Starting phenix.real_space_refine on Wed Jun 26 22:26:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/06_2024/8xvx_38721.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/06_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_38721/06_2024/8xvx_38721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/06_2024/8xvx_38721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/06_2024/8xvx_38721.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvx_38721/06_2024/8xvx_38721.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 6.23, per 1000 atoms: 0.56 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: 4.20 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: 1.15 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: 3.34 Time building geometry restraints manager: 4.68 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 2.520 nonbonded pdb=" O MET A 82 " pdb=" NH2 ARG A 606 " model vdw 2.137 2.520 nonbonded pdb=" OH TYR A 167 " pdb=" O PHE A 657 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR B 167 " pdb=" O PHE B 657 " model vdw 2.219 2.440 nonbonded pdb=" O PHE A 420 " pdb=" OG SER A 423 " model vdw 2.237 2.440 ... (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 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: 3.970 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: 3.520 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.560 Find NCS groups from input model: 0.570 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.470 ------------------------------------------------------------------------------- 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 : 1.312 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: 0.1613 time to fit residues: 48.1057 Evaluate side-chains 153 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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: 9.9990 chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 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: 0.7746 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11422 Z= 0.217 Angle : 0.628 8.114 15550 Z= 0.329 Chirality : 0.044 0.185 1762 Planarity : 0.006 0.067 1944 Dihedral : 5.175 35.721 1494 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.29 % Allowed : 7.55 % 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: 0.08 (0.24), residues: 1384 helix: 1.47 (0.17), residues: 944 sheet: -3.17 (0.81), residues: 30 loop : -3.23 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.020 0.001 PHE B 428 TYR 0.037 0.002 TYR A 181 ARG 0.001 0.000 ARG B 682 *********************** 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 175 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: B 151 ASN cc_start: 0.6937 (t0) cc_final: 0.6414 (t0) REVERT: B 165 MET cc_start: 0.7932 (mmp) cc_final: 0.7462 (mmm) REVERT: B 260 ASP cc_start: 0.7799 (t0) cc_final: 0.7581 (t0) REVERT: B 428 PHE cc_start: 0.8203 (t80) cc_final: 0.7963 (t80) REVERT: A 19 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7062 (t80) REVERT: A 31 GLN cc_start: 0.7898 (mm110) cc_final: 0.7697 (mm-40) REVERT: A 72 PHE cc_start: 0.7995 (p90) cc_final: 0.7689 (p90) REVERT: A 151 ASN cc_start: 0.6871 (t0) cc_final: 0.6611 (t0) REVERT: A 257 ASN cc_start: 0.8461 (m110) cc_final: 0.8238 (m110) REVERT: A 260 ASP cc_start: 0.7960 (t0) cc_final: 0.7695 (t0) REVERT: A 521 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7649 (ttp) outliers start: 15 outliers final: 13 residues processed: 169 average time/residue: 0.1673 time to fit residues: 44.8942 Evaluate side-chains 160 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 521 MET 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: 0.9980 chunk 85 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 0.0570 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.1310 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= 0.209 Angle : 0.590 8.983 15550 Z= 0.306 Chirality : 0.042 0.191 1762 Planarity : 0.006 0.064 1944 Dihedral : 4.942 34.576 1494 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 1.89 % Allowed : 10.38 % Favored : 87.74 % 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: 0.22 (0.24), residues: 1384 helix: 1.54 (0.17), residues: 958 sheet: -2.82 (0.85), residues: 30 loop : -3.29 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 624 HIS 0.005 0.001 HIS A 628 PHE 0.017 0.001 PHE B 21 TYR 0.030 0.001 TYR A 181 ARG 0.002 0.000 ARG A 555 *********************** 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 183 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.263 Fit side-chains REVERT: B 151 ASN cc_start: 0.6842 (t0) cc_final: 0.6359 (t0) REVERT: B 260 ASP cc_start: 0.7808 (t0) cc_final: 0.7502 (t0) REVERT: B 521 MET cc_start: 0.7982 (ttm) cc_final: 0.7679 (ttp) REVERT: B 587 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8867 (p) REVERT: A 19 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7016 (t80) REVERT: A 72 PHE cc_start: 0.8058 (p90) cc_final: 0.7733 (p90) REVERT: A 151 ASN cc_start: 0.6820 (t0) cc_final: 0.6546 (t0) REVERT: A 165 MET cc_start: 0.7821 (mmp) cc_final: 0.7563 (mmm) REVERT: A 260 ASP cc_start: 0.7993 (t0) cc_final: 0.7681 (t0) REVERT: A 397 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7963 (mm-40) REVERT: A 534 MET cc_start: 0.7782 (mmm) cc_final: 0.7423 (mtt) outliers start: 22 outliers final: 17 residues processed: 173 average time/residue: 0.1625 time to fit residues: 45.2733 Evaluate side-chains 164 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 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 240 CYS 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: 50.0000 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.0070 chunk 119 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 611 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: 0.7707 moved from start: 0.1589 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= 0.182 Angle : 0.574 8.901 15550 Z= 0.296 Chirality : 0.041 0.190 1762 Planarity : 0.006 0.064 1944 Dihedral : 4.795 33.300 1494 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.06 % Allowed : 14.92 % Favored : 83.02 % 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: 0.41 (0.24), residues: 1384 helix: 1.68 (0.17), residues: 956 sheet: -2.81 (0.86), residues: 30 loop : -3.18 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.016 0.001 PHE B 21 TYR 0.024 0.001 TYR A 181 ARG 0.003 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 183 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.059 Fit side-chains REVERT: B 151 ASN cc_start: 0.6736 (t0) cc_final: 0.6258 (t0) REVERT: B 157 MET cc_start: 0.4185 (tmm) cc_final: 0.3816 (tmm) REVERT: B 208 ASN cc_start: 0.8712 (t0) cc_final: 0.8505 (t0) REVERT: B 260 ASP cc_start: 0.7892 (t0) cc_final: 0.7560 (t0) REVERT: B 521 MET cc_start: 0.8046 (ttm) cc_final: 0.7713 (ttp) REVERT: B 587 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 19 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7023 (t80) REVERT: A 72 PHE cc_start: 0.8012 (p90) cc_final: 0.7717 (p90) REVERT: A 82 MET cc_start: 0.8889 (ttm) cc_final: 0.8634 (ttm) REVERT: A 151 ASN cc_start: 0.7102 (t0) cc_final: 0.6785 (t0) REVERT: A 260 ASP cc_start: 0.7892 (t0) cc_final: 0.7641 (t0) REVERT: A 378 MET cc_start: 0.6914 (mmm) cc_final: 0.6364 (mmm) REVERT: A 521 MET cc_start: 0.7930 (ttp) cc_final: 0.7529 (ttp) REVERT: A 534 MET cc_start: 0.7744 (mmm) cc_final: 0.7424 (mtt) outliers start: 24 outliers final: 18 residues processed: 175 average time/residue: 0.1656 time to fit residues: 45.9628 Evaluate side-chains 170 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 240 CYS 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 612 VAL 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: 2.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- 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: 0.7746 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11422 Z= 0.237 Angle : 0.587 8.976 15550 Z= 0.303 Chirality : 0.042 0.189 1762 Planarity : 0.006 0.065 1944 Dihedral : 4.739 33.947 1494 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.49 % Allowed : 16.47 % Favored : 81.05 % 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: 0.40 (0.24), residues: 1384 helix: 1.69 (0.17), residues: 956 sheet: -2.86 (0.89), residues: 30 loop : -3.22 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 624 HIS 0.005 0.001 HIS A 628 PHE 0.017 0.001 PHE B 21 TYR 0.028 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 176 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.222 Fit side-chains REVERT: B 151 ASN cc_start: 0.6888 (t0) cc_final: 0.6336 (t0) REVERT: B 157 MET cc_start: 0.4356 (tmm) cc_final: 0.4017 (tmm) REVERT: B 260 ASP cc_start: 0.7808 (t0) cc_final: 0.7462 (t0) REVERT: B 521 MET cc_start: 0.8147 (ttm) cc_final: 0.7799 (ttp) REVERT: B 587 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8819 (p) REVERT: A 19 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7039 (t80) REVERT: A 72 PHE cc_start: 0.7955 (p90) cc_final: 0.7660 (p90) REVERT: A 82 MET cc_start: 0.8941 (ttm) cc_final: 0.8726 (ttm) REVERT: A 151 ASN cc_start: 0.7084 (t0) cc_final: 0.6783 (t0) REVERT: A 155 TYR cc_start: 0.5804 (t80) cc_final: 0.5449 (t80) REVERT: A 260 ASP cc_start: 0.7925 (t0) cc_final: 0.7667 (t0) REVERT: A 521 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7701 (ttp) REVERT: A 534 MET cc_start: 0.7762 (mmm) cc_final: 0.7403 (mtt) outliers start: 29 outliers final: 22 residues processed: 165 average time/residue: 0.1587 time to fit residues: 42.3782 Evaluate side-chains 169 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 170 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 240 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1785 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= 0.191 Angle : 0.574 9.032 15550 Z= 0.293 Chirality : 0.041 0.191 1762 Planarity : 0.006 0.063 1944 Dihedral : 4.676 32.895 1494 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.83 % Allowed : 16.81 % Favored : 80.36 % 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: 0.49 (0.24), residues: 1384 helix: 1.74 (0.17), residues: 956 sheet: -2.78 (0.89), residues: 30 loop : -3.16 (0.28), residues: 398 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 0.017 0.001 PHE B 21 TYR 0.023 0.001 TYR B 181 ARG 0.002 0.000 ARG A 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 186 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.231 Fit side-chains REVERT: B 151 ASN cc_start: 0.6792 (t0) cc_final: 0.6250 (t0) REVERT: B 157 MET cc_start: 0.4151 (tmm) cc_final: 0.3803 (tmm) REVERT: B 208 ASN cc_start: 0.8771 (t0) cc_final: 0.8549 (t0) REVERT: B 260 ASP cc_start: 0.7808 (t0) cc_final: 0.7455 (t0) REVERT: B 521 MET cc_start: 0.8135 (ttm) cc_final: 0.7774 (ttp) REVERT: B 587 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 19 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.6817 (t80) REVERT: A 23 ILE cc_start: 0.9218 (mm) cc_final: 0.8974 (mm) REVERT: A 72 PHE cc_start: 0.7904 (p90) cc_final: 0.7692 (p90) REVERT: A 78 GLU cc_start: 0.7571 (pp20) cc_final: 0.7286 (pp20) REVERT: A 151 ASN cc_start: 0.7043 (t0) cc_final: 0.6760 (t0) REVERT: A 155 TYR cc_start: 0.5916 (t80) cc_final: 0.5232 (t80) REVERT: A 260 ASP cc_start: 0.7994 (t0) cc_final: 0.7728 (t0) REVERT: A 378 MET cc_start: 0.6892 (mmm) cc_final: 0.6230 (mmm) REVERT: A 521 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7563 (ttp) REVERT: A 534 MET cc_start: 0.7720 (mmm) cc_final: 0.7378 (mtt) outliers start: 33 outliers final: 23 residues processed: 175 average time/residue: 0.1595 time to fit residues: 44.9198 Evaluate side-chains 173 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 657 PHE 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 240 CYS 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 612 VAL 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: 1.9990 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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: 0.7726 moved from start: 0.1881 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 : 0.582 9.230 15550 Z= 0.297 Chirality : 0.042 0.190 1762 Planarity : 0.006 0.064 1944 Dihedral : 4.612 33.057 1494 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.09 % Allowed : 16.98 % Favored : 79.93 % 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: 1.81 (0.17), residues: 946 sheet: -2.73 (0.90), residues: 30 loop : -3.12 (0.28), residues: 408 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 0.013 0.001 PHE B 21 TYR 0.023 0.001 TYR A 181 ARG 0.002 0.000 ARG A 555 *********************** 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 190 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 1.013 Fit side-chains REVERT: B 151 ASN cc_start: 0.6740 (t0) cc_final: 0.6212 (t0) REVERT: B 157 MET cc_start: 0.4245 (tmm) cc_final: 0.3927 (tmm) REVERT: B 208 ASN cc_start: 0.8795 (t0) cc_final: 0.8583 (t0) REVERT: B 260 ASP cc_start: 0.7808 (t0) cc_final: 0.7454 (t0) REVERT: B 521 MET cc_start: 0.8142 (ttm) cc_final: 0.7791 (ttp) REVERT: B 587 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8810 (p) REVERT: A 78 GLU cc_start: 0.7585 (pp20) cc_final: 0.7288 (pp20) REVERT: A 151 ASN cc_start: 0.7080 (t0) cc_final: 0.6793 (t0) REVERT: A 260 ASP cc_start: 0.8002 (t0) cc_final: 0.7734 (t0) REVERT: A 378 MET cc_start: 0.6896 (mmm) cc_final: 0.6293 (mmm) REVERT: A 521 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: A 534 MET cc_start: 0.7732 (mmm) cc_final: 0.7423 (mtt) outliers start: 36 outliers final: 29 residues processed: 176 average time/residue: 0.1602 time to fit residues: 45.7911 Evaluate side-chains 184 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 170 THR 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 657 PHE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 240 CYS 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 612 VAL 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: 10.0000 chunk 79 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7721 moved from start: 0.1959 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 : 0.592 9.203 15550 Z= 0.298 Chirality : 0.042 0.190 1762 Planarity : 0.006 0.065 1944 Dihedral : 4.586 32.885 1494 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.74 % Allowed : 17.50 % 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: 0.49 (0.24), residues: 1384 helix: 1.79 (0.17), residues: 938 sheet: -2.66 (0.92), residues: 30 loop : -3.08 (0.28), residues: 416 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 0.022 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 187 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.282 Fit side-chains REVERT: B 151 ASN cc_start: 0.6737 (t0) cc_final: 0.6218 (t0) REVERT: B 157 MET cc_start: 0.4339 (tmm) cc_final: 0.4045 (tmm) REVERT: B 208 ASN cc_start: 0.8801 (t0) cc_final: 0.8573 (t0) REVERT: B 260 ASP cc_start: 0.7803 (t0) cc_final: 0.7448 (t0) REVERT: B 378 MET cc_start: 0.6945 (mmm) cc_final: 0.6523 (mmm) REVERT: B 521 MET cc_start: 0.8149 (ttm) cc_final: 0.7776 (ttp) REVERT: B 587 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8746 (p) REVERT: A 19 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.6972 (t80) REVERT: A 78 GLU cc_start: 0.7576 (pp20) cc_final: 0.7275 (pp20) REVERT: A 82 MET cc_start: 0.8924 (ttm) cc_final: 0.8663 (ttm) REVERT: A 151 ASN cc_start: 0.7024 (t0) cc_final: 0.6745 (t0) REVERT: A 260 ASP cc_start: 0.8003 (t0) cc_final: 0.7737 (t0) REVERT: A 378 MET cc_start: 0.6875 (mmm) cc_final: 0.6295 (mmm) REVERT: A 521 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7595 (ttp) REVERT: A 534 MET cc_start: 0.7716 (mmm) cc_final: 0.7378 (mtt) outliers start: 32 outliers final: 29 residues processed: 174 average time/residue: 0.1772 time to fit residues: 49.6541 Evaluate side-chains 183 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 170 THR 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 514 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 657 PHE 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 240 CYS 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 612 VAL 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: 0.7980 chunk 116 optimal weight: 0.0770 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 53 optimal weight: 0.0020 chunk 97 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 overall best weight: 0.4146 ------------------------------------------------------------------------------- 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 611 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: 0.7675 moved from start: 0.2177 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= 0.169 Angle : 0.570 9.089 15550 Z= 0.287 Chirality : 0.041 0.188 1762 Planarity : 0.006 0.064 1944 Dihedral : 4.482 31.356 1494 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.66 % Allowed : 17.50 % 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: 0.60 (0.24), residues: 1384 helix: 1.89 (0.18), residues: 936 sheet: -2.49 (0.94), residues: 30 loop : -3.06 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 624 HIS 0.003 0.000 HIS A 628 PHE 0.015 0.001 PHE A 72 TYR 0.015 0.001 TYR B 181 ARG 0.001 0.000 ARG B 207 *********************** 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 194 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.288 Fit side-chains REVERT: B 151 ASN cc_start: 0.6710 (t0) cc_final: 0.6183 (t0) REVERT: B 157 MET cc_start: 0.4299 (tmm) cc_final: 0.4032 (tmm) REVERT: B 208 ASN cc_start: 0.8722 (t0) cc_final: 0.8462 (t0) REVERT: B 260 ASP cc_start: 0.7848 (t0) cc_final: 0.7492 (t0) REVERT: B 521 MET cc_start: 0.8002 (ttm) cc_final: 0.7604 (ttp) REVERT: B 587 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8727 (p) REVERT: A 19 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6976 (t80) REVERT: A 78 GLU cc_start: 0.7577 (pp20) cc_final: 0.7274 (pp20) REVERT: A 82 MET cc_start: 0.8928 (ttm) cc_final: 0.8727 (ttm) REVERT: A 151 ASN cc_start: 0.6973 (t0) cc_final: 0.6726 (t0) REVERT: A 260 ASP cc_start: 0.7931 (t0) cc_final: 0.7690 (t0) REVERT: A 378 MET cc_start: 0.6740 (mmm) cc_final: 0.6176 (mmm) REVERT: A 521 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7622 (ttp) REVERT: A 613 TYR cc_start: 0.7927 (m-10) cc_final: 0.7691 (m-10) outliers start: 31 outliers final: 26 residues processed: 179 average time/residue: 0.1645 time to fit residues: 46.7790 Evaluate side-chains 188 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU 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 429 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 657 PHE 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 240 CYS 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 612 VAL Chi-restraints excluded: chain A residue 614 ASN 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: 2.9990 chunk 91 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 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** ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2188 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= 0.201 Angle : 0.598 9.366 15550 Z= 0.298 Chirality : 0.041 0.211 1762 Planarity : 0.006 0.065 1944 Dihedral : 4.464 32.034 1494 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.74 % Allowed : 17.84 % 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: 0.61 (0.24), residues: 1384 helix: 1.88 (0.17), residues: 938 sheet: -2.41 (0.95), residues: 30 loop : -3.06 (0.28), residues: 416 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 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 192 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.229 Fit side-chains REVERT: B 151 ASN cc_start: 0.6702 (t0) cc_final: 0.6190 (t0) REVERT: B 157 MET cc_start: 0.4310 (tmm) cc_final: 0.4053 (tmm) REVERT: B 208 ASN cc_start: 0.8801 (t0) cc_final: 0.8548 (t0) REVERT: B 260 ASP cc_start: 0.7764 (t0) cc_final: 0.7491 (t0) REVERT: B 378 MET cc_start: 0.6914 (mmm) cc_final: 0.6494 (mmm) REVERT: B 521 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7697 (ttp) REVERT: B 587 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8727 (p) REVERT: A 19 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7062 (t80) REVERT: A 78 GLU cc_start: 0.7592 (pp20) cc_final: 0.7283 (pp20) REVERT: A 151 ASN cc_start: 0.6977 (t0) cc_final: 0.6711 (t0) REVERT: A 260 ASP cc_start: 0.7936 (t0) cc_final: 0.7700 (t0) REVERT: A 378 MET cc_start: 0.6796 (mmm) cc_final: 0.6240 (mmm) REVERT: A 521 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7663 (ttp) REVERT: A 534 MET cc_start: 0.7745 (mmm) cc_final: 0.7393 (mtt) REVERT: A 539 ILE cc_start: 0.8487 (mm) cc_final: 0.8272 (mt) REVERT: A 613 TYR cc_start: 0.7968 (m-10) cc_final: 0.7664 (m-10) outliers start: 32 outliers final: 27 residues processed: 176 average time/residue: 0.1600 time to fit residues: 45.3956 Evaluate side-chains 190 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 376 LEU 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 470 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 657 PHE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 240 CYS 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 612 VAL 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: 0.8980 chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** A 208 ASN A 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126454 restraints weight = 13110.151| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.07 r_work: 0.3300 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2258 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= 0.186 Angle : 0.585 8.600 15550 Z= 0.294 Chirality : 0.041 0.197 1762 Planarity : 0.006 0.064 1944 Dihedral : 4.433 31.876 1494 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.83 % Allowed : 18.10 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.90 (0.17), residues: 940 sheet: -2.35 (0.97), residues: 30 loop : -3.15 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 PHE 0.014 0.001 PHE A 72 TYR 0.019 0.001 TYR A 181 ARG 0.002 0.000 ARG B 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.91 seconds wall clock time: 42 minutes 50.61 seconds (2570.61 seconds total)