003 0.049 15029 Z= 0.219 Angle : 0.596 7.463 20462 Z= 0.345 Chirality : 0.042 0.164 2270 Planarity : 0.006 0.058 2478 Dihedral : 13.173 84.409 5850 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 4.69 % 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: -3.21 (0.16), residues: 1691 helix: -2.20 (0.13), residues: 817 sheet: -1.68 (0.36), residues: 167 loop : -1.95 (0.19), residues: 707 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 310 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 29 residues processed: 362 average time/residue: 0.3139 time to fit residues: 159.6783 Evaluate side-chains 247 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1489 time to fit residues: 9.7507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 100 ASN A 239 ASN A 508 ASN B 367 GLN B 413 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15029 Z= 0.189 Angle : 0.492 9.165 20462 Z= 0.259 Chirality : 0.039 0.144 2270 Planarity : 0.004 0.058 2478 Dihedral : 7.820 84.273 2365 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.85 % 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: -1.36 (0.19), residues: 1691 helix: -0.22 (0.17), residues: 827 sheet: -1.02 (0.38), residues: 165 loop : -1.63 (0.21), residues: 699 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.578 Fit side-chains outliers start: 28 outliers final: 18 residues processed: 226 average time/residue: 0.2877 time to fit residues: 94.3489 Evaluate side-chains 216 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1379 time to fit residues: 6.8891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 508 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 15029 Z= 0.364 Angle : 0.579 11.565 20462 Z= 0.301 Chirality : 0.043 0.171 2270 Planarity : 0.005 0.051 2478 Dihedral : 8.032 85.758 2365 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 2.05 % 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: -0.79 (0.19), residues: 1691 helix: 0.39 (0.18), residues: 822 sheet: -0.88 (0.38), residues: 168 loop : -1.49 (0.21), residues: 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.738 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 230 average time/residue: 0.2937 time to fit residues: 98.3970 Evaluate side-chains 208 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1407 time to fit residues: 5.5277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15029 Z= 0.217 Angle : 0.502 11.751 20462 Z= 0.261 Chirality : 0.039 0.147 2270 Planarity : 0.004 0.049 2478 Dihedral : 7.889 84.993 2365 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.65 % 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: -0.30 (0.20), residues: 1691 helix: 0.85 (0.18), residues: 827 sheet: -0.80 (0.37), residues: 168 loop : -1.29 (0.22), residues: 696 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 211 time to evaluate : 1.598 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 226 average time/residue: 0.2943 time to fit residues: 96.6955 Evaluate side-chains 209 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1635 time to fit residues: 5.8143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 15029 Z= 0.309 Angle : 0.542 12.392 20462 Z= 0.281 Chirality : 0.041 0.164 2270 Planarity : 0.004 0.049 2478 Dihedral : 7.941 85.680 2365 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.59 % 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: -0.21 (0.20), residues: 1691 helix: 0.92 (0.18), residues: 826 sheet: -0.74 (0.37), residues: 168 loop : -1.25 (0.22), residues: 697 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 1.683 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 216 average time/residue: 0.2895 time to fit residues: 92.2126 Evaluate side-chains 207 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1467 time to fit residues: 6.3573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 15029 Z= 0.197 Angle : 0.488 13.185 20462 Z= 0.254 Chirality : 0.039 0.145 2270 Planarity : 0.004 0.049 2478 Dihedral : 7.817 84.980 2365 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.66 % 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: 0.08 (0.20), residues: 1691 helix: 1.16 (0.19), residues: 827 sheet: -0.59 (0.38), residues: 168 loop : -1.11 (0.22), residues: 696 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 1.735 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 211 average time/residue: 0.2904 time to fit residues: 90.2660 Evaluate side-chains 201 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1639 time to fit residues: 4.2933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 15029 Z= 0.228 Angle : 0.497 13.124 20462 Z= 0.258 Chirality : 0.039 0.148 2270 Planarity : 0.004 0.049 2478 Dihedral : 7.790 85.393 2365 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.12 % 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: 0.14 (0.20), residues: 1691 helix: 1.20 (0.19), residues: 827 sheet: -0.55 (0.37), residues: 170 loop : -1.07 (0.23), residues: 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 1.585 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 213 average time/residue: 0.2826 time to fit residues: 87.8558 Evaluate side-chains 205 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1413 time to fit residues: 4.7972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 0.3980 chunk 144 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15029 Z= 0.219 Angle : 0.489 12.880 20462 Z= 0.254 Chirality : 0.039 0.145 2270 Planarity : 0.004 0.051 2478 Dihedral : 7.744 85.389 2365 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.99 % 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: 0.19 (0.21), residues: 1691 helix: 1.23 (0.19), residues: 829 sheet: -0.63 (0.37), residues: 182 loop : -1.00 (0.23), residues: 680 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 1.702 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 207 average time/residue: 0.2933 time to fit residues: 89.2869 Evaluate side-chains 210 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1403 time to fit residues: 5.1576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 101 optimal weight: 0.0270 chunk 163 optimal weight: 1.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 15029 Z= 0.209 Angle : 0.490 12.619 20462 Z= 0.254 Chirality : 0.039 0.144 2270 Planarity : 0.004 0.050 2478 Dihedral : 7.711 85.421 2365 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.40 % 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: 0.29 (0.21), residues: 1691 helix: 1.32 (0.19), residues: 825 sheet: -0.59 (0.37), residues: 182 loop : -0.95 (0.23), residues: 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 1.741 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 202 average time/residue: 0.3026 time to fit residues: 89.5387 Evaluate side-chains 203 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1470 time to fit residues: 3.9404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15029 Z= 0.175 Angle : 0.472 12.028 20462 Z= 0.245 Chirality : 0.038 0.150 2270 Planarity : 0.004 0.046 2478 Dihedral : 7.642 85.362 2365 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1691 helix: 1.41 (0.19), residues: 827 sheet: -0.51 (0.37), residues: 181 loop : -0.90 (0.23), residues: 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 1.735 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 208 average time/residue: 0.3005 time to fit residues: 91.1372 Evaluate side-chains 200 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1890 time to fit residues: 3.3854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 7 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.121331 restraints weight = 24179.687| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.75 r_work: 0.3178 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 15029 Z= 0.127 Angle : 0.464 11.803 20462 Z= 0.241 Chirality : 0.037 0.154 2270 Planarity : 0.004 0.046 2478 Dihedral : 7.557 85.324 2365 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.26 % 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: 0.58 (0.21), residues: 1691 helix: 1.55 (0.19), residues: 830 sheet: -0.43 (0.38), residues: 181 loop : -0.81 (0.23), residues: 680 =============================================================================== Job complete usr+sys time: 3169.93 seconds wall clock time: 58 minutes 32.24 seconds (3512.24 seconds total)