Starting phenix.real_space_refine on Sat Jul 20 11:37:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/07_2024/8wot_37698_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/07_2024/8wot_37698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/07_2024/8wot_37698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/07_2024/8wot_37698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/07_2024/8wot_37698_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wot_37698/07_2024/8wot_37698_neut.cif" } resolution = 3.18 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= 0.014 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 41": "OD1" <-> "OD2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 791": "OD1" <-> "OD2" Residue "B ASP 795": "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: 6.44, per 1000 atoms: 0.60 Number of scatterers: 10672 At special positions: 0 Unit cell: (98.716, 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: 4.46 Conformation dependent library (CDL) restraints added in 1.8 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 800 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 796 " 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: 34 helices and 10 sheets defined 49.8% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 302 through 336 removed outlier: 3.871A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.989A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.925A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 529 removed outlier: 3.927A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.607A pdb=" N GLU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.557A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.928A pdb=" N PHE A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 594 removed outlier: 3.812A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 622 removed outlier: 3.898A 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: 3.700A 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 'B' and resid 38 through 43 removed outlier: 3.517A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) 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: 3.777A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 474 removed outlier: 3.549A 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: 3.997A 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: 3.879A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.563A pdb=" N GLU B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 3.782A pdb=" N VAL B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 4.086A pdb=" N PHE B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.853A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 622 removed outlier: 3.773A 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: 3.647A pdb=" N GLN B 768 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 794 through 817 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: 4.753A 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 62 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: 4.765A 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 181 612 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: 2.98 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3170 1.34 - 1.46: 2831 1.46 - 1.58: 4885 1.58 - 1.70: 0 1.70 - 1.81: 90 Bond restraints: 10976 Sorted by residual: bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 318 106.95 - 113.72: 6180 113.72 - 120.48: 4315 120.48 - 127.25: 4061 127.25 - 134.01: 106 Bond angle restraints: 14980 Sorted by residual: angle pdb=" C SER A 600 " pdb=" CA SER A 600 " pdb=" CB SER A 600 " ideal model delta sigma weight residual 116.54 110.44 6.10 1.15e+00 7.56e-01 2.81e+01 angle pdb=" C SER B 600 " pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 116.54 110.48 6.06 1.15e+00 7.56e-01 2.78e+01 angle pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " pdb=" CG LEU B 789 " ideal model delta sigma weight residual 116.30 129.42 -13.12 3.50e+00 8.16e-02 1.41e+01 angle pdb=" CA SER A 600 " pdb=" C SER A 600 " pdb=" N ALA A 601 " ideal model delta sigma weight residual 119.52 116.57 2.95 7.90e-01 1.60e+00 1.39e+01 angle pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N ALA B 601 " ideal model delta sigma weight residual 119.52 116.63 2.89 7.90e-01 1.60e+00 1.33e+01 ... (remaining 14975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.66: 6356 25.66 - 51.33: 481 51.33 - 76.99: 59 76.99 - 102.66: 22 102.66 - 128.32: 10 Dihedral angle restraints: 6928 sinusoidal: 3148 harmonic: 3780 Sorted by residual: 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 65.36 -128.32 1 3.00e+01 1.11e-03 1.73e+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 65.32 -128.28 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sinusoidal sigma weight residual 175.11 62.53 112.58 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1596 0.069 - 0.138: 151 0.138 - 0.207: 3 0.207 - 0.276: 0 0.276 - 0.345: 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 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+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 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+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 -2.21 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1749 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.002 2.00e-02 2.50e+03 1.90e-02 4.50e+00 pdb=" CG ASN B 83 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 747 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 748 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 748 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 748 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 747 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 748 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " -0.023 5.00e-02 4.00e+02 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 113 2.60 - 3.17: 9668 3.17 - 3.75: 15866 3.75 - 4.32: 20935 4.32 - 4.90: 35956 Nonbonded interactions: 82538 Sorted by model distance: nonbonded pdb=" OG SER B 701 " pdb=" OH TYR B 717 " model vdw 2.020 2.440 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.073 2.440 nonbonded pdb=" OG SER A 740 " pdb=" OE2 GLU A 742 " model vdw 2.097 2.440 nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 2.103 2.440 nonbonded pdb=" N GLU B 137 " pdb=" OE1 GLU B 137 " model vdw 2.121 2.520 ... (remaining 82533 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: 2.660 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: 0.080 Set scattering table: 0.120 Process input model: 32.040 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 0.052 10976 Z= 0.190 Angle : 0.519 13.124 14980 Z= 0.273 Chirality : 0.040 0.345 1752 Planarity : 0.003 0.045 1802 Dihedral : 17.953 128.319 4470 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.27 % Allowed : 29.86 % Favored : 69.88 % 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: 1.30 (0.25), residues: 1256 helix: 3.00 (0.21), residues: 580 sheet: 0.62 (0.33), residues: 268 loop : -2.36 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 446 HIS 0.001 0.000 HIS B 636 PHE 0.025 0.001 PHE B 705 TYR 0.016 0.001 TYR B 709 ARG 0.002 0.000 ARG B 37 *********************** 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 132 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 689 MET cc_start: 0.8366 (pmm) cc_final: 0.7892 (pmm) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 0.2121 time to fit residues: 42.0806 Evaluate side-chains 131 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 714 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: 3.9990 chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0824 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= 0.217 Angle : 0.616 9.562 14980 Z= 0.301 Chirality : 0.047 0.492 1752 Planarity : 0.004 0.052 1802 Dihedral : 12.733 112.646 2158 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.07 % Rotamer: Outliers : 3.00 % Allowed : 26.24 % Favored : 70.76 % 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: 0.70 (0.24), residues: 1256 helix: 2.18 (0.21), residues: 590 sheet: 0.70 (0.32), residues: 268 loop : -2.51 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.026 0.001 PHE A 705 TYR 0.032 0.001 TYR A 717 ARG 0.004 0.000 ARG A 712 *********************** 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 176 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.146 Fit side-chains REVERT: A 287 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6932 (tt) REVERT: A 520 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8332 (tp) REVERT: A 540 LYS cc_start: 0.6072 (tmtt) cc_final: 0.5765 (tmtt) REVERT: A 586 MET cc_start: 0.8136 (mmp) cc_final: 0.7898 (mmp) REVERT: A 689 MET cc_start: 0.8413 (pmm) cc_final: 0.7990 (pmm) REVERT: A 722 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8859 (m-10) outliers start: 34 outliers final: 20 residues processed: 165 average time/residue: 0.1793 time to fit residues: 45.2170 Evaluate side-chains 155 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 750 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.0060 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1039 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= 0.209 Angle : 0.605 10.620 14980 Z= 0.296 Chirality : 0.046 0.490 1752 Planarity : 0.004 0.051 1802 Dihedral : 11.952 110.207 2154 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 3.89 % Allowed : 25.88 % Favored : 70.23 % 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: 0.55 (0.24), residues: 1256 helix: 1.98 (0.21), residues: 590 sheet: 0.68 (0.32), residues: 276 loop : -2.56 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.028 0.001 PHE B 705 TYR 0.032 0.001 TYR A 717 ARG 0.003 0.000 ARG A 712 *********************** 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 183 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 139 time to evaluate : 1.199 Fit side-chains REVERT: A 287 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6943 (tt) REVERT: A 520 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8378 (tp) REVERT: A 540 LYS cc_start: 0.6111 (tmtt) cc_final: 0.5627 (tmtt) REVERT: A 689 MET cc_start: 0.8449 (pmm) cc_final: 0.8033 (pmm) outliers start: 44 outliers final: 29 residues processed: 170 average time/residue: 0.1892 time to fit residues: 48.4522 Evaluate side-chains 162 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10976 Z= 0.247 Angle : 0.626 10.532 14980 Z= 0.305 Chirality : 0.047 0.509 1752 Planarity : 0.004 0.051 1802 Dihedral : 11.501 109.451 2154 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.29 % Favored : 93.55 % Rotamer: Outliers : 3.80 % Allowed : 26.77 % Favored : 69.43 % 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: 0.43 (0.24), residues: 1256 helix: 1.87 (0.21), residues: 586 sheet: 0.63 (0.32), residues: 276 loop : -2.56 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.026 0.001 PHE B 705 TYR 0.028 0.001 TYR A 717 ARG 0.003 0.000 ARG A 712 *********************** 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 185 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6928 (tt) REVERT: A 520 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8442 (tp) REVERT: A 540 LYS cc_start: 0.6213 (tmtt) cc_final: 0.5681 (tmtt) outliers start: 43 outliers final: 33 residues processed: 174 average time/residue: 0.1818 time to fit residues: 47.8088 Evaluate side-chains 167 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.0040 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 482 ASN ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** 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: 0.8244 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10976 Z= 0.170 Angle : 0.605 11.211 14980 Z= 0.291 Chirality : 0.046 0.497 1752 Planarity : 0.004 0.050 1802 Dihedral : 11.108 108.550 2154 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 3.80 % Allowed : 27.03 % Favored : 69.17 % 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: 592 sheet: 0.75 (0.32), residues: 276 loop : -2.57 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 446 HIS 0.003 0.001 HIS A 636 PHE 0.033 0.001 PHE B 705 TYR 0.030 0.001 TYR A 717 ARG 0.003 0.000 ARG A 712 *********************** 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 188 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6885 (tt) REVERT: A 520 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8432 (tp) REVERT: A 540 LYS cc_start: 0.6148 (tmtt) cc_final: 0.5544 (tmtt) REVERT: A 584 LEU cc_start: 0.9128 (mt) cc_final: 0.8909 (mp) outliers start: 43 outliers final: 30 residues processed: 176 average time/residue: 0.1773 time to fit residues: 47.4165 Evaluate side-chains 165 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 750 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10976 Z= 0.292 Angle : 0.643 7.512 14980 Z= 0.314 Chirality : 0.047 0.516 1752 Planarity : 0.004 0.049 1802 Dihedral : 10.870 108.533 2154 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.45 % Favored : 93.39 % Rotamer: Outliers : 5.04 % Allowed : 26.77 % Favored : 68.20 % 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: 1.73 (0.21), residues: 590 sheet: 0.63 (0.32), residues: 276 loop : -2.62 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 446 HIS 0.004 0.001 HIS B 800 PHE 0.033 0.002 PHE B 705 TYR 0.032 0.002 TYR A 717 ARG 0.004 0.000 ARG A 712 *********************** 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 191 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 134 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6919 (tt) REVERT: A 520 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8465 (tp) outliers start: 57 outliers final: 45 residues processed: 179 average time/residue: 0.1770 time to fit residues: 48.8499 Evaluate side-chains 175 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 128 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 76 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10976 Z= 0.172 Angle : 0.617 11.694 14980 Z= 0.296 Chirality : 0.046 0.501 1752 Planarity : 0.004 0.045 1802 Dihedral : 10.630 107.808 2154 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.75 % Rotamer: Outliers : 3.89 % Allowed : 28.00 % Favored : 68.11 % 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: 0.39 (0.24), residues: 1256 helix: 1.78 (0.21), residues: 592 sheet: 0.70 (0.32), residues: 276 loop : -2.60 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.037 0.001 PHE B 705 TYR 0.034 0.001 TYR A 717 ARG 0.004 0.000 ARG A 712 *********************** 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 179 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6885 (tt) REVERT: A 326 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7857 (mt) REVERT: A 520 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8477 (tp) REVERT: B 709 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6762 (p90) outliers start: 44 outliers final: 35 residues processed: 169 average time/residue: 0.1813 time to fit residues: 46.6474 Evaluate side-chains 168 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 0.0020 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10976 Z= 0.249 Angle : 0.654 11.552 14980 Z= 0.313 Chirality : 0.047 0.516 1752 Planarity : 0.004 0.044 1802 Dihedral : 10.402 107.431 2154 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 4.51 % Allowed : 27.65 % Favored : 67.84 % 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: 0.31 (0.24), residues: 1256 helix: 1.71 (0.21), residues: 592 sheet: 0.65 (0.32), residues: 276 loop : -2.65 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.039 0.001 PHE B 705 TYR 0.035 0.001 TYR A 717 ARG 0.004 0.000 ARG A 712 *********************** 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 180 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 129 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6902 (tt) REVERT: A 520 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8515 (tp) outliers start: 51 outliers final: 43 residues processed: 170 average time/residue: 0.1834 time to fit residues: 47.9620 Evaluate side-chains 172 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU 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 788 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 10976 Z= 0.430 Angle : 0.749 9.619 14980 Z= 0.368 Chirality : 0.051 0.571 1752 Planarity : 0.004 0.042 1802 Dihedral : 10.483 107.832 2154 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.25 % Favored : 92.60 % Rotamer: Outliers : 4.68 % Allowed : 27.47 % Favored : 67.84 % 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: -0.06 (0.24), residues: 1256 helix: 1.46 (0.21), residues: 586 sheet: 0.30 (0.31), residues: 276 loop : -2.72 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 106 HIS 0.003 0.001 HIS A 50 PHE 0.048 0.002 PHE A 705 TYR 0.030 0.002 TYR A 717 ARG 0.002 0.000 ARG B 79 *********************** 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 191 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 138 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8525 (pt) cc_final: 0.8137 (tt) REVERT: A 287 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6835 (tt) REVERT: A 520 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8614 (tp) REVERT: B 686 MET cc_start: 0.5652 (pmm) cc_final: 0.5024 (pmm) outliers start: 53 outliers final: 42 residues processed: 177 average time/residue: 0.1827 time to fit residues: 48.9655 Evaluate side-chains 175 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 131 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10976 Z= 0.207 Angle : 0.659 10.700 14980 Z= 0.318 Chirality : 0.047 0.532 1752 Planarity : 0.004 0.050 1802 Dihedral : 10.220 106.313 2154 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 3.53 % Allowed : 28.89 % 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: 0.16 (0.24), residues: 1256 helix: 1.70 (0.21), residues: 578 sheet: 0.49 (0.32), residues: 276 loop : -2.68 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 446 HIS 0.003 0.001 HIS A 636 PHE 0.050 0.002 PHE A 705 TYR 0.033 0.001 TYR A 717 ARG 0.005 0.000 ARG B 712 ********************** 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 181 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8519 (pt) cc_final: 0.8124 (tt) REVERT: A 287 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6816 (tt) REVERT: A 520 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8602 (tp) REVERT: B 686 MET cc_start: 0.5539 (pmm) cc_final: 0.4911 (pmm) outliers start: 40 outliers final: 37 residues processed: 170 average time/residue: 0.1870 time to fit residues: 48.0382 Evaluate side-chains 176 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098702 restraints weight = 16917.237| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.53 r_work: 0.3263 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10976 Z= 0.412 Angle : 0.745 12.580 14980 Z= 0.363 Chirality : 0.051 0.590 1752 Planarity : 0.005 0.042 1802 Dihedral : 10.239 107.594 2154 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.09 % Favored : 92.75 % Rotamer: Outliers : 3.80 % Allowed : 29.24 % Favored : 66.96 % 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: -0.08 (0.24), residues: 1256 helix: 1.57 (0.21), residues: 578 sheet: 0.26 (0.31), residues: 276 loop : -2.82 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 446 HIS 0.005 0.001 HIS A 800 PHE 0.055 0.002 PHE B 705 TYR 0.031 0.002 TYR A 717 ARG 0.008 0.000 ARG B 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.02 seconds wall clock time: 41 minutes 2.66 seconds (2462.66 seconds total)