Starting phenix.real_space_refine on Sun Apr 7 15:08:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t12_40952/04_2024/8t12_40952_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t12_40952/04_2024/8t12_40952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t12_40952/04_2024/8t12_40952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t12_40952/04_2024/8t12_40952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t12_40952/04_2024/8t12_40952_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t12_40952/04_2024/8t12_40952_neut.pdb" } resolution = 3.34 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 59 5.16 5 C 6835 2.51 5 N 1913 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B GLU 802": "OE1" <-> "OE2" Residue "B GLU 825": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10813 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3778 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 446} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 7033 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 876, 7019 Classifications: {'peptide': 876} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 30, 'TRANS': 845} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 876, 7019 Classifications: {'peptide': 876} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 30, 'TRANS': 845} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 7161 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9551 SG CYS B 728 22.760 32.299 108.451 1.00111.75 S ATOM 10533 SG CYS B 847 20.266 33.374 105.715 1.00121.42 S ATOM 7310 SG CYS B 450 56.443 53.293 128.737 1.00115.64 S Time building chain proxies: 8.94, per 1000 atoms: 0.83 Number of scatterers: 10813 At special positions: 0 Unit cell: (87.69, 104.34, 156.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 59 16.00 O 2004 8.00 N 1913 7.00 C 6835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 714 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 712 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 728 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 847 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 442 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 450 " Number of angles added : 2 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 53.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 removed outlier: 4.273A pdb=" N ASP A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 25 removed outlier: 3.726A pdb=" N HIS A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 35 removed outlier: 3.602A pdb=" N GLN A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.625A pdb=" N ALA A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 76 removed outlier: 3.646A pdb=" N CYS A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.656A pdb=" N ASP A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 127 removed outlier: 3.736A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 184 removed outlier: 3.710A pdb=" N LYS A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 247 Proline residue: A 233 - end of helix removed outlier: 3.739A pdb=" N ILE A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 284 Processing helix chain 'A' and resid 292 through 315 removed outlier: 4.593A pdb=" N ASP A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 removed outlier: 4.126A pdb=" N GLY A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 removed outlier: 4.423A pdb=" N ALA A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.791A pdb=" N PHE A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 21 through 29 removed outlier: 3.896A pdb=" N ILE B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.874A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 68 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.822A pdb=" N GLY B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.795A pdb=" N PHE B 134 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 170 removed outlier: 3.574A pdb=" N GLU B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.944A pdb=" N LYS B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 243 removed outlier: 3.586A pdb=" N SER B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.606A pdb=" N ILE B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ARG B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 removed outlier: 3.637A pdb=" N TRP B 292 " --> pdb=" O GLU B 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 289 through 292' Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.683A pdb=" N THR B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 367 through 386 removed outlier: 3.565A pdb=" N GLY B 386 " --> pdb=" O TRP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.556A pdb=" N PHE B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 428 removed outlier: 4.114A pdb=" N GLU B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 443 removed outlier: 4.196A pdb=" N TRP B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.610A pdb=" N PHE B 465 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 466' Processing helix chain 'B' and resid 479 through 490 Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 514 through 523 removed outlier: 3.650A pdb=" N ILE B 518 " --> pdb=" O LYS B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.136A pdb=" N ILE B 542 " --> pdb=" O ASP B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.580A pdb=" N LEU B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.553A pdb=" N ASN B 555 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 572 removed outlier: 3.541A pdb=" N LYS B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 627 removed outlier: 3.606A pdb=" N GLY B 627 " --> pdb=" O MET B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 656 removed outlier: 5.741A pdb=" N ARG B 652 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 656 " --> pdb=" O ARG B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 677 removed outlier: 3.726A pdb=" N ALA B 677 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 730 through 739 removed outlier: 3.579A pdb=" N LEU B 734 " --> pdb=" O ASN B 730 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 739 " --> pdb=" O ILE B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 4.023A pdb=" N THR B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 765 Processing helix chain 'B' and resid 769 through 783 removed outlier: 3.668A pdb=" N LEU B 774 " --> pdb=" O ARG B 770 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 775 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 776 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN B 777 " --> pdb=" O ARG B 773 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 778 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 780 " --> pdb=" O ALA B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 818 removed outlier: 3.709A pdb=" N VAL B 812 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 848 removed outlier: 4.064A pdb=" N GLN B 845 " --> pdb=" O LYS B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 860 Processing helix chain 'B' and resid 866 through 874 removed outlier: 4.384A pdb=" N SER B 872 " --> pdb=" O ASN B 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 316 through 323 removed outlier: 5.051A pdb=" N VAL A 318 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG A 345 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR A 341 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 340 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.298A pdb=" N LEU A 334 " --> pdb=" O ILE A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.519A pdb=" N VAL A 359 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 386 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 357 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR A 358 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 436 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.710A pdb=" N GLU B 35 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 127 removed outlier: 8.859A pdb=" N ARG B 125 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 100 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLN B 127 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY B 102 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY B 75 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 99 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 204 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 310 removed outlier: 6.209A pdb=" N TYR B 305 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER B 594 " --> pdb=" O TYR B 305 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 307 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN B 581 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 413 " --> pdb=" O MET B 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 658 through 660 Processing sheet with id=AA9, first strand: chain 'B' and resid 714 through 717 497 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3586 1.35 - 1.46: 2501 1.46 - 1.58: 4861 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 11045 Sorted by residual: bond pdb=" N GLY A 50 " pdb=" CA GLY A 50 " ideal model delta sigma weight residual 1.447 1.476 -0.030 1.01e-02 9.80e+03 8.71e+00 bond pdb=" N ASP A 52 " pdb=" CA ASP A 52 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.46e+00 bond pdb=" N LYS B 460 " pdb=" CA LYS B 460 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.40e-02 5.10e+03 6.38e+00 bond pdb=" N ASP A 53 " pdb=" CA ASP A 53 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.06e+00 bond pdb=" N HIS A 24 " pdb=" CA HIS A 24 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.25e-02 6.40e+03 5.13e+00 ... (remaining 11040 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.57: 196 105.57 - 112.72: 5853 112.72 - 119.86: 3788 119.86 - 127.01: 4928 127.01 - 134.16: 171 Bond angle restraints: 14936 Sorted by residual: angle pdb=" C ARG B 458 " pdb=" N GLU B 459 " pdb=" CA GLU B 459 " ideal model delta sigma weight residual 121.83 113.56 8.27 1.48e+00 4.57e-01 3.12e+01 angle pdb=" CA GLU B 459 " pdb=" C GLU B 459 " pdb=" O GLU B 459 " ideal model delta sigma weight residual 121.67 117.45 4.22 9.30e-01 1.16e+00 2.06e+01 angle pdb=" CA GLN A 3 " pdb=" CB GLN A 3 " pdb=" CG GLN A 3 " ideal model delta sigma weight residual 114.10 122.80 -8.70 2.00e+00 2.50e-01 1.89e+01 angle pdb=" C ALA A 48 " pdb=" N LEU A 49 " pdb=" CA LEU A 49 " ideal model delta sigma weight residual 123.20 117.57 5.63 1.38e+00 5.25e-01 1.66e+01 angle pdb=" CA MET B 187 " pdb=" CB MET B 187 " pdb=" CG MET B 187 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 ... (remaining 14931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 5581 17.04 - 34.07: 768 34.07 - 51.11: 242 51.11 - 68.14: 43 68.14 - 85.18: 20 Dihedral angle restraints: 6654 sinusoidal: 2769 harmonic: 3885 Sorted by residual: dihedral pdb=" CA MET B 187 " pdb=" C MET B 187 " pdb=" N PRO B 188 " pdb=" CA PRO B 188 " ideal model delta harmonic sigma weight residual -180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA TYR B 758 " pdb=" C TYR B 758 " pdb=" N ALA B 759 " pdb=" CA ALA B 759 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LEU B 853 " pdb=" C LEU B 853 " pdb=" N THR B 854 " pdb=" CA THR B 854 " ideal model delta harmonic sigma weight residual -180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1452 0.064 - 0.128: 170 0.128 - 0.193: 4 0.193 - 0.257: 2 0.257 - 0.321: 1 Chirality restraints: 1629 Sorted by residual: chirality pdb=" CB ILE A 247 " pdb=" CA ILE A 247 " pdb=" CG1 ILE A 247 " pdb=" CG2 ILE A 247 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA TYR B 758 " pdb=" N TYR B 758 " pdb=" C TYR B 758 " pdb=" CB TYR B 758 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ARG B 698 " pdb=" N ARG B 698 " pdb=" C ARG B 698 " pdb=" CB ARG B 698 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1626 not shown) Planarity restraints: 1915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 151 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO B 152 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 152 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 152 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 458 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ARG B 458 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG B 458 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 459 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 871 " -0.173 9.50e-02 1.11e+02 7.77e-02 4.11e+00 pdb=" NE ARG B 871 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 871 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 871 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 871 " -0.003 2.00e-02 2.50e+03 ... (remaining 1912 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 284 2.70 - 3.25: 10468 3.25 - 3.80: 16056 3.80 - 4.35: 19551 4.35 - 4.90: 33366 Nonbonded interactions: 79725 Sorted by model distance: nonbonded pdb=" OE1 GLU B 438 " pdb="ZN ZN B1002 " model vdw 2.147 2.230 nonbonded pdb=" N GLU B 365 " pdb=" OE1 GLU B 365 " model vdw 2.196 2.520 nonbonded pdb=" OG1 THR B 805 " pdb=" OE1 GLU B 807 " model vdw 2.208 2.440 nonbonded pdb=" OE1 GLN A 165 " pdb=" NH2 ARG A 209 " model vdw 2.219 2.520 nonbonded pdb=" OE1 GLN A 95 " pdb=" OG SER B 316 " model vdw 2.226 2.440 ... (remaining 79720 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 13.720 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 37.090 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 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 : 0.004 0.059 11045 Z= 0.251 Angle : 0.694 10.152 14936 Z= 0.387 Chirality : 0.042 0.321 1629 Planarity : 0.004 0.078 1915 Dihedral : 17.589 85.179 4140 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.63 % Favored : 94.00 % Rotamer: Outliers : 0.60 % Allowed : 25.79 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1336 helix: 2.13 (0.23), residues: 592 sheet: 0.29 (0.45), residues: 153 loop : -1.96 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 238 HIS 0.005 0.001 HIS B 110 PHE 0.017 0.001 PHE A 433 TYR 0.026 0.001 TYR A 402 ARG 0.011 0.001 ARG B 871 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8050 (tttt) cc_final: 0.7696 (pttp) REVERT: A 324 MET cc_start: 0.2831 (tpp) cc_final: 0.2444 (tpt) REVERT: A 433 PHE cc_start: 0.6515 (m-80) cc_final: 0.6040 (t80) REVERT: B 49 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7613 (tt0) REVERT: B 84 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7319 (mtt180) REVERT: B 111 GLU cc_start: 0.7777 (mm-30) cc_final: 0.6559 (mm-30) REVERT: B 135 THR cc_start: 0.7473 (m) cc_final: 0.7151 (p) REVERT: B 170 ASN cc_start: 0.8057 (t0) cc_final: 0.7158 (m110) REVERT: B 245 MET cc_start: 0.7227 (mpp) cc_final: 0.6703 (mpp) REVERT: B 288 HIS cc_start: 0.7254 (m90) cc_final: 0.6902 (m90) REVERT: B 289 GLU cc_start: 0.8125 (tt0) cc_final: 0.7916 (tm-30) REVERT: B 401 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7495 (ttp-170) REVERT: B 690 ASP cc_start: 0.7559 (t0) cc_final: 0.7306 (p0) outliers start: 7 outliers final: 3 residues processed: 178 average time/residue: 0.2642 time to fit residues: 64.7196 Evaluate side-chains 119 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 460 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.0770 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 127 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 HIS ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11045 Z= 0.217 Angle : 0.580 6.533 14936 Z= 0.302 Chirality : 0.041 0.269 1629 Planarity : 0.004 0.052 1915 Dihedral : 5.012 59.672 1459 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.03 % Favored : 94.75 % Rotamer: Outliers : 2.30 % Allowed : 24.68 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1336 helix: 2.15 (0.22), residues: 597 sheet: 0.22 (0.44), residues: 158 loop : -2.10 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 475 HIS 0.004 0.001 HIS B 714 PHE 0.013 0.001 PHE B 243 TYR 0.021 0.001 TYR A 402 ARG 0.006 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.220 Fit side-chains REVERT: A 34 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: A 117 ARG cc_start: 0.5587 (mmp80) cc_final: 0.5380 (ttp-110) REVERT: A 211 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7792 (tppt) REVERT: A 280 LYS cc_start: 0.8098 (tttt) cc_final: 0.7690 (pttm) REVERT: A 324 MET cc_start: 0.2585 (tpp) cc_final: 0.2200 (tpt) REVERT: A 433 PHE cc_start: 0.6641 (m-80) cc_final: 0.6159 (t80) REVERT: B 49 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7544 (tt0) REVERT: B 84 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7716 (mtt180) REVERT: B 135 THR cc_start: 0.7299 (m) cc_final: 0.6997 (p) REVERT: B 242 ARG cc_start: 0.6599 (tpp80) cc_final: 0.6307 (tpp80) REVERT: B 245 MET cc_start: 0.7157 (mpp) cc_final: 0.6899 (mpp) REVERT: B 289 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: B 460 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.4629 (tppt) REVERT: B 570 LYS cc_start: 0.7468 (ttmm) cc_final: 0.6793 (mttm) REVERT: B 634 HIS cc_start: 0.8245 (t70) cc_final: 0.8019 (t70) outliers start: 27 outliers final: 11 residues processed: 141 average time/residue: 0.2660 time to fit residues: 51.2886 Evaluate side-chains 126 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 769 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 97 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 271 HIS ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11045 Z= 0.191 Angle : 0.540 6.756 14936 Z= 0.281 Chirality : 0.040 0.235 1629 Planarity : 0.004 0.050 1915 Dihedral : 4.860 59.440 1457 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.33 % Favored : 94.45 % Rotamer: Outliers : 3.40 % Allowed : 23.32 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1336 helix: 2.16 (0.22), residues: 604 sheet: 0.37 (0.45), residues: 148 loop : -2.13 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 475 HIS 0.004 0.001 HIS B 714 PHE 0.009 0.001 PHE A 60 TYR 0.018 0.001 TYR B 758 ARG 0.004 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 116 time to evaluate : 1.353 Fit side-chains REVERT: A 34 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: A 88 ARG cc_start: 0.4938 (mtt90) cc_final: 0.4734 (mtm110) REVERT: A 156 MET cc_start: 0.6236 (tpp) cc_final: 0.5969 (tmm) REVERT: A 211 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7883 (tppt) REVERT: A 280 LYS cc_start: 0.8055 (tttt) cc_final: 0.7715 (pttm) REVERT: A 319 GLU cc_start: 0.5495 (tp30) cc_final: 0.4445 (tt0) REVERT: A 448 THR cc_start: 0.6757 (OUTLIER) cc_final: 0.6548 (p) REVERT: B 49 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7408 (tt0) REVERT: B 135 THR cc_start: 0.7245 (m) cc_final: 0.6936 (p) REVERT: B 206 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7701 (m) REVERT: B 242 ARG cc_start: 0.6619 (tpp80) cc_final: 0.6270 (tpp80) REVERT: B 245 MET cc_start: 0.6670 (mpp) cc_final: 0.6366 (mpp) REVERT: B 289 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: B 320 MET cc_start: 0.8145 (mmp) cc_final: 0.7514 (mmm) REVERT: B 341 MET cc_start: 0.8625 (ttt) cc_final: 0.8337 (ptm) REVERT: B 570 LYS cc_start: 0.7502 (ttmm) cc_final: 0.6862 (mttm) outliers start: 40 outliers final: 19 residues processed: 145 average time/residue: 0.2400 time to fit residues: 49.5305 Evaluate side-chains 130 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 658 MET Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 865 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11045 Z= 0.233 Angle : 0.572 6.693 14936 Z= 0.299 Chirality : 0.041 0.234 1629 Planarity : 0.004 0.050 1915 Dihedral : 4.508 45.051 1453 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.78 % Favored : 94.00 % Rotamer: Outliers : 3.06 % Allowed : 24.34 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1336 helix: 2.13 (0.22), residues: 606 sheet: 0.25 (0.45), residues: 146 loop : -2.13 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 466 HIS 0.004 0.001 HIS B 714 PHE 0.011 0.001 PHE A 60 TYR 0.020 0.001 TYR B 758 ARG 0.003 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 1.347 Fit side-chains REVERT: A 34 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: A 52 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.5559 (m-30) REVERT: A 88 ARG cc_start: 0.4972 (mtt90) cc_final: 0.4746 (mtm110) REVERT: A 211 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7982 (tppt) REVERT: A 280 LYS cc_start: 0.8118 (tttt) cc_final: 0.7787 (pttm) REVERT: A 319 GLU cc_start: 0.5446 (tp30) cc_final: 0.4385 (tt0) REVERT: A 346 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5723 (mm) REVERT: A 459 MET cc_start: 0.7167 (tpp) cc_final: 0.6733 (tpt) REVERT: A 460 ASN cc_start: 0.7100 (p0) cc_final: 0.6518 (m-40) REVERT: B 49 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7161 (tt0) REVERT: B 206 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7887 (m) REVERT: B 245 MET cc_start: 0.6825 (mpp) cc_final: 0.6542 (mpp) REVERT: B 289 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: B 320 MET cc_start: 0.8107 (mmp) cc_final: 0.7599 (mmm) REVERT: B 570 LYS cc_start: 0.7517 (ttmm) cc_final: 0.6886 (mttm) REVERT: B 705 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: B 842 ARG cc_start: 0.7197 (tmm160) cc_final: 0.6949 (tmm160) REVERT: B 869 GLN cc_start: 0.7296 (tm-30) cc_final: 0.7019 (tm-30) outliers start: 35 outliers final: 24 residues processed: 142 average time/residue: 0.2576 time to fit residues: 51.4695 Evaluate side-chains 139 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 882 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 115 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11045 Z= 0.196 Angle : 0.539 8.670 14936 Z= 0.282 Chirality : 0.040 0.214 1629 Planarity : 0.004 0.048 1915 Dihedral : 4.355 42.898 1453 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.63 % Favored : 94.22 % Rotamer: Outliers : 3.06 % Allowed : 25.28 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1336 helix: 2.18 (0.22), residues: 608 sheet: 0.21 (0.45), residues: 146 loop : -2.12 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 475 HIS 0.009 0.001 HIS B 247 PHE 0.012 0.001 PHE B 243 TYR 0.018 0.001 TYR B 758 ARG 0.003 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.158 Fit side-chains REVERT: A 34 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: A 88 ARG cc_start: 0.5007 (mtt90) cc_final: 0.4731 (mtm110) REVERT: A 280 LYS cc_start: 0.7994 (tttt) cc_final: 0.7609 (pttm) REVERT: A 319 GLU cc_start: 0.5777 (tp30) cc_final: 0.4621 (tt0) REVERT: A 459 MET cc_start: 0.6975 (tpp) cc_final: 0.6546 (tpt) REVERT: A 460 ASN cc_start: 0.7090 (p0) cc_final: 0.6521 (m-40) REVERT: B 49 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: B 206 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7857 (m) REVERT: B 245 MET cc_start: 0.6770 (mpp) cc_final: 0.6478 (mpp) REVERT: B 289 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: B 320 MET cc_start: 0.8067 (mmp) cc_final: 0.7593 (mmm) REVERT: B 570 LYS cc_start: 0.7494 (ttmm) cc_final: 0.6872 (mmtp) REVERT: B 705 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: B 873 LEU cc_start: 0.8253 (tp) cc_final: 0.7972 (tt) outliers start: 36 outliers final: 26 residues processed: 136 average time/residue: 0.2436 time to fit residues: 46.9114 Evaluate side-chains 143 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 882 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 128 optimal weight: 0.0060 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11045 Z= 0.177 Angle : 0.531 8.831 14936 Z= 0.275 Chirality : 0.039 0.201 1629 Planarity : 0.003 0.048 1915 Dihedral : 4.196 39.295 1453 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Rotamer: Outliers : 3.40 % Allowed : 24.94 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1336 helix: 2.28 (0.22), residues: 608 sheet: 0.18 (0.45), residues: 146 loop : -2.02 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 475 HIS 0.004 0.001 HIS B 714 PHE 0.014 0.001 PHE B 243 TYR 0.017 0.001 TYR B 758 ARG 0.003 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 112 time to evaluate : 1.299 Fit side-chains REVERT: A 34 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: A 88 ARG cc_start: 0.4947 (mtt90) cc_final: 0.4524 (mtm110) REVERT: A 280 LYS cc_start: 0.7975 (tttt) cc_final: 0.7768 (tptm) REVERT: A 319 GLU cc_start: 0.5915 (tp30) cc_final: 0.4846 (tt0) REVERT: A 346 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.6039 (mm) REVERT: A 400 PHE cc_start: 0.5730 (OUTLIER) cc_final: 0.5491 (t80) REVERT: A 459 MET cc_start: 0.6942 (tpp) cc_final: 0.6546 (tpt) REVERT: A 460 ASN cc_start: 0.7039 (p0) cc_final: 0.6486 (m-40) REVERT: B 49 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: B 206 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7817 (m) REVERT: B 245 MET cc_start: 0.6814 (mpp) cc_final: 0.6556 (mpp) REVERT: B 289 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: B 320 MET cc_start: 0.8121 (mmp) cc_final: 0.7673 (mmm) REVERT: B 428 ASP cc_start: 0.6383 (t70) cc_final: 0.6044 (m-30) REVERT: B 570 LYS cc_start: 0.7498 (ttmm) cc_final: 0.6910 (mmtp) REVERT: B 705 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: B 842 ARG cc_start: 0.7220 (tmm160) cc_final: 0.6980 (tmm160) outliers start: 40 outliers final: 25 residues processed: 142 average time/residue: 0.2307 time to fit residues: 47.7156 Evaluate side-chains 140 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 882 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.0470 chunk 80 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11045 Z= 0.174 Angle : 0.527 7.899 14936 Z= 0.273 Chirality : 0.039 0.191 1629 Planarity : 0.003 0.046 1915 Dihedral : 4.091 35.216 1453 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.25 % Favored : 94.60 % Rotamer: Outliers : 3.40 % Allowed : 25.19 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1336 helix: 2.31 (0.22), residues: 608 sheet: 0.18 (0.45), residues: 146 loop : -1.99 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 475 HIS 0.004 0.001 HIS B 714 PHE 0.014 0.001 PHE B 243 TYR 0.016 0.001 TYR B 758 ARG 0.007 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 1.141 Fit side-chains REVERT: A 34 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: A 88 ARG cc_start: 0.5019 (mtt90) cc_final: 0.4631 (mtm110) REVERT: A 280 LYS cc_start: 0.7979 (tttt) cc_final: 0.7747 (tptm) REVERT: A 319 GLU cc_start: 0.5998 (tp30) cc_final: 0.5005 (tt0) REVERT: A 346 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6069 (mm) REVERT: A 459 MET cc_start: 0.7032 (tpp) cc_final: 0.6670 (tpt) REVERT: A 460 ASN cc_start: 0.7061 (OUTLIER) cc_final: 0.6612 (m-40) REVERT: B 49 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: B 168 VAL cc_start: 0.8251 (p) cc_final: 0.8000 (p) REVERT: B 195 GLU cc_start: 0.7862 (tp30) cc_final: 0.7618 (tp30) REVERT: B 245 MET cc_start: 0.6661 (mpp) cc_final: 0.6389 (mpp) REVERT: B 289 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: B 320 MET cc_start: 0.8094 (mmp) cc_final: 0.7721 (mmm) REVERT: B 428 ASP cc_start: 0.6400 (t70) cc_final: 0.6064 (m-30) REVERT: B 570 LYS cc_start: 0.7501 (ttmm) cc_final: 0.6919 (mmtp) REVERT: B 690 ASP cc_start: 0.7670 (t0) cc_final: 0.7331 (p0) REVERT: B 705 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: B 842 ARG cc_start: 0.7238 (tmm160) cc_final: 0.6985 (tmm160) outliers start: 40 outliers final: 30 residues processed: 134 average time/residue: 0.2413 time to fit residues: 46.2096 Evaluate side-chains 138 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 882 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.0060 chunk 51 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11045 Z= 0.147 Angle : 0.508 9.318 14936 Z= 0.263 Chirality : 0.038 0.189 1629 Planarity : 0.003 0.047 1915 Dihedral : 3.898 32.076 1453 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.88 % Favored : 94.97 % Rotamer: Outliers : 2.47 % Allowed : 26.21 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1336 helix: 2.41 (0.22), residues: 610 sheet: 0.21 (0.45), residues: 148 loop : -1.95 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 746 HIS 0.004 0.000 HIS B 714 PHE 0.014 0.001 PHE B 243 TYR 0.014 0.001 TYR B 758 ARG 0.007 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.309 Fit side-chains REVERT: A 34 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: A 88 ARG cc_start: 0.5014 (mtt90) cc_final: 0.4632 (mtm110) REVERT: A 280 LYS cc_start: 0.7947 (tttt) cc_final: 0.7746 (tptm) REVERT: A 319 GLU cc_start: 0.5939 (tp30) cc_final: 0.4969 (tt0) REVERT: A 346 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6370 (mm) REVERT: A 459 MET cc_start: 0.7148 (tpp) cc_final: 0.6772 (tpt) REVERT: A 460 ASN cc_start: 0.6981 (p0) cc_final: 0.6536 (m-40) REVERT: B 49 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: B 168 VAL cc_start: 0.8236 (p) cc_final: 0.7983 (p) REVERT: B 195 GLU cc_start: 0.7908 (tp30) cc_final: 0.7654 (tp30) REVERT: B 245 MET cc_start: 0.6907 (mpp) cc_final: 0.6649 (mpp) REVERT: B 289 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: B 320 MET cc_start: 0.8164 (mmp) cc_final: 0.7959 (mmm) REVERT: B 570 LYS cc_start: 0.7476 (ttmm) cc_final: 0.6905 (mmtp) REVERT: B 690 ASP cc_start: 0.7750 (t0) cc_final: 0.7459 (p0) REVERT: B 842 ARG cc_start: 0.7234 (tmm160) cc_final: 0.6970 (tmm160) outliers start: 29 outliers final: 23 residues processed: 126 average time/residue: 0.2456 time to fit residues: 44.2488 Evaluate side-chains 129 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 882 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11045 Z= 0.177 Angle : 0.528 8.759 14936 Z= 0.273 Chirality : 0.039 0.194 1629 Planarity : 0.003 0.045 1915 Dihedral : 4.000 30.181 1453 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Rotamer: Outliers : 3.15 % Allowed : 25.36 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1336 helix: 2.38 (0.22), residues: 609 sheet: 0.23 (0.45), residues: 146 loop : -1.93 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 475 HIS 0.004 0.001 HIS B 714 PHE 0.029 0.001 PHE B 413 TYR 0.014 0.001 TYR B 758 ARG 0.008 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 1.161 Fit side-chains REVERT: A 34 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: A 88 ARG cc_start: 0.5044 (mtt90) cc_final: 0.4637 (mtm110) REVERT: A 319 GLU cc_start: 0.6028 (tp30) cc_final: 0.5043 (tt0) REVERT: A 346 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6373 (mm) REVERT: A 459 MET cc_start: 0.7120 (tpp) cc_final: 0.6734 (tpt) REVERT: A 460 ASN cc_start: 0.7051 (p0) cc_final: 0.6665 (m-40) REVERT: B 49 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6864 (tt0) REVERT: B 168 VAL cc_start: 0.8252 (p) cc_final: 0.8000 (p) REVERT: B 245 MET cc_start: 0.6940 (mpp) cc_final: 0.6689 (mpp) REVERT: B 320 MET cc_start: 0.8293 (mmp) cc_final: 0.7897 (mmm) REVERT: B 428 ASP cc_start: 0.6420 (t70) cc_final: 0.6105 (m-30) REVERT: B 570 LYS cc_start: 0.7556 (ttmm) cc_final: 0.6972 (mmtp) REVERT: B 690 ASP cc_start: 0.7820 (t0) cc_final: 0.7511 (p0) REVERT: B 705 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: B 842 ARG cc_start: 0.7237 (tmm160) cc_final: 0.6975 (tmm160) outliers start: 37 outliers final: 30 residues processed: 131 average time/residue: 0.2355 time to fit residues: 44.9903 Evaluate side-chains 136 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 705 GLN Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 882 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 0.0770 chunk 112 optimal weight: 0.4980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11045 Z= 0.154 Angle : 0.517 8.827 14936 Z= 0.267 Chirality : 0.038 0.181 1629 Planarity : 0.003 0.046 1915 Dihedral : 3.841 17.511 1451 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.88 % Favored : 94.97 % Rotamer: Outliers : 2.13 % Allowed : 26.38 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1336 helix: 2.46 (0.22), residues: 604 sheet: 0.25 (0.45), residues: 148 loop : -1.88 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 746 HIS 0.004 0.000 HIS B 714 PHE 0.027 0.001 PHE B 413 TYR 0.012 0.001 TYR B 758 ARG 0.007 0.000 ARG B 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.275 Fit side-chains REVERT: A 34 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: A 88 ARG cc_start: 0.5311 (mtt90) cc_final: 0.4858 (mtm110) REVERT: A 319 GLU cc_start: 0.6017 (tp30) cc_final: 0.5060 (tt0) REVERT: A 346 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6379 (mm) REVERT: A 459 MET cc_start: 0.7114 (tpp) cc_final: 0.6728 (tpt) REVERT: A 460 ASN cc_start: 0.7175 (p0) cc_final: 0.6876 (m-40) REVERT: B 49 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: B 168 VAL cc_start: 0.8201 (p) cc_final: 0.7955 (p) REVERT: B 195 GLU cc_start: 0.7903 (tp30) cc_final: 0.7652 (tp30) REVERT: B 245 MET cc_start: 0.6995 (mpp) cc_final: 0.6722 (mpp) REVERT: B 320 MET cc_start: 0.8240 (mmp) cc_final: 0.7867 (mmm) REVERT: B 428 ASP cc_start: 0.6309 (t70) cc_final: 0.6011 (m-30) REVERT: B 570 LYS cc_start: 0.7531 (ttmm) cc_final: 0.6935 (mmtp) REVERT: B 690 ASP cc_start: 0.7826 (t0) cc_final: 0.7519 (p0) REVERT: B 842 ARG cc_start: 0.7247 (tmm160) cc_final: 0.6984 (tmm160) outliers start: 25 outliers final: 22 residues processed: 123 average time/residue: 0.2416 time to fit residues: 42.4791 Evaluate side-chains 126 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 769 ARG Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 882 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 6 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.160143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111568 restraints weight = 24652.337| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.84 r_work: 0.3128 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11045 Z= 0.213 Angle : 0.554 9.427 14936 Z= 0.287 Chirality : 0.040 0.202 1629 Planarity : 0.004 0.045 1915 Dihedral : 4.043 19.368 1451 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.70 % Favored : 94.15 % Rotamer: Outliers : 2.72 % Allowed : 25.79 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1336 helix: 2.31 (0.22), residues: 608 sheet: 0.18 (0.45), residues: 146 loop : -1.95 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 475 HIS 0.004 0.001 HIS B 714 PHE 0.029 0.001 PHE B 413 TYR 0.015 0.001 TYR B 758 ARG 0.007 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2605.47 seconds wall clock time: 48 minutes 5.75 seconds (2885.75 seconds total)