Starting phenix.real_space_refine on Sun Dec 10 13:28:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/12_2023/6t0s_10358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/12_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_10358/12_2023/6t0s_10358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/12_2023/6t0s_10358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/12_2023/6t0s_10358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0s_10358/12_2023/6t0s_10358.pdb" } resolution = 3.04 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: 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.78, 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: 5.71 Conformation dependent library (CDL) restraints added in 3.5 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: 5.45 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: 5.15 Time building geometry restraints manager: 6.14 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: 8257 16.88 - 33.76: 640 33.76 - 50.65: 165 50.65 - 67.53: 60 67.53 - 84.41: 18 Dihedral angle restraints: 9140 sinusoidal: 4171 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 9137 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: 1.640 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: 7.320 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 48.670 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.370 ------------------------------------------------------------------------------- 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 : 14.045 84.409 5924 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 % Allowed : 6.41 % Favored : 88.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 49 HIS 0.004 0.001 HIS A 41 PHE 0.015 0.002 PHE A 211 TYR 0.020 0.002 TYR B 557 ARG 0.003 0.000 ARG A 578 *********************** 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 : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 29 residues processed: 362 average time/residue: 0.3083 time to fit residues: 156.3135 Evaluate side-chains 247 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1559 time to fit residues: 10.1349 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15029 Z= 0.191 Angle : 0.491 9.502 20462 Z= 0.258 Chirality : 0.039 0.141 2270 Planarity : 0.004 0.058 2478 Dihedral : 10.950 84.281 2439 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.92 % Allowed : 10.71 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1691 helix: -0.20 (0.17), residues: 826 sheet: -1.01 (0.38), residues: 165 loop : -1.61 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 188 HIS 0.002 0.001 HIS B 605 PHE 0.015 0.001 PHE A 191 TYR 0.021 0.001 TYR B 557 ARG 0.007 0.000 ARG C 175 *********************** 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 251 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 222 time to evaluate : 1.643 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 234 average time/residue: 0.2881 time to fit residues: 98.3266 Evaluate side-chains 217 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 1.655 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1414 time to fit residues: 6.7302 ------------------------------------------------------------------------------- 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: 3.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8407 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15029 Z= 0.346 Angle : 0.567 11.674 20462 Z= 0.294 Chirality : 0.042 0.167 2270 Planarity : 0.005 0.051 2478 Dihedral : 10.998 85.622 2439 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.05 % Allowed : 11.76 % Favored : 86.19 % 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: -0.73 (0.19), residues: 1691 helix: 0.44 (0.18), residues: 823 sheet: -0.88 (0.38), residues: 168 loop : -1.46 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 438 HIS 0.004 0.001 HIS A 41 PHE 0.021 0.002 PHE A 211 TYR 0.025 0.002 TYR B 557 ARG 0.005 0.001 ARG B 118 *********************** 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 : 1.667 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 231 average time/residue: 0.2932 time to fit residues: 98.3221 Evaluate side-chains 209 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1369 time to fit residues: 5.2036 ------------------------------------------------------------------------------- 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: 0.7980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 166 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8385 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15029 Z= 0.243 Angle : 0.515 12.020 20462 Z= 0.267 Chirality : 0.040 0.150 2270 Planarity : 0.004 0.049 2478 Dihedral : 10.937 85.111 2439 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 13.22 % Favored : 84.93 % 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: -0.35 (0.20), residues: 1691 helix: 0.80 (0.18), residues: 827 sheet: -0.81 (0.37), residues: 168 loop : -1.30 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.002 0.001 HIS B 605 PHE 0.016 0.001 PHE A 211 TYR 0.021 0.002 TYR A 131 ARG 0.006 0.000 ARG A 124 *********************** 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 237 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 1.617 Fit side-chains outliers start: 28 outliers final: 14 residues processed: 224 average time/residue: 0.2894 time to fit residues: 94.0074 Evaluate side-chains 214 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1574 time to fit residues: 6.1806 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 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: 2.9990 chunk 149 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8391 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15029 Z= 0.258 Angle : 0.513 12.530 20462 Z= 0.266 Chirality : 0.040 0.153 2270 Planarity : 0.004 0.049 2478 Dihedral : 10.910 85.425 2439 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.26 % Allowed : 13.68 % Favored : 85.06 % 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: 1691 helix: 0.99 (0.18), residues: 827 sheet: -0.66 (0.37), residues: 168 loop : -1.20 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.003 0.001 HIS B 605 PHE 0.017 0.001 PHE A 211 TYR 0.021 0.002 TYR A 131 ARG 0.007 0.000 ARG A 179 *********************** 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 220 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 1.699 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 216 average time/residue: 0.2884 time to fit residues: 91.2259 Evaluate side-chains 206 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1416 time to fit residues: 5.2449 ------------------------------------------------------------------------------- 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: 0.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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: 0.8351 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15029 Z= 0.155 Angle : 0.463 11.557 20462 Z= 0.242 Chirality : 0.038 0.146 2270 Planarity : 0.004 0.049 2478 Dihedral : 10.844 84.918 2439 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.79 % Allowed : 14.34 % Favored : 84.86 % 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: 1.26 (0.19), residues: 828 sheet: -0.47 (0.38), residues: 172 loop : -1.06 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.002 0.000 HIS A 41 PHE 0.012 0.001 PHE A 211 TYR 0.021 0.001 TYR A 131 ARG 0.006 0.000 ARG B 118 *********************** 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 223 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 1.612 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 218 average time/residue: 0.2942 time to fit residues: 92.9295 Evaluate side-chains 207 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1303 time to fit residues: 3.4207 ------------------------------------------------------------------------------- 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: 6.9990 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.8385 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 0.046 15029 Z= 0.254 Angle : 0.511 13.555 20462 Z= 0.265 Chirality : 0.040 0.149 2270 Planarity : 0.004 0.048 2478 Dihedral : 10.844 85.660 2439 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.06 % Allowed : 14.28 % Favored : 84.67 % 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: 0.18 (0.20), residues: 1691 helix: 1.23 (0.19), residues: 825 sheet: -0.47 (0.38), residues: 172 loop : -1.05 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.002 0.001 HIS B 605 PHE 0.017 0.001 PHE A 211 TYR 0.020 0.002 TYR B 557 ARG 0.007 0.000 ARG C 175 *********************** 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 219 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 1.939 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 211 average time/residue: 0.2953 time to fit residues: 92.1042 Evaluate side-chains 206 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.622 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1452 time to fit residues: 5.0420 ------------------------------------------------------------------------------- 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: 0.9980 chunk 49 optimal weight: 4.9990 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: 2.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15029 Z= 0.241 Angle : 0.507 13.466 20462 Z= 0.262 Chirality : 0.040 0.146 2270 Planarity : 0.004 0.048 2478 Dihedral : 10.841 85.464 2439 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.12 % Allowed : 14.21 % Favored : 84.67 % 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: 0.20 (0.20), residues: 1691 helix: 1.23 (0.19), residues: 825 sheet: -0.50 (0.38), residues: 173 loop : -1.02 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.002 0.001 HIS B 394 PHE 0.017 0.001 PHE A 191 TYR 0.022 0.002 TYR A 131 ARG 0.007 0.000 ARG C 175 *********************** 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 218 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.605 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 212 average time/residue: 0.2888 time to fit residues: 90.0414 Evaluate side-chains 204 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 197 time to evaluate : 1.622 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1475 time to fit residues: 4.1882 ------------------------------------------------------------------------------- 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: 1.9990 chunk 158 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8372 moved from start: 0.2398 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= 0.208 Angle : 0.489 12.888 20462 Z= 0.253 Chirality : 0.039 0.151 2270 Planarity : 0.004 0.048 2478 Dihedral : 10.820 85.393 2439 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.26 % Allowed : 15.47 % Favored : 84.27 % 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: 0.31 (0.21), residues: 1691 helix: 1.32 (0.19), residues: 825 sheet: -0.42 (0.38), residues: 173 loop : -0.96 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.002 0.001 HIS B 465 PHE 0.015 0.001 PHE A 191 TYR 0.021 0.001 TYR A 131 ARG 0.007 0.000 ARG C 175 *********************** 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 211 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 1.633 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 209 average time/residue: 0.3506 time to fit residues: 108.7069 Evaluate side-chains 202 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1356 time to fit residues: 2.7180 ------------------------------------------------------------------------------- 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: 4.9990 chunk 77 optimal weight: 0.0270 chunk 113 optimal weight: 0.5980 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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: 0.8320 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15029 Z= 0.129 Angle : 0.457 12.369 20462 Z= 0.236 Chirality : 0.037 0.156 2270 Planarity : 0.003 0.047 2478 Dihedral : 10.767 85.153 2439 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.33 % Allowed : 15.93 % Favored : 83.74 % 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: 0.52 (0.21), residues: 1691 helix: 1.50 (0.19), residues: 829 sheet: -0.47 (0.37), residues: 182 loop : -0.83 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 49 HIS 0.002 0.001 HIS B 465 PHE 0.012 0.001 PHE A 191 TYR 0.023 0.001 TYR A 131 ARG 0.008 0.000 ARG C 175 ********************** 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 222 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 1.694 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 218 average time/residue: 0.2907 time to fit residues: 92.5628 Evaluate side-chains 204 residues out of total 1511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1597 time to fit residues: 3.1089 ------------------------------------------------------------------------------- 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: 4.9990 chunk 125 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.145600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119327 restraints weight = 24264.744| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.64 r_work: 0.3101 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15029 Z= 0.279 Angle : 0.526 13.289 20462 Z= 0.271 Chirality : 0.040 0.150 2270 Planarity : 0.004 0.049 2478 Dihedral : 10.786 86.070 2439 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.59 % Allowed : 15.80 % Favored : 83.61 % 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: 0.39 (0.21), residues: 1691 helix: 1.35 (0.19), residues: 827 sheet: -0.49 (0.38), residues: 182 loop : -0.85 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 49 HIS 0.003 0.001 HIS B 605 PHE 0.017 0.001 PHE A 211 TYR 0.020 0.002 TYR B 557 ARG 0.006 0.000 ARG C 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3313.23 seconds wall clock time: 61 minutes 1.18 seconds (3661.18 seconds total)