Starting phenix.real_space_refine on Sat Jul 20 11:40:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/07_2024/8wos_37697_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/07_2024/8wos_37697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/07_2024/8wos_37697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/07_2024/8wos_37697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/07_2024/8wos_37697_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wos_37697/07_2024/8wos_37697_neut.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 58 5.16 5 C 7106 2.51 5 N 1644 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 786": "OE1" <-> "OE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 625": "OD1" <-> "OD2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 819": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "B" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.16, per 1000 atoms: 0.67 Number of scatterers: 10672 At special positions: 0 Unit cell: (97.865, 86.802, 137.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1862 8.00 N 1644 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 67 " " NAG A 902 " - " ASN A 136 " " NAG B 901 " - " ASN B 67 " " NAG B 902 " - " ASN B 136 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 57 " " NAG E 1 " - " ASN B 83 " " NAG F 1 " - " ASN B 57 " Time building additional restraints: 4.90 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 907 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 907 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 800 " 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 50.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 302 through 336 removed outlier: 3.884A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 474 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.941A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 529 removed outlier: 3.863A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.602A pdb=" N GLU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.609A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 4.228A pdb=" N PHE A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 594 removed outlier: 3.748A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 622 removed outlier: 3.922A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 649 Processing helix chain 'A' and resid 689 through 709 Processing helix chain 'A' and resid 713 through 740 Processing helix chain 'A' and resid 745 through 768 removed outlier: 3.667A pdb=" N GLN A 768 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 794 through 817 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'B' and resid 38 through 43 Processing helix chain 'B' and resid 302 through 336 removed outlier: 3.866A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 474 removed outlier: 3.564A pdb=" N VAL B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 4.030A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 529 removed outlier: 3.833A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.637A pdb=" N GLU B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 3.522A pdb=" N TYR B 546 " --> pdb=" O PHE B 542 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.872A pdb=" N PHE B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.926A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 621 removed outlier: 3.660A pdb=" N TYR B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 649 Processing helix chain 'B' and resid 689 through 709 Processing helix chain 'B' and resid 713 through 740 Processing helix chain 'B' and resid 745 through 768 removed outlier: 3.524A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 768 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 794 through 817 Processing helix chain 'B' and resid 818 through 822 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.739A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 70 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 171 removed outlier: 4.919A pdb=" N LYS B 192 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 615 hydrogen bonds defined for protein. 1758 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: 3.45 Time building geometry restraints manager: 5.26 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: 3170 1.34 - 1.46: 2808 1.46 - 1.58: 4908 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 10976 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.93: 316 106.93 - 113.70: 6190 113.70 - 120.48: 4302 120.48 - 127.25: 4069 127.25 - 134.03: 103 Bond angle restraints: 14980 Sorted by residual: angle pdb=" C SER B 600 " pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 116.54 110.30 6.24 1.15e+00 7.56e-01 2.94e+01 angle pdb=" C LEU A 789 " pdb=" CA LEU A 789 " pdb=" CB LEU A 789 " ideal model delta sigma weight residual 116.63 111.62 5.01 1.16e+00 7.43e-01 1.87e+01 angle pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N ALA B 601 " ideal model delta sigma weight residual 119.52 116.43 3.09 7.90e-01 1.60e+00 1.53e+01 angle pdb=" C LEU A 704 " pdb=" N PHE A 705 " pdb=" CA PHE A 705 " ideal model delta sigma weight residual 122.06 114.81 7.25 1.86e+00 2.89e-01 1.52e+01 angle pdb=" C LEU B 789 " pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " ideal model delta sigma weight residual 117.23 112.78 4.45 1.36e+00 5.41e-01 1.07e+01 ... (remaining 14975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 6322 25.77 - 51.54: 518 51.54 - 77.30: 55 77.30 - 103.07: 23 103.07 - 128.84: 10 Dihedral angle restraints: 6928 sinusoidal: 3148 harmonic: 3780 Sorted by residual: dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 128.21 -35.21 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" C2 NAG B 901 " pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C5 NAG B 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.88 -128.84 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.20 -128.16 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1612 0.074 - 0.149: 135 0.149 - 0.223: 3 0.223 - 0.298: 0 0.298 - 0.372: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1749 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.001 2.00e-02 2.50e+03 2.76e-02 9.53e+00 pdb=" CG ASN B 83 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 702 " -0.024 2.00e-02 2.50e+03 2.16e-02 8.15e+00 pdb=" CG PHE A 702 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 702 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 702 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 702 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 702 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 702 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 717 " -0.023 2.00e-02 2.50e+03 1.43e-02 4.10e+00 pdb=" CG TYR A 717 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 717 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 717 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 717 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 717 " -0.007 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 98 2.53 - 3.13: 8838 3.13 - 3.72: 16130 3.72 - 4.31: 21203 4.31 - 4.90: 36523 Nonbonded interactions: 82792 Sorted by model distance: nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 1.943 2.440 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 1.961 2.440 nonbonded pdb=" OG SER B 701 " pdb=" OH TYR B 717 " model vdw 1.981 2.440 nonbonded pdb=" OG SER A 740 " pdb=" OE2 GLU A 742 " model vdw 2.036 2.440 nonbonded pdb=" OH TYR A 321 " pdb=" O LEU A 506 " model vdw 2.086 2.440 ... (remaining 82787 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' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.480 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.960 Find NCS groups from input model: 0.860 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10976 Z= 0.201 Angle : 0.552 7.753 14980 Z= 0.301 Chirality : 0.041 0.372 1752 Planarity : 0.003 0.049 1802 Dihedral : 18.351 128.840 4470 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.35 % Allowed : 33.39 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1256 helix: 2.71 (0.21), residues: 568 sheet: 0.51 (0.33), residues: 272 loop : -2.17 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.050 0.001 PHE A 702 TYR 0.032 0.001 TYR A 717 ARG 0.001 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 767 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.6557 (m-80) outliers start: 4 outliers final: 3 residues processed: 148 average time/residue: 0.1674 time to fit residues: 38.9595 Evaluate side-chains 143 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 767 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 0.0570 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 594 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10976 Z= 0.259 Angle : 0.670 9.674 14980 Z= 0.327 Chirality : 0.047 0.496 1752 Planarity : 0.004 0.054 1802 Dihedral : 12.978 114.788 2162 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.61 % Favored : 93.23 % Rotamer: Outliers : 3.62 % Allowed : 28.80 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1256 helix: 1.93 (0.21), residues: 578 sheet: 0.55 (0.32), residues: 280 loop : -2.35 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 446 HIS 0.009 0.001 HIS B 636 PHE 0.021 0.002 PHE B 705 TYR 0.045 0.002 TYR A 717 ARG 0.004 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 326 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5514 (mt) REVERT: A 605 TYR cc_start: 0.8495 (m-80) cc_final: 0.8268 (m-80) REVERT: A 713 ASP cc_start: 0.7954 (t0) cc_final: 0.7717 (t0) REVERT: B 36 ARG cc_start: 0.4920 (OUTLIER) cc_final: 0.3203 (mtt180) REVERT: B 208 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.5596 (ppp) REVERT: B 613 MET cc_start: 0.8488 (mmm) cc_final: 0.8248 (mmm) REVERT: B 722 PHE cc_start: 0.8634 (m-10) cc_final: 0.8402 (m-10) REVERT: B 736 MET cc_start: 0.8052 (mmt) cc_final: 0.7819 (mmt) REVERT: B 767 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7541 (m-80) outliers start: 41 outliers final: 16 residues processed: 177 average time/residue: 0.1810 time to fit residues: 48.8075 Evaluate side-chains 155 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 594 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10976 Z= 0.210 Angle : 0.624 9.963 14980 Z= 0.304 Chirality : 0.046 0.482 1752 Planarity : 0.004 0.046 1802 Dihedral : 12.293 113.238 2158 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.11 % Rotamer: Outliers : 4.33 % Allowed : 29.77 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1256 helix: 1.82 (0.21), residues: 578 sheet: 0.62 (0.32), residues: 280 loop : -2.32 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 446 HIS 0.008 0.001 HIS B 636 PHE 0.024 0.001 PHE A 445 TYR 0.055 0.001 TYR A 717 ARG 0.003 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 159 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5433 (mt) REVERT: A 605 TYR cc_start: 0.8496 (m-80) cc_final: 0.8263 (m-80) REVERT: A 702 PHE cc_start: 0.7986 (m-80) cc_final: 0.7304 (m-80) REVERT: B 208 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.5504 (ppp) REVERT: B 613 MET cc_start: 0.8492 (mmm) cc_final: 0.8239 (mmm) REVERT: B 722 PHE cc_start: 0.8646 (m-10) cc_final: 0.8386 (m-10) REVERT: B 736 MET cc_start: 0.8043 (mmt) cc_final: 0.7777 (mmt) REVERT: B 767 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7510 (m-80) outliers start: 49 outliers final: 25 residues processed: 200 average time/residue: 0.1655 time to fit residues: 51.0758 Evaluate side-chains 166 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10976 Z= 0.383 Angle : 0.725 10.082 14980 Z= 0.355 Chirality : 0.050 0.526 1752 Planarity : 0.004 0.046 1802 Dihedral : 12.025 115.211 2156 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 5.65 % Allowed : 29.86 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1256 helix: 1.60 (0.21), residues: 566 sheet: 0.56 (0.33), residues: 268 loop : -2.36 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 446 HIS 0.006 0.001 HIS A 50 PHE 0.022 0.002 PHE B 705 TYR 0.034 0.002 TYR A 717 ARG 0.004 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 145 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: A 326 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5385 (mm) REVERT: A 455 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: A 702 PHE cc_start: 0.8042 (m-80) cc_final: 0.7311 (m-80) REVERT: B 36 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.3439 (mmt90) REVERT: B 208 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.5774 (ppp) REVERT: B 454 PHE cc_start: 0.8521 (m-80) cc_final: 0.7881 (m-80) REVERT: B 613 MET cc_start: 0.8462 (mmm) cc_final: 0.8182 (mmm) REVERT: B 722 PHE cc_start: 0.8714 (m-10) cc_final: 0.8414 (m-10) REVERT: B 767 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7640 (m-80) outliers start: 64 outliers final: 39 residues processed: 191 average time/residue: 0.1712 time to fit residues: 50.8733 Evaluate side-chains 186 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10976 Z= 0.265 Angle : 0.666 11.441 14980 Z= 0.323 Chirality : 0.047 0.521 1752 Planarity : 0.004 0.039 1802 Dihedral : 11.700 115.048 2156 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.63 % Rotamer: Outliers : 5.65 % Allowed : 29.68 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1256 helix: 1.72 (0.22), residues: 558 sheet: 0.44 (0.32), residues: 280 loop : -2.48 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 446 HIS 0.006 0.001 HIS B 636 PHE 0.024 0.001 PHE A 445 TYR 0.042 0.001 TYR A 717 ARG 0.003 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 152 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: A 326 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5270 (mm) REVERT: A 455 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: A 702 PHE cc_start: 0.7944 (m-80) cc_final: 0.7460 (m-80) REVERT: B 36 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.3492 (mtt-85) REVERT: B 208 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.5712 (ppp) REVERT: B 454 PHE cc_start: 0.8434 (m-80) cc_final: 0.7775 (m-80) REVERT: B 613 MET cc_start: 0.8470 (mmm) cc_final: 0.8156 (mmm) REVERT: B 722 PHE cc_start: 0.8733 (m-10) cc_final: 0.8400 (m-10) REVERT: B 736 MET cc_start: 0.8050 (mmt) cc_final: 0.7848 (mmt) REVERT: B 767 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7643 (m-80) outliers start: 64 outliers final: 45 residues processed: 197 average time/residue: 0.1665 time to fit residues: 51.1253 Evaluate side-chains 191 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 140 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 0.0570 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 482 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10976 Z= 0.176 Angle : 0.642 11.217 14980 Z= 0.305 Chirality : 0.047 0.500 1752 Planarity : 0.004 0.038 1802 Dihedral : 11.239 114.487 2156 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.33 % Favored : 94.51 % Rotamer: Outliers : 3.98 % Allowed : 31.10 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1256 helix: 1.81 (0.22), residues: 558 sheet: 0.77 (0.33), residues: 268 loop : -2.46 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 446 HIS 0.006 0.001 HIS B 636 PHE 0.025 0.001 PHE A 445 TYR 0.016 0.001 TYR A 709 ARG 0.003 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 154 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8183 (tp30) REVERT: A 702 PHE cc_start: 0.7803 (m-80) cc_final: 0.7412 (m-80) REVERT: A 713 ASP cc_start: 0.7825 (t0) cc_final: 0.7568 (t0) REVERT: B 36 ARG cc_start: 0.4975 (OUTLIER) cc_final: 0.3416 (mtt180) REVERT: B 208 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.5347 (ppp) REVERT: B 518 ARG cc_start: 0.7438 (ttt-90) cc_final: 0.7026 (ttm110) REVERT: B 722 PHE cc_start: 0.8742 (m-10) cc_final: 0.8407 (m-10) REVERT: B 736 MET cc_start: 0.8024 (mmt) cc_final: 0.7777 (mmt) REVERT: B 767 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7484 (m-80) outliers start: 45 outliers final: 32 residues processed: 189 average time/residue: 0.1692 time to fit residues: 49.6834 Evaluate side-chains 182 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 482 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10976 Z= 0.266 Angle : 0.664 11.637 14980 Z= 0.320 Chirality : 0.047 0.501 1752 Planarity : 0.004 0.038 1802 Dihedral : 11.110 114.981 2156 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 5.30 % Allowed : 30.30 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1256 helix: 1.80 (0.22), residues: 558 sheet: 0.73 (0.33), residues: 268 loop : -2.47 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 446 HIS 0.006 0.001 HIS B 800 PHE 0.025 0.002 PHE A 445 TYR 0.024 0.001 TYR A 188 ARG 0.006 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 153 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: A 326 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5337 (mt) REVERT: A 455 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: A 702 PHE cc_start: 0.7868 (m-80) cc_final: 0.7475 (m-80) REVERT: B 36 ARG cc_start: 0.4979 (OUTLIER) cc_final: 0.3445 (mtt180) REVERT: B 208 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.5452 (ppp) REVERT: B 613 MET cc_start: 0.8517 (mmm) cc_final: 0.8167 (mmm) REVERT: B 722 PHE cc_start: 0.8744 (m-10) cc_final: 0.8419 (m-10) REVERT: B 736 MET cc_start: 0.8056 (mmt) cc_final: 0.7798 (mmt) REVERT: B 767 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7640 (m-80) outliers start: 60 outliers final: 46 residues processed: 199 average time/residue: 0.1606 time to fit residues: 50.2786 Evaluate side-chains 200 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 148 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 0.0060 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 482 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10976 Z= 0.174 Angle : 0.647 12.160 14980 Z= 0.306 Chirality : 0.046 0.491 1752 Planarity : 0.004 0.036 1802 Dihedral : 10.810 114.304 2156 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 4.15 % Allowed : 31.36 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1256 helix: 1.91 (0.22), residues: 556 sheet: 0.87 (0.34), residues: 268 loop : -2.47 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 446 HIS 0.005 0.001 HIS B 636 PHE 0.028 0.001 PHE A 705 TYR 0.019 0.001 TYR A 188 ARG 0.002 0.000 ARG A 524 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 153 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5491 (mt) REVERT: A 553 MET cc_start: 0.8011 (mpp) cc_final: 0.7790 (mpp) REVERT: A 555 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8188 (tp30) REVERT: A 702 PHE cc_start: 0.7858 (m-80) cc_final: 0.7477 (m-80) REVERT: A 713 ASP cc_start: 0.7788 (t0) cc_final: 0.7581 (t0) REVERT: B 36 ARG cc_start: 0.4892 (OUTLIER) cc_final: 0.3378 (mtt180) REVERT: B 208 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.5310 (ppp) REVERT: B 221 MET cc_start: 0.7785 (mmm) cc_final: 0.7499 (mmm) REVERT: B 613 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8098 (mmm) REVERT: B 722 PHE cc_start: 0.8736 (m-10) cc_final: 0.8390 (m-10) REVERT: B 736 MET cc_start: 0.8071 (mmt) cc_final: 0.7770 (mmt) REVERT: B 767 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7502 (m-80) outliers start: 47 outliers final: 35 residues processed: 188 average time/residue: 0.1670 time to fit residues: 49.6409 Evaluate side-chains 182 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10976 Z= 0.213 Angle : 0.660 12.195 14980 Z= 0.313 Chirality : 0.047 0.493 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.667 114.507 2156 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 4.33 % Allowed : 31.36 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1256 helix: 1.86 (0.22), residues: 558 sheet: 0.85 (0.33), residues: 268 loop : -2.42 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 446 HIS 0.004 0.001 HIS B 636 PHE 0.028 0.001 PHE A 705 TYR 0.032 0.001 TYR A 717 ARG 0.002 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 148 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: A 326 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5382 (mt) REVERT: A 555 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8203 (tp30) REVERT: A 689 MET cc_start: 0.8795 (mmt) cc_final: 0.8530 (mmp) REVERT: A 702 PHE cc_start: 0.7926 (m-80) cc_final: 0.7527 (m-80) REVERT: B 36 ARG cc_start: 0.4813 (OUTLIER) cc_final: 0.3285 (mtt180) REVERT: B 208 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5358 (ppp) REVERT: B 613 MET cc_start: 0.8441 (mmm) cc_final: 0.8114 (mmm) REVERT: B 722 PHE cc_start: 0.8744 (m-10) cc_final: 0.8413 (m-10) REVERT: B 736 MET cc_start: 0.8075 (mmt) cc_final: 0.7765 (mmt) REVERT: B 767 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7578 (m-80) outliers start: 49 outliers final: 41 residues processed: 186 average time/residue: 0.1656 time to fit residues: 48.4081 Evaluate side-chains 189 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 482 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10976 Z= 0.194 Angle : 0.664 12.323 14980 Z= 0.312 Chirality : 0.048 0.495 1752 Planarity : 0.004 0.036 1802 Dihedral : 10.470 114.352 2156 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 4.33 % Allowed : 31.45 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1256 helix: 1.87 (0.22), residues: 554 sheet: 0.91 (0.34), residues: 268 loop : -2.41 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 446 HIS 0.005 0.001 HIS B 636 PHE 0.032 0.001 PHE A 705 TYR 0.031 0.001 TYR A 717 ARG 0.002 0.000 ARG A 524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 148 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: A 326 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5426 (mt) REVERT: A 455 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: A 555 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8148 (tp30) REVERT: A 689 MET cc_start: 0.8822 (mmt) cc_final: 0.8531 (mmp) REVERT: A 702 PHE cc_start: 0.7859 (m-80) cc_final: 0.7461 (m-80) REVERT: B 36 ARG cc_start: 0.4793 (OUTLIER) cc_final: 0.3288 (mtt180) REVERT: B 208 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.5245 (ppp) REVERT: B 221 MET cc_start: 0.7844 (mmm) cc_final: 0.7518 (mmm) REVERT: B 613 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8137 (mmm) REVERT: B 722 PHE cc_start: 0.8767 (m-10) cc_final: 0.8437 (m-10) REVERT: B 736 MET cc_start: 0.8012 (mmt) cc_final: 0.7700 (mmt) REVERT: B 767 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7591 (m-80) outliers start: 49 outliers final: 40 residues processed: 186 average time/residue: 0.1688 time to fit residues: 49.2312 Evaluate side-chains 192 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 145 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 732 PHE Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 816 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 0.0070 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 87 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.143427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108441 restraints weight = 19570.447| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.74 r_work: 0.3472 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10976 Z= 0.169 Angle : 0.656 12.364 14980 Z= 0.307 Chirality : 0.047 0.493 1752 Planarity : 0.004 0.037 1802 Dihedral : 10.180 113.753 2156 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 3.62 % Allowed : 32.24 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1256 helix: 1.93 (0.22), residues: 554 sheet: 0.90 (0.33), residues: 276 loop : -2.43 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 446 HIS 0.005 0.001 HIS B 636 PHE 0.035 0.001 PHE A 705 TYR 0.038 0.001 TYR A 717 ARG 0.002 0.000 ARG A 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2251.20 seconds wall clock time: 41 minutes 27.05 seconds (2487.05 seconds total)