Starting phenix.real_space_refine on Fri Mar 15 04:28:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7k_9937/03_2024/6k7k_9937.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7k_9937/03_2024/6k7k_9937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7k_9937/03_2024/6k7k_9937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7k_9937/03_2024/6k7k_9937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7k_9937/03_2024/6k7k_9937.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7k_9937/03_2024/6k7k_9937.pdb" } resolution = 3.04 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= 0.004 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 6851 2.51 5 N 1755 2.21 5 O 1915 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A ASP 748": "OD1" <-> "OD2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 897": "OE1" <-> "OE2" Residue "A ARG 898": "NH1" <-> "NH2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10586 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7835 Classifications: {'peptide': 984} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 953} Chain breaks: 3 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.20, per 1000 atoms: 0.59 Number of scatterers: 10586 At special positions: 0 Unit cell: (69.72, 109.56, 167.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 56 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 1915 8.00 N 1755 7.00 C 6851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.04 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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 ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 48.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 131 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.695A pdb=" N ASP A 273 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 324 Processing helix chain 'A' and resid 341 through 352 removed outlier: 4.008A pdb=" N PHE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.956A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.288A pdb=" N ILE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.959A pdb=" N ASP A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 4.019A pdb=" N LYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 617 Processing helix chain 'A' and resid 621 through 632 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 742 through 752 Processing helix chain 'A' and resid 762 through 778 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.442A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 866 removed outlier: 4.294A pdb=" N ILE A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 880 Processing helix chain 'A' and resid 888 through 896 removed outlier: 4.579A pdb=" N GLY A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 896 " --> pdb=" O THR A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.534A pdb=" N THR A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.295A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 removed outlier: 3.656A pdb=" N HIS A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 3.971A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1061 removed outlier: 5.121A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.755A pdb=" N LEU C 95 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 146 through 151 removed outlier: 4.357A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.525A pdb=" N ARG C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.705A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 4.021A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.085A pdb=" N GLU A 144 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.856A pdb=" N TRP A 262 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 174 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.617A pdb=" N TYR A 182 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.564A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.985A pdb=" N VAL A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 542 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 530 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 546 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU A 528 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 7.357A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.103A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 163 508 hydrogen bonds defined for protein. 1461 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: 3.77 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1833 1.32 - 1.45: 2848 1.45 - 1.57: 6060 1.57 - 1.70: 3 1.70 - 1.82: 89 Bond restraints: 10833 Sorted by residual: bond pdb=" C4 ADP A1201 " pdb=" C5 ADP A1201 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.796 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.794 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.793 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.790 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 10828 not shown) Histogram of bond angle deviations from ideal: 87.20 - 105.53: 234 105.53 - 123.86: 14119 123.86 - 142.19: 357 142.19 - 160.52: 0 160.52 - 178.85: 2 Bond angle restraints: 14712 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.85 -70.17 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 178.35 -68.72 3.00e+00 1.11e-01 5.25e+02 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 87.20 23.01 3.00e+00 1.11e-01 5.88e+01 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.69 87.79 21.90 3.00e+00 1.11e-01 5.33e+01 angle pdb=" C ASN C 163 " pdb=" N GLU C 164 " pdb=" CA GLU C 164 " ideal model delta sigma weight residual 121.54 133.48 -11.94 1.91e+00 2.74e-01 3.91e+01 ... (remaining 14707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 6162 25.03 - 50.07: 347 50.07 - 75.10: 35 75.10 - 100.14: 9 100.14 - 125.17: 2 Dihedral angle restraints: 6555 sinusoidal: 2735 harmonic: 3820 Sorted by residual: dihedral pdb=" CA GLU C 164 " pdb=" C GLU C 164 " pdb=" N ASP C 165 " pdb=" CA ASP C 165 " ideal model delta harmonic sigma weight residual 180.00 131.13 48.87 0 5.00e+00 4.00e-02 9.55e+01 dihedral pdb=" CA THR C 100 " pdb=" C THR C 100 " pdb=" N PRO C 101 " pdb=" CA PRO C 101 " ideal model delta harmonic sigma weight residual 0.00 34.24 -34.24 0 5.00e+00 4.00e-02 4.69e+01 dihedral pdb=" O1B ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PB ADP A1201 " pdb=" PA ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 174.82 125.17 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 6552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1340 0.079 - 0.158: 297 0.158 - 0.237: 40 0.237 - 0.317: 5 0.317 - 0.396: 1 Chirality restraints: 1683 Sorted by residual: chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB ILE A 41 " pdb=" CA ILE A 41 " pdb=" CG1 ILE A 41 " pdb=" CG2 ILE A 41 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB THR C 263 " pdb=" CA THR C 263 " pdb=" OG1 THR C 263 " pdb=" CG2 THR C 263 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1680 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.295 2.00e-02 2.50e+03 2.51e-01 7.90e+02 pdb=" C7 NAG C 402 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.438 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.186 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" C7 NAG C 401 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.135 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.253 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.088 2.00e-02 2.50e+03 7.52e-02 7.07e+01 pdb=" C7 NAG B 2 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.121 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.072 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 97 2.58 - 3.16: 8078 3.16 - 3.74: 16667 3.74 - 4.32: 23714 4.32 - 4.90: 39925 Nonbonded interactions: 88481 Sorted by model distance: nonbonded pdb=" F3 ALF A1202 " pdb="MG MG A1204 " model vdw 2.000 2.120 nonbonded pdb=" O THR A 411 " pdb="MG MG A1204 " model vdw 2.082 2.170 nonbonded pdb=" OD1 ASP A 786 " pdb="MG MG A1204 " model vdw 2.156 2.170 nonbonded pdb=" O THR A 411 " pdb=" F3 ALF A1202 " model vdw 2.248 2.390 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.255 2.440 ... (remaining 88476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.700 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.310 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.800 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.011 0.132 10833 Z= 0.721 Angle : 1.452 70.169 14712 Z= 0.668 Chirality : 0.067 0.396 1683 Planarity : 0.011 0.251 1832 Dihedral : 15.373 125.173 4082 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.35 % Allowed : 6.01 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.19), residues: 1299 helix: -2.32 (0.16), residues: 575 sheet: -0.87 (0.36), residues: 174 loop : -2.73 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 260 HIS 0.007 0.002 HIS C 131 PHE 0.026 0.004 PHE C 61 TYR 0.030 0.003 TYR C 122 ARG 0.009 0.001 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7186 (mmp-170) cc_final: 0.6412 (ttp-110) REVERT: A 139 ARG cc_start: 0.6177 (ttp-110) cc_final: 0.5442 (ttp80) REVERT: A 275 LYS cc_start: 0.6335 (mptt) cc_final: 0.6097 (mttt) REVERT: A 278 GLN cc_start: 0.6169 (tt0) cc_final: 0.5906 (tt0) REVERT: A 420 GLN cc_start: 0.6832 (pt0) cc_final: 0.6413 (mt0) REVERT: A 525 ARG cc_start: 0.7167 (ttt-90) cc_final: 0.6940 (ttp80) REVERT: A 532 LEU cc_start: 0.6262 (mm) cc_final: 0.6025 (mm) REVERT: A 675 GLU cc_start: 0.6618 (pm20) cc_final: 0.5759 (mm-30) REVERT: A 754 LYS cc_start: 0.6286 (mttp) cc_final: 0.4620 (ttpt) REVERT: C 55 PHE cc_start: 0.8529 (m-80) cc_final: 0.8294 (m-80) REVERT: C 155 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7612 (mtmt) REVERT: C 200 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8283 (tttm) outliers start: 4 outliers final: 3 residues processed: 167 average time/residue: 0.2898 time to fit residues: 64.8821 Evaluate side-chains 134 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 136 GLN A 147 HIS A 227 HIS A 249 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 ASN A 397 ASN A 453 GLN A 580 HIS A 635 ASN A 765 GLN A 798 HIS A 917 ASN A 993 HIS C 216 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10833 Z= 0.228 Angle : 0.679 9.213 14712 Z= 0.342 Chirality : 0.046 0.215 1683 Planarity : 0.005 0.071 1832 Dihedral : 10.064 123.956 1602 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.48 % Allowed : 10.01 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.22), residues: 1299 helix: -0.69 (0.20), residues: 577 sheet: -0.69 (0.37), residues: 161 loop : -2.12 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.020 0.002 PHE A 968 TYR 0.017 0.002 TYR C 122 ARG 0.004 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7115 (mmp-170) cc_final: 0.6326 (ttp-110) REVERT: A 139 ARG cc_start: 0.6171 (ttp-110) cc_final: 0.5553 (ttp80) REVERT: A 278 GLN cc_start: 0.6240 (tt0) cc_final: 0.6012 (tt0) REVERT: A 420 GLN cc_start: 0.6870 (pt0) cc_final: 0.6495 (mm-40) REVERT: A 527 GLU cc_start: 0.6772 (tp30) cc_final: 0.6480 (tp30) REVERT: A 675 GLU cc_start: 0.6580 (pm20) cc_final: 0.5673 (mm-30) REVERT: A 754 LYS cc_start: 0.6375 (mttp) cc_final: 0.4596 (ttpt) REVERT: C 291 TYR cc_start: 0.8751 (m-80) cc_final: 0.7990 (m-80) outliers start: 17 outliers final: 11 residues processed: 152 average time/residue: 0.2611 time to fit residues: 54.9024 Evaluate side-chains 144 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 193 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 353 ASN C 131 HIS C 283 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10833 Z= 0.296 Angle : 0.683 8.672 14712 Z= 0.342 Chirality : 0.047 0.174 1683 Planarity : 0.005 0.071 1832 Dihedral : 9.540 120.317 1600 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.52 % Allowed : 11.84 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1299 helix: -0.15 (0.21), residues: 583 sheet: -0.44 (0.36), residues: 179 loop : -1.95 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 927 HIS 0.004 0.001 HIS C 131 PHE 0.023 0.002 PHE A 968 TYR 0.020 0.002 TYR C 122 ARG 0.004 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6227 (p) REVERT: A 74 ARG cc_start: 0.7085 (mmp-170) cc_final: 0.6352 (ttp-170) REVERT: A 258 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.6767 (mmm-85) REVERT: A 275 LYS cc_start: 0.6412 (mptt) cc_final: 0.6172 (mttt) REVERT: A 278 GLN cc_start: 0.6244 (tt0) cc_final: 0.6015 (tt0) REVERT: A 405 TYR cc_start: 0.8748 (m-80) cc_final: 0.8496 (m-80) REVERT: A 420 GLN cc_start: 0.6780 (pt0) cc_final: 0.6513 (mm-40) REVERT: A 583 GLN cc_start: 0.6225 (tt0) cc_final: 0.5878 (tp-100) REVERT: A 675 GLU cc_start: 0.6635 (pm20) cc_final: 0.5640 (mm-30) REVERT: A 754 LYS cc_start: 0.6278 (mttp) cc_final: 0.4517 (ttpt) REVERT: C 263 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8616 (m) REVERT: C 277 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6706 (mm-30) REVERT: C 291 TYR cc_start: 0.8747 (m-80) cc_final: 0.7946 (m-80) outliers start: 29 outliers final: 17 residues processed: 156 average time/residue: 0.2491 time to fit residues: 55.2286 Evaluate side-chains 157 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 0.0670 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10833 Z= 0.159 Angle : 0.603 8.703 14712 Z= 0.300 Chirality : 0.043 0.164 1683 Planarity : 0.004 0.067 1832 Dihedral : 8.911 116.193 1600 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.26 % Allowed : 13.32 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1299 helix: 0.38 (0.22), residues: 589 sheet: -0.16 (0.37), residues: 179 loop : -1.73 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.002 0.001 HIS C 283 PHE 0.019 0.001 PHE A 935 TYR 0.015 0.001 TYR A1054 ARG 0.002 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7028 (mmp-170) cc_final: 0.6327 (ttp-170) REVERT: A 139 ARG cc_start: 0.5926 (ttp-110) cc_final: 0.5122 (ttp80) REVERT: A 258 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.6886 (mmm-85) REVERT: A 278 GLN cc_start: 0.6174 (tt0) cc_final: 0.5888 (tt0) REVERT: A 421 PHE cc_start: 0.7815 (t80) cc_final: 0.7604 (t80) REVERT: A 468 MET cc_start: 0.7469 (ttp) cc_final: 0.7258 (ttp) REVERT: A 583 GLN cc_start: 0.6182 (tt0) cc_final: 0.5825 (tp-100) REVERT: A 675 GLU cc_start: 0.6632 (pm20) cc_final: 0.5629 (mm-30) REVERT: A 754 LYS cc_start: 0.6198 (mttp) cc_final: 0.4554 (ttpt) REVERT: A 758 CYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6768 (m) REVERT: C 263 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8610 (m) REVERT: C 291 TYR cc_start: 0.8701 (m-80) cc_final: 0.7959 (m-80) outliers start: 26 outliers final: 17 residues processed: 155 average time/residue: 0.2373 time to fit residues: 51.6063 Evaluate side-chains 153 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 86 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10833 Z= 0.190 Angle : 0.605 9.154 14712 Z= 0.299 Chirality : 0.044 0.151 1683 Planarity : 0.004 0.068 1832 Dihedral : 8.622 113.534 1599 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.35 % Allowed : 13.93 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1299 helix: 0.56 (0.22), residues: 589 sheet: -0.04 (0.37), residues: 179 loop : -1.67 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.004 0.001 HIS A 124 PHE 0.017 0.001 PHE A 968 TYR 0.016 0.001 TYR C 122 ARG 0.003 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6553 (OUTLIER) cc_final: 0.6211 (p) REVERT: A 74 ARG cc_start: 0.7047 (mmp-170) cc_final: 0.6344 (ttp-170) REVERT: A 258 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7403 (mmm-85) REVERT: A 405 TYR cc_start: 0.8684 (m-80) cc_final: 0.8473 (m-80) REVERT: A 421 PHE cc_start: 0.7827 (t80) cc_final: 0.7581 (t80) REVERT: A 583 GLN cc_start: 0.6239 (tt0) cc_final: 0.5868 (tp-100) REVERT: A 675 GLU cc_start: 0.6719 (pm20) cc_final: 0.5682 (mm-30) REVERT: A 754 LYS cc_start: 0.6103 (mttp) cc_final: 0.4482 (ttpt) REVERT: C 263 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8585 (m) REVERT: C 291 TYR cc_start: 0.8683 (m-80) cc_final: 0.7982 (m-80) outliers start: 27 outliers final: 20 residues processed: 150 average time/residue: 0.2475 time to fit residues: 51.7486 Evaluate side-chains 154 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN C 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10833 Z= 0.394 Angle : 0.700 8.733 14712 Z= 0.347 Chirality : 0.048 0.168 1683 Planarity : 0.005 0.068 1832 Dihedral : 8.763 111.154 1599 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.70 % Allowed : 14.80 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.86 (0.23), residues: 1299 helix: 0.29 (0.21), residues: 589 sheet: -0.03 (0.37), residues: 176 loop : -1.72 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 927 HIS 0.005 0.001 HIS A 323 PHE 0.022 0.002 PHE A 968 TYR 0.024 0.002 TYR C 122 ARG 0.005 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6296 (p) REVERT: A 74 ARG cc_start: 0.7076 (mmp-170) cc_final: 0.6364 (ttp-170) REVERT: A 258 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7427 (mmm-85) REVERT: A 275 LYS cc_start: 0.6458 (mptt) cc_final: 0.6193 (mttt) REVERT: A 405 TYR cc_start: 0.8764 (m-80) cc_final: 0.8515 (m-80) REVERT: A 583 GLN cc_start: 0.6224 (tt0) cc_final: 0.5863 (tp40) REVERT: A 754 LYS cc_start: 0.6097 (mttp) cc_final: 0.4473 (ttpt) REVERT: A 758 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7372 (m) REVERT: C 263 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8616 (m) REVERT: C 291 TYR cc_start: 0.8707 (m-80) cc_final: 0.8061 (m-80) outliers start: 31 outliers final: 21 residues processed: 154 average time/residue: 0.2420 time to fit residues: 52.5061 Evaluate side-chains 160 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10833 Z= 0.171 Angle : 0.600 9.245 14712 Z= 0.298 Chirality : 0.044 0.155 1683 Planarity : 0.004 0.070 1832 Dihedral : 8.341 108.363 1599 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.61 % Allowed : 15.67 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.48 (0.24), residues: 1299 helix: 0.64 (0.22), residues: 593 sheet: 0.14 (0.37), residues: 176 loop : -1.57 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.003 0.001 HIS A 124 PHE 0.018 0.001 PHE A 935 TYR 0.015 0.001 TYR A1054 ARG 0.002 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6581 (OUTLIER) cc_final: 0.6233 (p) REVERT: A 74 ARG cc_start: 0.7081 (mmp-170) cc_final: 0.6351 (ttp-170) REVERT: A 258 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7403 (mmm-85) REVERT: A 331 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7028 (t0) REVERT: A 405 TYR cc_start: 0.8732 (m-80) cc_final: 0.8486 (m-80) REVERT: A 421 PHE cc_start: 0.7864 (t80) cc_final: 0.7582 (t80) REVERT: A 525 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7244 (ttp80) REVERT: A 583 GLN cc_start: 0.6208 (tt0) cc_final: 0.5853 (tp40) REVERT: A 754 LYS cc_start: 0.5971 (mttp) cc_final: 0.4414 (ttpt) REVERT: C 263 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8605 (m) REVERT: C 291 TYR cc_start: 0.8666 (m-80) cc_final: 0.8019 (m-80) outliers start: 30 outliers final: 20 residues processed: 142 average time/residue: 0.2512 time to fit residues: 50.1086 Evaluate side-chains 150 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 98 optimal weight: 0.0060 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10833 Z= 0.269 Angle : 0.640 9.113 14712 Z= 0.316 Chirality : 0.045 0.157 1683 Planarity : 0.005 0.069 1832 Dihedral : 8.231 108.523 1599 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.44 % Allowed : 16.28 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.52 (0.23), residues: 1299 helix: 0.58 (0.22), residues: 594 sheet: 0.14 (0.37), residues: 175 loop : -1.57 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 PHE 0.018 0.002 PHE A 968 TYR 0.020 0.002 TYR C 122 ARG 0.004 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6628 (OUTLIER) cc_final: 0.6277 (p) REVERT: A 74 ARG cc_start: 0.7056 (mmp-170) cc_final: 0.6334 (ttp-170) REVERT: A 405 TYR cc_start: 0.8749 (m-80) cc_final: 0.8508 (m-80) REVERT: A 421 PHE cc_start: 0.7957 (t80) cc_final: 0.7718 (t80) REVERT: A 525 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7258 (ttp80) REVERT: A 583 GLN cc_start: 0.6252 (tt0) cc_final: 0.5885 (tp40) REVERT: A 754 LYS cc_start: 0.6005 (mttp) cc_final: 0.4449 (ttpt) REVERT: C 263 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8606 (m) REVERT: C 291 TYR cc_start: 0.8681 (m-80) cc_final: 0.8005 (m-80) outliers start: 28 outliers final: 21 residues processed: 147 average time/residue: 0.2568 time to fit residues: 52.7522 Evaluate side-chains 151 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10833 Z= 0.179 Angle : 0.596 9.331 14712 Z= 0.295 Chirality : 0.043 0.159 1683 Planarity : 0.004 0.070 1832 Dihedral : 7.792 107.241 1599 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.44 % Allowed : 16.10 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 1299 helix: 0.77 (0.22), residues: 594 sheet: 0.22 (0.37), residues: 177 loop : -1.47 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.003 0.001 HIS A 124 PHE 0.017 0.001 PHE A 935 TYR 0.015 0.001 TYR A1054 ARG 0.002 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6589 (OUTLIER) cc_final: 0.6247 (p) REVERT: A 74 ARG cc_start: 0.7080 (mmp-170) cc_final: 0.6340 (ttp-170) REVERT: A 405 TYR cc_start: 0.8741 (m-80) cc_final: 0.8484 (m-80) REVERT: A 421 PHE cc_start: 0.7908 (t80) cc_final: 0.7653 (t80) REVERT: A 525 ARG cc_start: 0.7540 (ttp80) cc_final: 0.7218 (ttp80) REVERT: A 583 GLN cc_start: 0.6264 (tt0) cc_final: 0.5888 (tp40) REVERT: A 587 GLU cc_start: 0.7773 (tt0) cc_final: 0.7517 (tp30) REVERT: C 263 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8610 (m) REVERT: C 291 TYR cc_start: 0.8661 (m-80) cc_final: 0.7998 (m-80) outliers start: 28 outliers final: 25 residues processed: 144 average time/residue: 0.2599 time to fit residues: 53.5732 Evaluate side-chains 152 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 119 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10833 Z= 0.163 Angle : 0.582 9.487 14712 Z= 0.286 Chirality : 0.043 0.160 1683 Planarity : 0.004 0.070 1832 Dihedral : 7.314 106.424 1599 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.26 % Allowed : 16.45 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 1299 helix: 0.91 (0.22), residues: 594 sheet: 0.37 (0.37), residues: 176 loop : -1.45 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.003 0.001 HIS A 798 PHE 0.017 0.001 PHE A 935 TYR 0.015 0.001 TYR A1054 ARG 0.002 0.000 ARG A 525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2598 Ramachandran restraints generated. 1299 Oldfield, 0 Emsley, 1299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6610 (OUTLIER) cc_final: 0.6291 (p) REVERT: A 74 ARG cc_start: 0.7062 (mmp-170) cc_final: 0.6331 (ttp-170) REVERT: A 405 TYR cc_start: 0.8720 (m-80) cc_final: 0.8464 (m-80) REVERT: A 421 PHE cc_start: 0.7854 (t80) cc_final: 0.7652 (t80) REVERT: A 502 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7684 (tt0) REVERT: A 525 ARG cc_start: 0.7574 (ttp80) cc_final: 0.7311 (ttp80) REVERT: A 527 GLU cc_start: 0.6302 (tp30) cc_final: 0.6016 (tp30) REVERT: A 583 GLN cc_start: 0.6259 (tt0) cc_final: 0.5871 (tp40) REVERT: A 587 GLU cc_start: 0.7596 (tt0) cc_final: 0.7374 (tp30) REVERT: A 758 CYS cc_start: 0.7356 (t) cc_final: 0.7008 (m) REVERT: A 1019 MET cc_start: 0.8140 (ptm) cc_final: 0.7924 (ptm) REVERT: A 1023 MET cc_start: 0.8310 (mmm) cc_final: 0.7741 (tpt) REVERT: C 78 ILE cc_start: 0.8917 (tp) cc_final: 0.8699 (tp) REVERT: C 89 SER cc_start: 0.8737 (m) cc_final: 0.8533 (t) REVERT: C 263 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8607 (m) REVERT: C 291 TYR cc_start: 0.8651 (m-80) cc_final: 0.7998 (m-80) outliers start: 26 outliers final: 22 residues processed: 147 average time/residue: 0.2322 time to fit residues: 48.7366 Evaluate side-chains 155 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 181 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 0.0570 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** 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 = 0.4008 r_free = 0.4008 target = 0.188276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.150913 restraints weight = 10734.223| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.20 r_work: 0.3235 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10833 Z= 0.161 Angle : 0.574 9.601 14712 Z= 0.284 Chirality : 0.043 0.163 1683 Planarity : 0.004 0.071 1832 Dihedral : 7.204 106.918 1599 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.18 % Allowed : 16.88 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: 1299 helix: 1.05 (0.22), residues: 592 sheet: 0.41 (0.37), residues: 179 loop : -1.49 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.002 0.001 HIS C 283 PHE 0.016 0.001 PHE A 935 TYR 0.015 0.001 TYR A1054 ARG 0.003 0.000 ARG A 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.26 seconds wall clock time: 44 minutes 37.52 seconds (2677.52 seconds total)