Starting phenix.real_space_refine on Sun Aug 4 17:46:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/08_2024/8xvx_38721.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/08_2024/8xvx_38721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/08_2024/8xvx_38721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/08_2024/8xvx_38721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/08_2024/8xvx_38721.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/08_2024/8xvx_38721.cif" } resolution = 3.32 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= 0.003 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7350 2.51 5 N 1810 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 682": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11110 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5555 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 36, 'TRANS': 659} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 5555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5555 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 36, 'TRANS': 659} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 6.65, per 1000 atoms: 0.60 Number of scatterers: 11110 At special positions: 0 Unit cell: (88.62, 143.48, 108.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1900 8.00 N 1810 7.00 C 7350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.1 seconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 2 sheets defined 76.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'B' and resid 3 through 31 removed outlier: 3.573A pdb=" N GLN B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.624A pdb=" N GLU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.928A pdb=" N ASP B 89 " --> pdb=" O PRO B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.552A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Proline residue: B 111 - end of helix Proline residue: B 122 - end of helix removed outlier: 3.521A pdb=" N THR B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 136 removed outlier: 4.276A pdb=" N MET B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 155 through 193 removed outlier: 3.755A pdb=" N PHE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.949A pdb=" N LEU B 283 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 284 " --> pdb=" O LEU B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 284' Processing helix chain 'B' and resid 290 through 314 removed outlier: 3.779A pdb=" N TYR B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 360 through 366 removed outlier: 4.145A pdb=" N ALA B 365 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 366 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 398 Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 399 through 408 removed outlier: 4.306A pdb=" N GLY B 404 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 406 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 4.513A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 440 Proline residue: B 430 - end of helix removed outlier: 4.493A pdb=" N PHE B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.602A pdb=" N ILE B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 452 " --> pdb=" O MET B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 489 Processing helix chain 'B' and resid 489 through 495 removed outlier: 4.679A pdb=" N ASN B 495 " --> pdb=" O ASN B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 534 removed outlier: 4.217A pdb=" N ILE B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Proline residue: B 510 - end of helix removed outlier: 3.785A pdb=" N THR B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 547 removed outlier: 3.579A pdb=" N LEU B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 565 through 587 Proline residue: B 571 - end of helix Proline residue: B 585 - end of helix Processing helix chain 'B' and resid 590 through 611 removed outlier: 3.841A pdb=" N ILE B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 Processing helix chain 'B' and resid 653 through 658 removed outlier: 3.614A pdb=" N PHE B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 removed outlier: 4.111A pdb=" N ILE B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.789A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 Processing helix chain 'A' and resid 4 through 31 removed outlier: 3.574A pdb=" N GLN A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.624A pdb=" N GLU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 3.927A pdb=" N ASP A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 126 removed outlier: 3.551A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Proline residue: A 111 - end of helix Proline residue: A 122 - end of helix removed outlier: 3.520A pdb=" N THR A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 removed outlier: 4.276A pdb=" N MET A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 155 through 193 removed outlier: 3.756A pdb=" N PHE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.949A pdb=" N LEU A 283 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 284 " --> pdb=" O LEU A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.779A pdb=" N TYR A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 360 through 366 removed outlier: 4.144A pdb=" N ALA A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 399 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 408 removed outlier: 4.305A pdb=" N GLY A 404 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 4.514A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 440 Proline residue: A 430 - end of helix removed outlier: 4.493A pdb=" N PHE A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.602A pdb=" N ILE A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 489 Processing helix chain 'A' and resid 489 through 495 removed outlier: 4.678A pdb=" N ASN A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 534 removed outlier: 4.217A pdb=" N ILE A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Proline residue: A 510 - end of helix removed outlier: 3.785A pdb=" N THR A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 547 removed outlier: 3.580A pdb=" N LEU A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 565 through 587 Proline residue: A 571 - end of helix Proline residue: A 585 - end of helix Processing helix chain 'A' and resid 590 through 611 removed outlier: 3.841A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.613A pdb=" N PHE A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 4.112A pdb=" N ILE A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.789A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 Processing sheet with id=AA1, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.545A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 351 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.543A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 351 " --> pdb=" O LEU A 205 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3409 1.34 - 1.46: 1875 1.46 - 1.57: 6046 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11422 Sorted by residual: bond pdb=" CA THR A 401 " pdb=" C THR A 401 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.62e+00 bond pdb=" CA THR B 401 " pdb=" C THR B 401 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.34e-02 5.57e+03 2.49e+00 bond pdb=" CB CYS A 672 " pdb=" SG CYS A 672 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB CYS B 672 " pdb=" SG CYS B 672 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CE1 TYR B 181 " pdb=" CZ TYR B 181 " ideal model delta sigma weight residual 1.378 1.344 0.034 2.40e-02 1.74e+03 2.04e+00 ... (remaining 11417 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.69: 366 106.69 - 113.54: 6358 113.54 - 120.40: 4651 120.40 - 127.25: 4018 127.25 - 134.11: 157 Bond angle restraints: 15550 Sorted by residual: angle pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" C ASN B 128 " ideal model delta sigma weight residual 114.62 110.19 4.43 1.14e+00 7.69e-01 1.51e+01 angle pdb=" N ASN A 128 " pdb=" CA ASN A 128 " pdb=" C ASN A 128 " ideal model delta sigma weight residual 114.62 110.22 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N PRO B 715 " pdb=" CA PRO B 715 " pdb=" C PRO B 715 " ideal model delta sigma weight residual 112.47 118.68 -6.21 2.06e+00 2.36e-01 9.08e+00 angle pdb=" N PRO A 715 " pdb=" CA PRO A 715 " pdb=" C PRO A 715 " ideal model delta sigma weight residual 112.47 118.59 -6.12 2.06e+00 2.36e-01 8.82e+00 angle pdb=" N LYS A 673 " pdb=" CA LYS A 673 " pdb=" C LYS A 673 " ideal model delta sigma weight residual 111.02 107.85 3.17 1.22e+00 6.72e-01 6.74e+00 ... (remaining 15545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 5861 15.85 - 31.70: 661 31.70 - 47.56: 168 47.56 - 63.41: 24 63.41 - 79.26: 16 Dihedral angle restraints: 6730 sinusoidal: 2612 harmonic: 4118 Sorted by residual: dihedral pdb=" CA LEU B 548 " pdb=" C LEU B 548 " pdb=" N VAL B 549 " pdb=" CA VAL B 549 " ideal model delta harmonic sigma weight residual 180.00 -143.06 -36.94 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA LEU A 548 " pdb=" C LEU A 548 " pdb=" N VAL A 549 " pdb=" CA VAL A 549 " ideal model delta harmonic sigma weight residual -180.00 -143.07 -36.93 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA ARG B 207 " pdb=" C ARG B 207 " pdb=" N ASN B 208 " pdb=" CA ASN B 208 " ideal model delta harmonic sigma weight residual 180.00 143.37 36.63 0 5.00e+00 4.00e-02 5.37e+01 ... (remaining 6727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1147 0.043 - 0.087: 462 0.087 - 0.130: 123 0.130 - 0.173: 20 0.173 - 0.216: 10 Chirality restraints: 1762 Sorted by residual: chirality pdb=" CB THR B 587 " pdb=" CA THR B 587 " pdb=" OG1 THR B 587 " pdb=" CG2 THR B 587 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR A 587 " pdb=" CA THR A 587 " pdb=" OG1 THR A 587 " pdb=" CG2 THR A 587 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA THR B 110 " pdb=" N THR B 110 " pdb=" C THR B 110 " pdb=" CB THR B 110 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1759 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 181 " 0.028 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR A 181 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 181 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 181 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 181 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 181 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 181 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " 0.028 2.00e-02 2.50e+03 2.25e-02 1.02e+01 pdb=" CG TYR B 181 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 624 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 625 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " 0.037 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 268 2.69 - 3.24: 11718 3.24 - 3.79: 17891 3.79 - 4.35: 22295 4.35 - 4.90: 38118 Nonbonded interactions: 90290 Sorted by model distance: nonbonded pdb=" O MET B 82 " pdb=" NH2 ARG B 606 " model vdw 2.136 3.120 nonbonded pdb=" O MET A 82 " pdb=" NH2 ARG A 606 " model vdw 2.137 3.120 nonbonded pdb=" OH TYR A 167 " pdb=" O PHE A 657 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 167 " pdb=" O PHE B 657 " model vdw 2.219 3.040 nonbonded pdb=" O PHE A 420 " pdb=" OG SER A 423 " model vdw 2.237 3.040 ... (remaining 90285 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' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.360 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.007 0.059 11422 Z= 0.457 Angle : 0.764 6.313 15550 Z= 0.430 Chirality : 0.050 0.216 1762 Planarity : 0.007 0.065 1944 Dihedral : 14.523 79.260 4054 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.50 (0.23), residues: 1384 helix: 0.98 (0.17), residues: 940 sheet: -3.31 (0.85), residues: 30 loop : -3.27 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 624 HIS 0.008 0.002 HIS B 229 PHE 0.014 0.002 PHE A 593 TYR 0.055 0.002 TYR A 181 ARG 0.004 0.001 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.250 Fit side-chains REVERT: B 376 LEU cc_start: 0.8419 (mt) cc_final: 0.8217 (mp) REVERT: B 659 ILE cc_start: 0.8501 (tp) cc_final: 0.8246 (tp) REVERT: A 151 ASN cc_start: 0.6780 (t0) cc_final: 0.6519 (t0) REVERT: A 257 ASN cc_start: 0.8542 (m110) cc_final: 0.8328 (m110) REVERT: A 378 MET cc_start: 0.6996 (mmm) cc_final: 0.6181 (mmm) REVERT: A 643 MET cc_start: 0.7433 (ttp) cc_final: 0.7065 (ttt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1626 time to fit residues: 48.3031 Evaluate side-chains 153 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 0.0050 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 0.0170 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN B 611 ASN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11422 Z= 0.200 Angle : 0.635 8.015 15550 Z= 0.334 Chirality : 0.044 0.207 1762 Planarity : 0.007 0.068 1944 Dihedral : 5.205 38.069 1494 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.54 % Allowed : 7.29 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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 (0.24), residues: 1384 helix: 1.43 (0.17), residues: 944 sheet: -3.17 (0.83), residues: 30 loop : -3.11 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 624 HIS 0.003 0.001 HIS A 628 PHE 0.017 0.001 PHE B 428 TYR 0.034 0.002 TYR A 181 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: B 151 ASN cc_start: 0.7038 (t0) cc_final: 0.6526 (t0) REVERT: B 165 MET cc_start: 0.7894 (mmp) cc_final: 0.7497 (mmm) REVERT: B 260 ASP cc_start: 0.7801 (t0) cc_final: 0.7574 (t0) REVERT: B 449 SER cc_start: 0.8851 (m) cc_final: 0.8564 (p) REVERT: A 19 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7055 (t80) REVERT: A 31 GLN cc_start: 0.7908 (mm110) cc_final: 0.7704 (mm-40) REVERT: A 72 PHE cc_start: 0.8054 (p90) cc_final: 0.7736 (p90) REVERT: A 151 ASN cc_start: 0.6905 (t0) cc_final: 0.6657 (t0) REVERT: A 257 ASN cc_start: 0.8453 (m110) cc_final: 0.8236 (m110) REVERT: A 260 ASP cc_start: 0.7962 (t0) cc_final: 0.7701 (t0) outliers start: 18 outliers final: 14 residues processed: 177 average time/residue: 0.1695 time to fit residues: 47.6382 Evaluate side-chains 163 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11422 Z= 0.212 Angle : 0.600 8.701 15550 Z= 0.313 Chirality : 0.043 0.190 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.968 36.905 1494 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 1.72 % Allowed : 10.12 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.24 (0.24), residues: 1384 helix: 1.52 (0.17), residues: 958 sheet: -2.87 (0.84), residues: 30 loop : -3.17 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.005 0.001 HIS A 628 PHE 0.017 0.001 PHE B 21 TYR 0.031 0.001 TYR A 181 ARG 0.003 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.160 Fit side-chains REVERT: B 151 ASN cc_start: 0.6969 (t0) cc_final: 0.6502 (t0) REVERT: B 157 MET cc_start: 0.4374 (tmm) cc_final: 0.3947 (tmm) REVERT: B 260 ASP cc_start: 0.7811 (t0) cc_final: 0.7506 (t0) REVERT: B 587 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8813 (p) REVERT: A 19 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7018 (t80) REVERT: A 72 PHE cc_start: 0.8047 (p90) cc_final: 0.7712 (p90) REVERT: A 151 ASN cc_start: 0.6879 (t0) cc_final: 0.6637 (t0) REVERT: A 260 ASP cc_start: 0.7994 (t0) cc_final: 0.7681 (t0) REVERT: A 378 MET cc_start: 0.6795 (mmm) cc_final: 0.6162 (mmm) outliers start: 20 outliers final: 15 residues processed: 167 average time/residue: 0.1732 time to fit residues: 46.4584 Evaluate side-chains 158 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 40.0000 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 0.0570 chunk 119 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11422 Z= 0.188 Angle : 0.592 9.542 15550 Z= 0.306 Chirality : 0.042 0.189 1762 Planarity : 0.006 0.065 1944 Dihedral : 4.829 35.720 1494 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.97 % Allowed : 14.67 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.47 (0.24), residues: 1384 helix: 1.66 (0.17), residues: 954 sheet: -2.94 (0.85), residues: 30 loop : -2.92 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.015 0.001 PHE A 493 TYR 0.023 0.001 TYR A 181 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.334 Fit side-chains REVERT: B 151 ASN cc_start: 0.6972 (t0) cc_final: 0.6518 (t0) REVERT: B 157 MET cc_start: 0.4225 (tmm) cc_final: 0.3842 (tmm) REVERT: B 260 ASP cc_start: 0.7894 (t0) cc_final: 0.7570 (t0) REVERT: B 587 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8791 (p) REVERT: A 19 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7025 (t80) REVERT: A 72 PHE cc_start: 0.8011 (p90) cc_final: 0.7709 (p90) REVERT: A 117 TRP cc_start: 0.7726 (m100) cc_final: 0.7265 (m100) REVERT: A 151 ASN cc_start: 0.6952 (t0) cc_final: 0.6681 (t0) REVERT: A 260 ASP cc_start: 0.7901 (t0) cc_final: 0.7653 (t0) REVERT: A 534 MET cc_start: 0.7801 (mmm) cc_final: 0.7429 (mtt) outliers start: 23 outliers final: 17 residues processed: 172 average time/residue: 0.1701 time to fit residues: 46.5106 Evaluate side-chains 167 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11422 Z= 0.247 Angle : 0.601 9.518 15550 Z= 0.312 Chirality : 0.043 0.190 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.781 36.383 1494 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.06 % Allowed : 16.30 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1384 helix: 1.62 (0.17), residues: 958 sheet: -2.94 (0.86), residues: 30 loop : -3.07 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 624 HIS 0.005 0.001 HIS A 628 PHE 0.016 0.001 PHE B 21 TYR 0.029 0.001 TYR A 181 ARG 0.003 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 1.265 Fit side-chains REVERT: B 151 ASN cc_start: 0.6981 (t0) cc_final: 0.6518 (t0) REVERT: B 157 MET cc_start: 0.4225 (tmm) cc_final: 0.3850 (tmm) REVERT: B 260 ASP cc_start: 0.7812 (t0) cc_final: 0.7472 (t0) REVERT: B 587 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8796 (p) REVERT: A 19 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7037 (t80) REVERT: A 72 PHE cc_start: 0.7964 (p90) cc_final: 0.7650 (p90) REVERT: A 151 ASN cc_start: 0.7145 (t0) cc_final: 0.6863 (t0) REVERT: A 155 TYR cc_start: 0.5967 (t80) cc_final: 0.5335 (t80) REVERT: A 260 ASP cc_start: 0.7923 (t0) cc_final: 0.7669 (t0) REVERT: A 534 MET cc_start: 0.7793 (mmm) cc_final: 0.7434 (mtt) outliers start: 24 outliers final: 19 residues processed: 165 average time/residue: 0.1649 time to fit residues: 43.5985 Evaluate side-chains 166 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11422 Z= 0.206 Angle : 0.590 9.539 15550 Z= 0.304 Chirality : 0.042 0.192 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.720 35.396 1494 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.14 % Allowed : 18.01 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1384 helix: 1.67 (0.17), residues: 958 sheet: -2.92 (0.90), residues: 30 loop : -3.03 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.016 0.001 PHE B 21 TYR 0.026 0.001 TYR B 181 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.403 Fit side-chains REVERT: B 151 ASN cc_start: 0.6979 (t0) cc_final: 0.6518 (t0) REVERT: B 157 MET cc_start: 0.4157 (tmm) cc_final: 0.3812 (tmm) REVERT: B 260 ASP cc_start: 0.7811 (t0) cc_final: 0.7459 (t0) REVERT: B 521 MET cc_start: 0.7750 (ttm) cc_final: 0.7507 (ttp) REVERT: B 587 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8771 (p) REVERT: A 19 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.6902 (t80) REVERT: A 72 PHE cc_start: 0.7873 (p90) cc_final: 0.7623 (p90) REVERT: A 151 ASN cc_start: 0.7114 (t0) cc_final: 0.6834 (t0) REVERT: A 155 TYR cc_start: 0.6048 (t80) cc_final: 0.5335 (t80) REVERT: A 260 ASP cc_start: 0.7928 (t0) cc_final: 0.7669 (t0) REVERT: A 378 MET cc_start: 0.6954 (mmm) cc_final: 0.6394 (mmm) REVERT: A 521 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7606 (ttp) REVERT: A 534 MET cc_start: 0.7736 (mmm) cc_final: 0.7380 (mtt) outliers start: 25 outliers final: 20 residues processed: 166 average time/residue: 0.1632 time to fit residues: 43.5629 Evaluate side-chains 166 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11422 Z= 0.215 Angle : 0.591 9.725 15550 Z= 0.304 Chirality : 0.042 0.190 1762 Planarity : 0.006 0.067 1944 Dihedral : 4.669 35.143 1494 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.66 % Allowed : 17.58 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.47 (0.24), residues: 1384 helix: 1.69 (0.17), residues: 960 sheet: -2.84 (0.91), residues: 30 loop : -3.10 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.013 0.001 PHE A 493 TYR 0.025 0.001 TYR A 181 ARG 0.002 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.355 Fit side-chains REVERT: B 78 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 151 ASN cc_start: 0.6985 (t0) cc_final: 0.6539 (t0) REVERT: B 157 MET cc_start: 0.4156 (tmm) cc_final: 0.3797 (tmm) REVERT: B 260 ASP cc_start: 0.7814 (t0) cc_final: 0.7467 (t0) REVERT: B 378 MET cc_start: 0.7052 (mmm) cc_final: 0.6604 (mmm) REVERT: B 521 MET cc_start: 0.7771 (ttm) cc_final: 0.7508 (ttp) REVERT: B 587 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8768 (p) REVERT: A 19 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7060 (t80) REVERT: A 72 PHE cc_start: 0.7911 (p90) cc_final: 0.7680 (p90) REVERT: A 151 ASN cc_start: 0.7132 (t0) cc_final: 0.6910 (t0) REVERT: A 155 TYR cc_start: 0.6148 (t80) cc_final: 0.5262 (t80) REVERT: A 260 ASP cc_start: 0.7924 (t0) cc_final: 0.7679 (t0) REVERT: A 378 MET cc_start: 0.6848 (mmm) cc_final: 0.6426 (mmm) REVERT: A 521 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7629 (ttp) REVERT: A 534 MET cc_start: 0.7751 (mmm) cc_final: 0.7383 (mtt) REVERT: A 587 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8533 (p) outliers start: 31 outliers final: 20 residues processed: 174 average time/residue: 0.1711 time to fit residues: 48.0279 Evaluate side-chains 172 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11422 Z= 0.197 Angle : 0.591 9.766 15550 Z= 0.300 Chirality : 0.042 0.192 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.603 34.271 1494 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.40 % Allowed : 18.18 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.60 (0.24), residues: 1384 helix: 1.77 (0.17), residues: 956 sheet: -2.80 (0.92), residues: 30 loop : -2.94 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.013 0.001 PHE B 493 TYR 0.022 0.001 TYR A 181 ARG 0.002 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.242 Fit side-chains REVERT: B 78 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 151 ASN cc_start: 0.6984 (t0) cc_final: 0.6536 (t0) REVERT: B 157 MET cc_start: 0.4128 (tmm) cc_final: 0.3862 (tmm) REVERT: B 222 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: B 260 ASP cc_start: 0.7809 (t0) cc_final: 0.7459 (t0) REVERT: B 378 MET cc_start: 0.7039 (mmm) cc_final: 0.6609 (mmm) REVERT: B 521 MET cc_start: 0.7872 (ttm) cc_final: 0.7597 (ttp) REVERT: B 587 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8865 (p) REVERT: A 78 GLU cc_start: 0.7558 (pp20) cc_final: 0.7251 (pp20) REVERT: A 151 ASN cc_start: 0.7125 (t0) cc_final: 0.6897 (t0) REVERT: A 260 ASP cc_start: 0.7927 (t0) cc_final: 0.7685 (t0) REVERT: A 521 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7602 (ttp) REVERT: A 534 MET cc_start: 0.7746 (mmm) cc_final: 0.7364 (mtt) REVERT: A 587 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8538 (p) REVERT: A 613 TYR cc_start: 0.8084 (m-10) cc_final: 0.7657 (m-10) outliers start: 28 outliers final: 23 residues processed: 171 average time/residue: 0.1625 time to fit residues: 44.2479 Evaluate side-chains 174 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 74 optimal weight: 0.0070 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11422 Z= 0.190 Angle : 0.589 10.045 15550 Z= 0.299 Chirality : 0.042 0.192 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.577 33.592 1494 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.23 % Allowed : 18.70 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1384 helix: 1.82 (0.17), residues: 934 sheet: -2.68 (0.93), residues: 30 loop : -3.00 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.015 0.001 PHE A 72 TYR 0.019 0.001 TYR A 181 ARG 0.002 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 1.342 Fit side-chains REVERT: B 78 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 151 ASN cc_start: 0.6991 (t0) cc_final: 0.6567 (t0) REVERT: B 157 MET cc_start: 0.4092 (tmm) cc_final: 0.3851 (tmm) REVERT: B 222 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: B 260 ASP cc_start: 0.7853 (t0) cc_final: 0.7499 (t0) REVERT: B 378 MET cc_start: 0.6921 (mmm) cc_final: 0.6499 (mmm) REVERT: B 521 MET cc_start: 0.7867 (ttm) cc_final: 0.7553 (ttp) REVERT: B 587 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8865 (p) REVERT: A 78 GLU cc_start: 0.7569 (pp20) cc_final: 0.7260 (pp20) REVERT: A 151 ASN cc_start: 0.7101 (t0) cc_final: 0.6872 (t0) REVERT: A 260 ASP cc_start: 0.7921 (t0) cc_final: 0.7684 (t0) REVERT: A 378 MET cc_start: 0.6789 (mmm) cc_final: 0.6145 (mmm) REVERT: A 521 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7629 (ttp) REVERT: A 534 MET cc_start: 0.7744 (mmm) cc_final: 0.7353 (mtt) REVERT: A 587 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8552 (p) REVERT: A 613 TYR cc_start: 0.8089 (m-10) cc_final: 0.7635 (m-10) outliers start: 26 outliers final: 21 residues processed: 172 average time/residue: 0.1638 time to fit residues: 45.1724 Evaluate side-chains 178 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 137 optimal weight: 0.1980 chunk 126 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11422 Z= 0.193 Angle : 0.602 10.074 15550 Z= 0.302 Chirality : 0.042 0.190 1762 Planarity : 0.006 0.066 1944 Dihedral : 4.523 33.242 1494 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.14 % Allowed : 18.61 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1384 helix: 1.85 (0.17), residues: 934 sheet: -2.56 (0.94), residues: 30 loop : -3.01 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.013 0.001 PHE A 72 TYR 0.020 0.001 TYR A 181 ARG 0.002 0.000 ARG A 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.273 Fit side-chains REVERT: B 151 ASN cc_start: 0.7110 (t0) cc_final: 0.6684 (t0) REVERT: B 157 MET cc_start: 0.4080 (tmm) cc_final: 0.3849 (tmm) REVERT: B 222 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: B 260 ASP cc_start: 0.7761 (t0) cc_final: 0.7489 (t0) REVERT: B 378 MET cc_start: 0.7003 (mmm) cc_final: 0.6568 (mmm) REVERT: B 521 MET cc_start: 0.7926 (ttm) cc_final: 0.7610 (ttp) REVERT: B 587 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8868 (p) REVERT: A 19 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.6980 (t80) REVERT: A 78 GLU cc_start: 0.7595 (pp20) cc_final: 0.7281 (pp20) REVERT: A 151 ASN cc_start: 0.7122 (t0) cc_final: 0.6903 (t0) REVERT: A 260 ASP cc_start: 0.7946 (t0) cc_final: 0.7715 (t0) REVERT: A 378 MET cc_start: 0.6754 (mmm) cc_final: 0.6114 (mmm) REVERT: A 521 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7621 (ttp) REVERT: A 534 MET cc_start: 0.7805 (mmm) cc_final: 0.7412 (mtt) REVERT: A 587 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8576 (p) REVERT: A 613 TYR cc_start: 0.8056 (m-10) cc_final: 0.7602 (m-10) outliers start: 25 outliers final: 19 residues processed: 173 average time/residue: 0.1643 time to fit residues: 45.5209 Evaluate side-chains 176 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.0370 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 96 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.180185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129191 restraints weight = 13102.125| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.64 r_work: 0.3301 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11422 Z= 0.175 Angle : 0.590 9.894 15550 Z= 0.297 Chirality : 0.041 0.190 1762 Planarity : 0.006 0.065 1944 Dihedral : 4.464 31.845 1494 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.23 % Allowed : 18.61 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.63 (0.24), residues: 1384 helix: 1.90 (0.18), residues: 934 sheet: -2.44 (0.94), residues: 30 loop : -2.98 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 624 HIS 0.003 0.000 HIS A 628 PHE 0.014 0.001 PHE A 72 TYR 0.017 0.001 TYR B 181 ARG 0.002 0.000 ARG A 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.06 seconds wall clock time: 40 minutes 55.55 seconds (2455.55 seconds total)