Starting phenix.real_space_refine on Sat Aug 10 22:35:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgy_18396/08_2024/8qgy_18396.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgy_18396/08_2024/8qgy_18396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgy_18396/08_2024/8qgy_18396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgy_18396/08_2024/8qgy_18396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgy_18396/08_2024/8qgy_18396.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qgy_18396/08_2024/8qgy_18396.cif" } resolution = 3.71 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6009 atoms to isotropic. 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 S 62 5.16 5 C 8184 2.51 5 N 2119 2.21 5 O 2379 1.98 5 H 12699 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25443 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 12499 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 26, 'TRANS': 753} Chain breaks: 4 Chain: "B" Number of atoms: 12944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 12944 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 29, 'TRANS': 779} Chain breaks: 2 Time building chain proxies: 12.26, per 1000 atoms: 0.48 Number of scatterers: 25443 At special positions: 0 Unit cell: (100.866, 115.87, 153.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 O 2379 8.00 N 2119 7.00 C 8184 6.00 H 12699 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 250 " distance=2.03 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: 21.10 Conformation dependent library (CDL) restraints added in 2.7 seconds 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3006 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 52.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.840A pdb=" N VAL A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 4.183A pdb=" N LEU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 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 161 through 175 removed outlier: 3.851A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N HIS A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 249 through 269 removed outlier: 4.181A pdb=" N SER A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 284 Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.512A pdb=" N ASN A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.593A pdb=" N VAL A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.689A pdb=" N LYS A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 353 " --> pdb=" O HIS A 349 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.775A pdb=" N LYS A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 386 through 404 removed outlier: 3.679A pdb=" N TYR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.073A pdb=" N ILE A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 3.691A pdb=" N LYS A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 3.960A pdb=" N PHE A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 504 removed outlier: 3.563A pdb=" N GLN A 496 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.709A pdb=" N LEU A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 removed outlier: 3.707A pdb=" N THR A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 654 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 776 through 797 removed outlier: 4.505A pdb=" N ILE A 780 " --> pdb=" O ASN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 854 Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 859 through 877 Processing helix chain 'A' and resid 908 through 919 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 939 Processing helix chain 'B' and resid 103 through 109 removed outlier: 4.039A pdb=" N VAL B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 109' Processing helix chain 'B' and resid 109 through 123 removed outlier: 4.041A pdb=" N LEU B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.841A pdb=" N TYR B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.553A pdb=" N ILE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 269 Processing helix chain 'B' and resid 269 through 287 removed outlier: 4.483A pdb=" N SER B 275 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 304 Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.858A pdb=" N ASN B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 349 through 363 removed outlier: 3.561A pdb=" N HIS B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 386 through 404 removed outlier: 3.947A pdb=" N TYR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 404 " --> pdb=" O MET B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 426 removed outlier: 3.520A pdb=" N HIS B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 removed outlier: 4.005A pdb=" N ILE B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 434 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 467 removed outlier: 4.168A pdb=" N VAL B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 488 Processing helix chain 'B' and resid 493 through 505 removed outlier: 3.540A pdb=" N ALA B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 525 removed outlier: 3.516A pdb=" N ILE B 520 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 521 " --> pdb=" O THR B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 549 removed outlier: 3.575A pdb=" N ALA B 549 " --> pdb=" O PHE B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 653 Processing helix chain 'B' and resid 719 through 731 removed outlier: 4.333A pdb=" N HIS B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'B' and resid 777 through 797 Processing helix chain 'B' and resid 822 through 826 removed outlier: 4.149A pdb=" N THR B 825 " --> pdb=" O ASP B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 859 through 877 removed outlier: 3.874A pdb=" N ASP B 863 " --> pdb=" O GLY B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 898 Processing helix chain 'B' and resid 908 through 919 Processing helix chain 'B' and resid 928 through 934 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 155 removed outlier: 6.588A pdb=" N VAL A 154 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N CYS A 185 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE A 182 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR A 215 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR A 184 " --> pdb=" O TYR A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 565 removed outlier: 3.637A pdb=" N ILE A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 612 through 614 Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 675 removed outlier: 7.219A pdb=" N VAL A 694 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE A 693 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY A 742 " --> pdb=" O PHE A 753 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 760 through 761 removed outlier: 3.971A pdb=" N VAL A 817 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.987A pdb=" N MET B 156 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 605 removed outlier: 4.088A pdb=" N GLU B 580 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 585 " --> pdb=" O ASN B 578 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 609 through 614 removed outlier: 6.669A pdb=" N TYR B 625 " --> pdb=" O ARG B 610 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 612 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE B 623 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 673 through 674 removed outlier: 4.533A pdb=" N GLY B 742 " --> pdb=" O PHE B 753 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B 755 " --> pdb=" O TYR B 740 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR B 740 " --> pdb=" O GLU B 755 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 760 through 761 removed outlier: 4.102A pdb=" N GLY B 760 " --> pdb=" O ILE B 811 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 811 " --> pdb=" O GLY B 760 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1761 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: 10.14 Time building geometry restraints manager: 21.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12669 1.03 - 1.23: 57 1.23 - 1.43: 5456 1.43 - 1.62: 7443 1.62 - 1.82: 94 Bond restraints: 25719 Sorted by residual: bond pdb=" N TYR B 95 " pdb=" CA TYR B 95 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N TYR B 95 " pdb=" H TYR B 95 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C PHE A 559 " pdb=" N PRO A 560 " ideal model delta sigma weight residual 1.335 1.347 -0.012 8.70e-03 1.32e+04 1.96e+00 bond pdb=" CA PHE B 272 " pdb=" CB PHE B 272 " ideal model delta sigma weight residual 1.535 1.555 -0.020 1.69e-02 3.50e+03 1.39e+00 bond pdb=" C LEU B 251 " pdb=" N PRO B 252 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.32e+00 ... (remaining 25714 not shown) Histogram of bond angle deviations from ideal: 61.11 - 75.70: 20 75.70 - 90.28: 12 90.28 - 104.87: 173 104.87 - 119.45: 35914 119.45 - 134.04: 10385 Bond angle restraints: 46504 Sorted by residual: angle pdb=" C LEU B 794 " pdb=" N HIS B 795 " pdb=" H HIS B 795 " ideal model delta sigma weight residual 125.00 71.15 53.86 3.00e+00 1.11e-01 3.22e+02 angle pdb=" CA HIS B 795 " pdb=" N HIS B 795 " pdb=" H HIS B 795 " ideal model delta sigma weight residual 114.70 61.11 53.59 3.00e+00 1.11e-01 3.19e+02 angle pdb=" C PRO B 855 " pdb=" CA PRO B 855 " pdb=" HA PRO B 855 " ideal model delta sigma weight residual 109.00 70.84 38.16 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C PRO B 923 " pdb=" CA PRO B 923 " pdb=" HA PRO B 923 " ideal model delta sigma weight residual 109.00 71.54 37.46 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C PHE B 839 " pdb=" CA PHE B 839 " pdb=" HA PHE B 839 " ideal model delta sigma weight residual 109.00 72.58 36.42 3.00e+00 1.11e-01 1.47e+02 ... (remaining 46499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 11052 17.70 - 35.40: 718 35.40 - 53.11: 238 53.11 - 70.81: 72 70.81 - 88.51: 7 Dihedral angle restraints: 12087 sinusoidal: 6507 harmonic: 5580 Sorted by residual: dihedral pdb=" CA TYR A 521 " pdb=" C TYR A 521 " pdb=" N LYS A 522 " pdb=" CA LYS A 522 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C LEU A 402 " pdb=" N LEU A 402 " pdb=" CA LEU A 402 " pdb=" CB LEU A 402 " ideal model delta harmonic sigma weight residual -122.60 -132.87 10.27 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" C LEU A 519 " pdb=" N LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta harmonic sigma weight residual -122.60 -132.35 9.75 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 12084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 1954 0.290 - 0.579: 9 0.579 - 0.869: 0 0.869 - 1.159: 0 1.159 - 1.448: 1 Chirality restraints: 1964 Sorted by residual: chirality pdb=" CB THR B 836 " pdb=" CA THR B 836 " pdb=" OG1 THR B 836 " pdb=" CG2 THR B 836 " both_signs ideal model delta sigma weight residual False 2.55 1.10 1.45 2.00e-01 2.50e+01 5.24e+01 chirality pdb=" CA PRO B 923 " pdb=" N PRO B 923 " pdb=" C PRO B 923 " pdb=" CB PRO B 923 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA GLU B 837 " pdb=" N GLU B 837 " pdb=" C GLU B 837 " pdb=" CB GLU B 837 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 1961 not shown) Planarity restraints: 3769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 162 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO B 163 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 162 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 163 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 571 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO B 572 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 572 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 572 " 0.020 5.00e-02 4.00e+02 ... (remaining 3766 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1057 2.19 - 2.79: 51948 2.79 - 3.40: 70613 3.40 - 4.00: 88251 4.00 - 4.60: 137085 Nonbonded interactions: 348954 Sorted by model distance: nonbonded pdb=" H HIS B 795 " pdb=" HA HIS B 795 " model vdw 1.591 1.816 nonbonded pdb=" H GLU B 837 " pdb=" HA GLU B 837 " model vdw 1.610 1.816 nonbonded pdb=" H THR B 836 " pdb=" HA THR B 836 " model vdw 1.613 1.816 nonbonded pdb=" H PHE B 839 " pdb=" HA PHE B 839 " model vdw 1.656 1.816 nonbonded pdb=" HA LEU A 519 " pdb=" HB2 LEU A 519 " model vdw 1.691 1.952 ... (remaining 348949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 95 through 225 or resid 247 through 653 or resid 670 throu \ gh 940)) selection = (chain 'B' and (resid 95 through 830 or resid 844 through 879 or resid 900 throu \ gh 940)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.380 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 82.430 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 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 0.035 13020 Z= 0.213 Angle : 0.616 11.966 17604 Z= 0.334 Chirality : 0.058 1.448 1964 Planarity : 0.004 0.051 2243 Dihedral : 11.945 77.328 4810 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 3.91 % Allowed : 5.41 % Favored : 90.68 % Cbeta Deviations : 0.07 % 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: 0.12 (0.22), residues: 1573 helix: 1.81 (0.19), residues: 729 sheet: -1.22 (0.39), residues: 170 loop : -1.57 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 476 HIS 0.005 0.001 HIS B 168 PHE 0.016 0.001 PHE B 212 TYR 0.014 0.001 TYR B 167 ARG 0.004 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 222 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 LYS cc_start: 0.7314 (tttt) cc_final: 0.7088 (tttm) REVERT: A 493 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7226 (mmt-90) REVERT: A 605 SER cc_start: 0.7893 (m) cc_final: 0.7509 (t) REVERT: A 614 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7947 (mt) REVERT: A 858 TYR cc_start: 0.6884 (m-80) cc_final: 0.6627 (m-80) REVERT: B 102 GLN cc_start: 0.5440 (OUTLIER) cc_final: 0.5203 (pm20) REVERT: B 201 GLN cc_start: 0.7619 (mm110) cc_final: 0.7284 (mm110) REVERT: B 287 TYR cc_start: 0.7521 (m-80) cc_final: 0.7311 (m-10) REVERT: B 290 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7211 (pmmt) REVERT: B 649 MET cc_start: 0.7340 (mtm) cc_final: 0.6973 (mtt) REVERT: B 694 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8176 (p) REVERT: B 698 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6366 (ptp-110) outliers start: 55 outliers final: 24 residues processed: 266 average time/residue: 0.6290 time to fit residues: 230.8483 Evaluate side-chains 183 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 698 ARG Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 634 GLN ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 430 GLN B 578 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13020 Z= 0.276 Angle : 0.587 12.523 17604 Z= 0.325 Chirality : 0.061 1.654 1964 Planarity : 0.004 0.044 2243 Dihedral : 6.789 59.552 1780 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.75 % Rotamer: Outliers : 3.20 % Allowed : 10.46 % Favored : 86.33 % 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: -0.02 (0.22), residues: 1573 helix: 1.62 (0.19), residues: 756 sheet: -1.28 (0.39), residues: 162 loop : -1.69 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 589 HIS 0.006 0.001 HIS A 523 PHE 0.018 0.002 PHE B 541 TYR 0.019 0.001 TYR B 167 ARG 0.006 0.001 ARG B 802 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7379 (mmtt) REVERT: A 420 LYS cc_start: 0.7400 (tttt) cc_final: 0.7148 (tttm) REVERT: A 493 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7917 (mmt180) REVERT: A 605 SER cc_start: 0.8137 (m) cc_final: 0.7589 (t) REVERT: A 858 TYR cc_start: 0.6953 (m-80) cc_final: 0.6696 (m-80) REVERT: B 197 GLU cc_start: 0.7601 (tp30) cc_final: 0.7166 (tp30) REVERT: B 201 GLN cc_start: 0.7653 (mm110) cc_final: 0.6968 (mm110) REVERT: B 216 MET cc_start: 0.2748 (mpp) cc_final: 0.2476 (mpp) REVERT: B 434 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6812 (m-40) REVERT: B 694 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8177 (p) outliers start: 45 outliers final: 27 residues processed: 195 average time/residue: 0.6367 time to fit residues: 176.7198 Evaluate side-chains 169 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN B 360 ASN B 430 GLN B 579 ASN B 776 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13020 Z= 0.196 Angle : 0.547 12.097 17604 Z= 0.300 Chirality : 0.059 1.542 1964 Planarity : 0.004 0.039 2243 Dihedral : 6.245 57.901 1762 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.68 % Favored : 93.26 % Rotamer: Outliers : 2.92 % Allowed : 12.31 % Favored : 84.77 % 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: -0.08 (0.22), residues: 1573 helix: 1.61 (0.19), residues: 760 sheet: -1.45 (0.38), residues: 163 loop : -1.76 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 509 HIS 0.004 0.001 HIS B 131 PHE 0.015 0.001 PHE B 541 TYR 0.017 0.001 TYR B 167 ARG 0.004 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.4912 (tpt) cc_final: 0.4503 (tpp) REVERT: A 290 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7279 (mmtt) REVERT: A 420 LYS cc_start: 0.7343 (tttt) cc_final: 0.7062 (tttm) REVERT: A 493 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7887 (mmt180) REVERT: A 605 SER cc_start: 0.8087 (m) cc_final: 0.7526 (t) REVERT: A 858 TYR cc_start: 0.6952 (m-80) cc_final: 0.6693 (m-80) REVERT: B 177 MET cc_start: 0.5708 (tmm) cc_final: 0.5487 (tmm) REVERT: B 201 GLN cc_start: 0.7649 (mm110) cc_final: 0.7409 (mm110) REVERT: B 314 VAL cc_start: 0.6650 (OUTLIER) cc_final: 0.6445 (p) REVERT: B 694 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8204 (p) outliers start: 41 outliers final: 29 residues processed: 175 average time/residue: 0.5942 time to fit residues: 148.0958 Evaluate side-chains 162 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 136 optimal weight: 0.0020 chunk 41 optimal weight: 4.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 131 HIS A 808 ASN B 360 ASN B 430 GLN B 523 HIS B 776 ASN B 795 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13020 Z= 0.192 Angle : 0.534 11.966 17604 Z= 0.292 Chirality : 0.058 1.506 1964 Planarity : 0.004 0.039 2243 Dihedral : 6.144 57.249 1761 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.94 % Rotamer: Outliers : 2.99 % Allowed : 13.02 % Favored : 83.99 % 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: -0.04 (0.22), residues: 1573 helix: 1.73 (0.19), residues: 756 sheet: -1.47 (0.38), residues: 163 loop : -1.81 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 509 HIS 0.004 0.001 HIS A 168 PHE 0.014 0.001 PHE B 897 TYR 0.017 0.001 TYR B 167 ARG 0.005 0.000 ARG B 717 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8381 (pm20) REVERT: A 290 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7285 (mmtt) REVERT: A 420 LYS cc_start: 0.7353 (tttt) cc_final: 0.7080 (tttm) REVERT: A 471 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8057 (tmtt) REVERT: A 493 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7910 (mmt180) REVERT: A 605 SER cc_start: 0.7986 (m) cc_final: 0.7460 (t) REVERT: A 858 TYR cc_start: 0.7011 (m-80) cc_final: 0.6771 (m-80) REVERT: B 197 GLU cc_start: 0.7617 (tp30) cc_final: 0.6969 (tp30) REVERT: B 364 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5855 (mm) REVERT: B 434 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6832 (m-40) REVERT: B 477 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7922 (mm-30) REVERT: B 603 ASN cc_start: 0.7659 (m-40) cc_final: 0.7263 (t0) REVERT: B 694 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8203 (p) outliers start: 42 outliers final: 32 residues processed: 180 average time/residue: 0.5964 time to fit residues: 153.7372 Evaluate side-chains 168 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN B 162 GLN B 325 GLN B 360 ASN B 430 GLN B 651 ASN B 776 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13020 Z= 0.293 Angle : 0.585 11.992 17604 Z= 0.323 Chirality : 0.058 1.486 1964 Planarity : 0.004 0.045 2243 Dihedral : 6.295 56.899 1759 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.95 % Favored : 91.99 % Rotamer: Outliers : 3.63 % Allowed : 13.02 % Favored : 83.35 % 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: -0.37 (0.21), residues: 1573 helix: 1.41 (0.19), residues: 758 sheet: -1.54 (0.38), residues: 163 loop : -1.97 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 509 HIS 0.007 0.001 HIS A 168 PHE 0.022 0.002 PHE A 480 TYR 0.022 0.001 TYR B 167 ARG 0.004 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 135 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LEU cc_start: 0.9040 (tp) cc_final: 0.8756 (tt) REVERT: A 420 LYS cc_start: 0.7404 (tttt) cc_final: 0.7131 (tttm) REVERT: A 493 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.8001 (mpt-90) REVERT: A 605 SER cc_start: 0.8065 (m) cc_final: 0.7505 (t) REVERT: A 858 TYR cc_start: 0.7018 (m-80) cc_final: 0.6768 (m-80) REVERT: B 364 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5904 (mm) REVERT: B 434 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6824 (m-40) REVERT: B 511 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5890 (tt) REVERT: B 694 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 883 GLU cc_start: 0.7644 (pm20) cc_final: 0.7370 (pm20) outliers start: 51 outliers final: 39 residues processed: 176 average time/residue: 0.5651 time to fit residues: 143.5644 Evaluate side-chains 175 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 776 ASN Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 808 ASN B 360 ASN B 430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13020 Z= 0.171 Angle : 0.544 11.914 17604 Z= 0.295 Chirality : 0.058 1.495 1964 Planarity : 0.004 0.045 2243 Dihedral : 6.134 56.941 1759 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 3.27 % Allowed : 13.45 % Favored : 83.27 % 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: -0.09 (0.22), residues: 1573 helix: 1.72 (0.19), residues: 756 sheet: -1.54 (0.38), residues: 164 loop : -1.87 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 509 HIS 0.006 0.001 HIS B 168 PHE 0.013 0.001 PHE A 502 TYR 0.016 0.001 TYR B 167 ARG 0.005 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6946 (pmm-80) REVERT: A 375 MET cc_start: 0.8503 (mmm) cc_final: 0.8301 (mmm) REVERT: A 420 LYS cc_start: 0.7316 (tttt) cc_final: 0.7058 (tttm) REVERT: A 471 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8106 (tmtt) REVERT: A 493 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7876 (mpt-90) REVERT: A 543 MET cc_start: 0.7203 (mmm) cc_final: 0.6665 (mmp) REVERT: A 605 SER cc_start: 0.7997 (m) cc_final: 0.7420 (t) REVERT: A 858 TYR cc_start: 0.6992 (m-80) cc_final: 0.6749 (m-80) REVERT: B 364 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5924 (mm) REVERT: B 434 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6782 (m-40) REVERT: B 511 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5872 (tt) REVERT: B 603 ASN cc_start: 0.7655 (m-40) cc_final: 0.7235 (t0) REVERT: B 694 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (p) REVERT: B 883 GLU cc_start: 0.7639 (pm20) cc_final: 0.7384 (pm20) outliers start: 46 outliers final: 33 residues processed: 177 average time/residue: 0.5847 time to fit residues: 148.9741 Evaluate side-chains 171 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN B 360 ASN B 430 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13020 Z= 0.233 Angle : 0.555 12.051 17604 Z= 0.305 Chirality : 0.058 1.501 1964 Planarity : 0.004 0.041 2243 Dihedral : 5.801 57.611 1753 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.76 % Favored : 92.18 % Rotamer: Outliers : 3.70 % Allowed : 13.67 % Favored : 82.63 % 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: -0.21 (0.22), residues: 1573 helix: 1.61 (0.19), residues: 759 sheet: -1.55 (0.38), residues: 163 loop : -1.95 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 509 HIS 0.006 0.001 HIS B 168 PHE 0.018 0.002 PHE B 892 TYR 0.019 0.001 TYR B 167 ARG 0.004 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 134 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.5162 (m-80) REVERT: A 205 MET cc_start: 0.7299 (tmm) cc_final: 0.7058 (tmm) REVERT: A 302 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7023 (pmm-80) REVERT: A 359 LEU cc_start: 0.8995 (tp) cc_final: 0.8742 (tt) REVERT: A 420 LYS cc_start: 0.7330 (tttt) cc_final: 0.7066 (tttm) REVERT: A 493 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7766 (mmt90) REVERT: A 605 SER cc_start: 0.8044 (m) cc_final: 0.7468 (t) REVERT: A 858 TYR cc_start: 0.7037 (m-80) cc_final: 0.6804 (m-80) REVERT: B 434 ASN cc_start: 0.7220 (OUTLIER) cc_final: 0.6798 (m-40) REVERT: B 511 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5944 (tt) REVERT: B 694 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 883 GLU cc_start: 0.7625 (pm20) cc_final: 0.7355 (pm20) outliers start: 52 outliers final: 36 residues processed: 181 average time/residue: 0.5642 time to fit residues: 148.0914 Evaluate side-chains 169 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A 808 ASN B 360 ASN B 430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13020 Z= 0.157 Angle : 0.532 11.933 17604 Z= 0.289 Chirality : 0.058 1.510 1964 Planarity : 0.003 0.040 2243 Dihedral : 5.675 58.125 1753 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.06 % Favored : 92.88 % Rotamer: Outliers : 3.13 % Allowed : 14.23 % Favored : 82.63 % 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: 0.02 (0.22), residues: 1573 helix: 1.83 (0.19), residues: 756 sheet: -1.57 (0.38), residues: 164 loop : -1.81 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 509 HIS 0.004 0.001 HIS B 168 PHE 0.014 0.001 PHE B 604 TYR 0.016 0.001 TYR B 167 ARG 0.004 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7317 (tmm) cc_final: 0.7098 (tmm) REVERT: A 359 LEU cc_start: 0.8987 (tp) cc_final: 0.8693 (tt) REVERT: A 420 LYS cc_start: 0.7261 (tttt) cc_final: 0.7014 (tttm) REVERT: A 471 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8145 (tmtt) REVERT: A 493 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7717 (mmt90) REVERT: A 605 SER cc_start: 0.8002 (m) cc_final: 0.7405 (t) REVERT: A 858 TYR cc_start: 0.7014 (m-80) cc_final: 0.6791 (m-80) REVERT: B 364 LEU cc_start: 0.6258 (mm) cc_final: 0.6013 (mm) REVERT: B 434 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6742 (m-40) REVERT: B 511 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5902 (tt) REVERT: B 603 ASN cc_start: 0.7653 (m-40) cc_final: 0.7225 (t0) REVERT: B 694 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 883 GLU cc_start: 0.7681 (pm20) cc_final: 0.7481 (pm20) outliers start: 44 outliers final: 35 residues processed: 176 average time/residue: 0.6050 time to fit residues: 151.4162 Evaluate side-chains 169 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN B 360 ASN B 430 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13020 Z= 0.152 Angle : 0.529 11.934 17604 Z= 0.285 Chirality : 0.058 1.513 1964 Planarity : 0.003 0.039 2243 Dihedral : 5.568 58.843 1753 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 3.13 % Allowed : 14.52 % Favored : 82.35 % 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: 0.17 (0.22), residues: 1573 helix: 1.93 (0.19), residues: 757 sheet: -1.48 (0.38), residues: 164 loop : -1.72 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 509 HIS 0.003 0.001 HIS B 168 PHE 0.015 0.001 PHE A 937 TYR 0.015 0.001 TYR B 521 ARG 0.003 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 139 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6530 (ptt180) REVERT: A 359 LEU cc_start: 0.8961 (tp) cc_final: 0.8672 (tt) REVERT: A 420 LYS cc_start: 0.7252 (tttt) cc_final: 0.7040 (tttm) REVERT: A 471 LYS cc_start: 0.8384 (ttpp) cc_final: 0.8098 (tmtt) REVERT: A 493 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7823 (mmt180) REVERT: A 605 SER cc_start: 0.7930 (m) cc_final: 0.7341 (t) REVERT: A 858 TYR cc_start: 0.7010 (m-80) cc_final: 0.6785 (m-80) REVERT: B 364 LEU cc_start: 0.6188 (mm) cc_final: 0.5957 (mm) REVERT: B 434 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6489 (m-40) REVERT: B 511 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5822 (tt) REVERT: B 603 ASN cc_start: 0.7611 (m-40) cc_final: 0.7183 (t0) REVERT: B 694 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8211 (p) REVERT: B 883 GLU cc_start: 0.7657 (pm20) cc_final: 0.7438 (pm20) outliers start: 44 outliers final: 32 residues processed: 179 average time/residue: 0.6368 time to fit residues: 162.5437 Evaluate side-chains 166 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN B 360 ASN B 430 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13020 Z= 0.186 Angle : 0.548 11.781 17604 Z= 0.296 Chirality : 0.058 1.493 1964 Planarity : 0.004 0.055 2243 Dihedral : 5.602 59.796 1751 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 2.78 % Allowed : 15.16 % Favored : 82.06 % 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: 0.06 (0.22), residues: 1573 helix: 1.84 (0.19), residues: 758 sheet: -1.60 (0.37), residues: 171 loop : -1.75 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 509 HIS 0.004 0.001 HIS B 168 PHE 0.014 0.001 PHE B 541 TYR 0.018 0.001 TYR B 167 ARG 0.007 0.000 ARG B 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3146 Ramachandran restraints generated. 1573 Oldfield, 0 Emsley, 1573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6680 (ptt180) REVERT: A 359 LEU cc_start: 0.8991 (tp) cc_final: 0.8700 (tt) REVERT: A 420 LYS cc_start: 0.7284 (tttt) cc_final: 0.7029 (tttm) REVERT: A 471 LYS cc_start: 0.8417 (ttpp) cc_final: 0.8136 (tmtt) REVERT: A 493 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7753 (mmt90) REVERT: A 605 SER cc_start: 0.7933 (m) cc_final: 0.7342 (t) REVERT: A 744 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6133 (p90) REVERT: A 858 TYR cc_start: 0.7024 (m-80) cc_final: 0.6793 (m-80) REVERT: B 364 LEU cc_start: 0.6183 (mm) cc_final: 0.5953 (mm) REVERT: B 434 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6508 (m-40) REVERT: B 511 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5890 (tt) REVERT: B 603 ASN cc_start: 0.7606 (m-40) cc_final: 0.7157 (t0) REVERT: B 694 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8176 (p) REVERT: B 883 GLU cc_start: 0.7681 (pm20) cc_final: 0.7469 (pm20) outliers start: 39 outliers final: 30 residues processed: 170 average time/residue: 0.6029 time to fit residues: 150.2545 Evaluate side-chains 165 residues out of total 1405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 PHE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 833 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 ASN B 360 ASN B 430 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.136151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.109674 restraints weight = 97268.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.113246 restraints weight = 52172.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.115537 restraints weight = 35975.653| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13020 Z= 0.194 Angle : 0.554 12.051 17604 Z= 0.300 Chirality : 0.058 1.533 1964 Planarity : 0.004 0.051 2243 Dihedral : 5.630 59.049 1751 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 2.99 % Allowed : 14.80 % Favored : 82.21 % 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: 0.00 (0.22), residues: 1573 helix: 1.78 (0.19), residues: 758 sheet: -1.63 (0.37), residues: 173 loop : -1.77 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 509 HIS 0.005 0.001 HIS B 168 PHE 0.014 0.001 PHE B 541 TYR 0.019 0.001 TYR B 167 ARG 0.006 0.000 ARG B 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5326.81 seconds wall clock time: 95 minutes 1.46 seconds (5701.46 seconds total)