Starting phenix.real_space_refine on Fri Mar 15 04:25:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7h_9932/03_2024/6k7h_9932.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7h_9932/03_2024/6k7h_9932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7h_9932/03_2024/6k7h_9932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7h_9932/03_2024/6k7h_9932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7h_9932/03_2024/6k7h_9932.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7h_9932/03_2024/6k7h_9932.pdb" } resolution = 3.22 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6857 2.51 5 N 1753 2.21 5 O 1911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 273": "OD1" <-> "OD2" 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 PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 513": "OD1" <-> "OD2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 807": "OE1" <-> "OE2" 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 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1051": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10577 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7860 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 30, 'TRANS': 956} 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: "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: 6.02, per 1000 atoms: 0.57 Number of scatterers: 10577 At special positions: 0 Unit cell: (67.23, 109.56, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1911 8.00 N 1753 7.00 C 6857 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=2.02 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: 4.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 49.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 101 through 127 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.752A pdb=" N GLY A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 142 " --> pdb=" O ARG A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.693A pdb=" N ASP A 273 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.811A pdb=" N ILE A 355 " --> pdb=" O ASN A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.985A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 458 through 472 removed outlier: 5.090A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE A 465 " --> pdb=" O ILE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.974A pdb=" N ARG A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 588 removed outlier: 4.499A pdb=" N GLU A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 618 removed outlier: 4.196A pdb=" N VAL A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 616 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 633 removed outlier: 3.731A pdb=" N LYS A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) 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 737 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 762 through 778 removed outlier: 4.198A pdb=" N GLN A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 778 " --> pdb=" O LYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 824 through 831 Processing helix chain 'A' and resid 832 through 856 removed outlier: 4.011A pdb=" N ASN A 851 " --> pdb=" O CYS A 847 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 862 Processing helix chain 'A' and resid 874 through 880 removed outlier: 3.515A pdb=" N ILE A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.005A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 909 through 919 removed outlier: 4.293A pdb=" N LYS A 913 " --> pdb=" O PRO A 909 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) removed outlier: 3.620A 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: 4.059A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1033 through 1062 removed outlier: 3.975A pdb=" N TRP A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A1038 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 4.990A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.603A 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 removed outlier: 3.985A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.721A 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 Processing helix chain 'C' and resid 157 through 161 removed outlier: 4.171A pdb=" N ARG C 161 " --> pdb=" O GLU C 158 " (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 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.839A pdb=" N PHE C 304 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C 305 " --> pdb=" O HIS C 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 305' Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.811A pdb=" N TRP A 262 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER A 174 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 185 removed outlier: 4.843A pdb=" N THR A 185 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASN A 193 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.723A pdb=" N GLY A 800 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 819 " --> pdb=" O GLY A 800 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY A 802 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.681A pdb=" N VAL A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 426 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 545 Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 81 removed outlier: 7.247A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.030A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 109 removed outlier: 5.078A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1371 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: 3.53 Time building geometry restraints manager: 4.84 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: 1752 1.32 - 1.44: 2903 1.44 - 1.57: 6085 1.57 - 1.69: 1 1.69 - 1.81: 85 Bond restraints: 10826 Sorted by residual: bond pdb=" CB VAL A 969 " pdb=" CG2 VAL A 969 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.99e+00 bond pdb=" CB PRO C 170 " pdb=" CG PRO C 170 " ideal model delta sigma weight residual 1.506 1.417 0.089 3.90e-02 6.57e+02 5.23e+00 bond pdb=" CD LYS C 308 " pdb=" CE LYS C 308 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" CB ARG C 262 " pdb=" CG ARG C 262 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.10e+00 bond pdb=" CG1 ILE A 996 " pdb=" CD1 ILE A 996 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 ... (remaining 10821 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.94: 186 104.94 - 112.41: 5339 112.41 - 119.87: 4259 119.87 - 127.34: 4776 127.34 - 134.81: 136 Bond angle restraints: 14696 Sorted by residual: angle pdb=" C ARG A 75 " pdb=" N ALA A 76 " pdb=" CA ALA A 76 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 angle pdb=" CA MET C 318 " pdb=" CB MET C 318 " pdb=" CG MET C 318 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" C MET A 830 " pdb=" N ILE A 831 " pdb=" CA ILE A 831 " ideal model delta sigma weight residual 122.76 116.22 6.54 1.57e+00 4.06e-01 1.74e+01 angle pdb=" C GLY C 251 " pdb=" N PHE C 252 " pdb=" CA PHE C 252 " ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 angle pdb=" C THR A 281 " pdb=" N SER A 282 " pdb=" CA SER A 282 " ideal model delta sigma weight residual 120.97 132.40 -11.43 2.84e+00 1.24e-01 1.62e+01 ... (remaining 14691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 5614 16.15 - 32.31: 724 32.31 - 48.46: 166 48.46 - 64.62: 41 64.62 - 80.77: 13 Dihedral angle restraints: 6558 sinusoidal: 2729 harmonic: 3829 Sorted by residual: dihedral pdb=" CA LYS A 483 " pdb=" C LYS A 483 " pdb=" N ILE A 484 " pdb=" CA ILE A 484 " ideal model delta harmonic sigma weight residual -180.00 -130.56 -49.44 0 5.00e+00 4.00e-02 9.78e+01 dihedral pdb=" CB CYS C 157 " pdb=" SG CYS C 157 " pdb=" SG CYS C 171 " pdb=" CB CYS C 171 " ideal model delta sinusoidal sigma weight residual 93.00 36.09 56.91 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA SER C 316 " pdb=" C SER C 316 " pdb=" N TRP C 317 " pdb=" CA TRP C 317 " ideal model delta harmonic sigma weight residual 180.00 152.98 27.02 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 6555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1175 0.063 - 0.125: 414 0.125 - 0.188: 80 0.188 - 0.251: 11 0.251 - 0.314: 2 Chirality restraints: 1682 Sorted by residual: chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL A 545 " pdb=" CA VAL A 545 " pdb=" CG1 VAL A 545 " pdb=" CG2 VAL A 545 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1679 not shown) Planarity restraints: 1839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.317 2.00e-02 2.50e+03 2.77e-01 9.59e+02 pdb=" C7 NAG C 402 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.497 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.238 2.00e-02 2.50e+03 1.97e-01 4.86e+02 pdb=" C7 NAG C 401 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.325 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.132 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" C7 NAG B 1 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.022 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.190 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.106 2.00e-02 2.50e+03 ... (remaining 1836 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2801 2.80 - 3.32: 9424 3.32 - 3.85: 17748 3.85 - 4.37: 21002 4.37 - 4.90: 36217 Nonbonded interactions: 87192 Sorted by model distance: nonbonded pdb=" O LEU A 400 " pdb=" OH TYR A 912 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 490 " pdb=" OD1 ASP A 492 " model vdw 2.308 2.440 nonbonded pdb=" OE2 GLU A 897 " pdb=" OG SER A 986 " model vdw 2.320 2.440 nonbonded pdb=" O SER A 814 " pdb=" OG SER A 814 " model vdw 2.325 2.440 nonbonded pdb=" ND2 ASN C 176 " pdb=" OD1 ASN C 235 " model vdw 2.333 2.520 ... (remaining 87187 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: 1.050 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: 4.190 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.640 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 0.089 10826 Z= 0.693 Angle : 1.109 13.796 14696 Z= 0.591 Chirality : 0.065 0.314 1682 Planarity : 0.012 0.277 1836 Dihedral : 15.571 80.770 4079 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.13 % Allowed : 10.94 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -3.82 (0.19), residues: 1302 helix: -2.60 (0.15), residues: 594 sheet: -1.24 (0.38), residues: 173 loop : -2.75 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A1003 HIS 0.008 0.002 HIS A 124 PHE 0.035 0.003 PHE C 179 TYR 0.029 0.003 TYR C 122 ARG 0.008 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.8754 (mttt) cc_final: 0.8185 (mtmt) REVERT: A 535 THR cc_start: 0.2267 (OUTLIER) cc_final: 0.1901 (t) REVERT: A 599 ILE cc_start: -0.1456 (OUTLIER) cc_final: -0.1895 (tp) REVERT: A 753 CYS cc_start: 0.7243 (m) cc_final: 0.6792 (m) REVERT: A 852 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8388 (mp) REVERT: C 146 ASP cc_start: 0.7661 (m-30) cc_final: 0.7333 (m-30) REVERT: C 201 LYS cc_start: 0.9085 (pttt) cc_final: 0.8829 (ptmt) REVERT: C 315 ILE cc_start: 0.8013 (pt) cc_final: 0.7719 (pt) outliers start: 13 outliers final: 2 residues processed: 144 average time/residue: 0.2693 time to fit residues: 52.8023 Evaluate side-chains 93 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain C residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 140 ASN A 147 HIS A 234 ASN A 320 ASN A 323 HIS A 333 ASN A 397 ASN A 453 GLN A 522 GLN A 583 GLN A 605 GLN A 679 ASN A 682 HIS A 744 GLN A 810 GLN A 949 GLN A 993 HIS C 92 ASN C 131 HIS C 142 GLN C 190 ASN C 254 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 10826 Z= 0.191 Angle : 0.626 8.300 14696 Z= 0.325 Chirality : 0.044 0.173 1682 Planarity : 0.005 0.052 1836 Dihedral : 7.113 58.028 1597 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.52 % Allowed : 13.54 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -2.22 (0.21), residues: 1302 helix: -0.89 (0.19), residues: 591 sheet: -0.79 (0.39), residues: 175 loop : -2.32 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1003 HIS 0.003 0.001 HIS A 993 PHE 0.016 0.001 PHE C 108 TYR 0.019 0.001 TYR A 555 ARG 0.002 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6133 (tt) REVERT: A 165 ILE cc_start: 0.8444 (mt) cc_final: 0.8209 (mt) REVERT: A 326 LYS cc_start: 0.8745 (mttt) cc_final: 0.8236 (mtmt) REVERT: A 535 THR cc_start: 0.2718 (OUTLIER) cc_final: 0.2381 (t) REVERT: A 599 ILE cc_start: -0.1121 (OUTLIER) cc_final: -0.1711 (tp) REVERT: A 693 MET cc_start: 0.3670 (mpp) cc_final: 0.2669 (ttt) REVERT: A 753 CYS cc_start: 0.7121 (m) cc_final: 0.6849 (m) REVERT: A 852 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 1059 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6543 (tpt-90) REVERT: C 92 ASN cc_start: 0.8627 (t0) cc_final: 0.8394 (t0) REVERT: C 146 ASP cc_start: 0.7483 (m-30) cc_final: 0.7226 (m-30) REVERT: C 201 LYS cc_start: 0.8921 (pttt) cc_final: 0.8696 (ptpt) REVERT: C 315 ILE cc_start: 0.7945 (pt) cc_final: 0.7705 (pt) outliers start: 29 outliers final: 11 residues processed: 130 average time/residue: 0.2312 time to fit residues: 43.7444 Evaluate side-chains 113 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 682 HIS Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 682 HIS C 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10826 Z= 0.426 Angle : 0.696 10.084 14696 Z= 0.356 Chirality : 0.048 0.212 1682 Planarity : 0.005 0.045 1836 Dihedral : 6.939 57.754 1597 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.73 % Allowed : 14.84 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -1.74 (0.22), residues: 1302 helix: -0.34 (0.21), residues: 584 sheet: -0.77 (0.38), residues: 181 loop : -2.17 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1003 HIS 0.014 0.002 HIS A 682 PHE 0.022 0.002 PHE C 179 TYR 0.023 0.002 TYR C 122 ARG 0.004 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 96 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.8504 (mt) cc_final: 0.8267 (mt) REVERT: A 326 LYS cc_start: 0.8790 (mttt) cc_final: 0.8232 (mtmt) REVERT: A 535 THR cc_start: 0.2894 (OUTLIER) cc_final: 0.2517 (t) REVERT: A 599 ILE cc_start: -0.0689 (OUTLIER) cc_final: -0.1453 (tp) REVERT: A 693 MET cc_start: 0.3949 (mpp) cc_final: 0.2946 (ttt) REVERT: A 727 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 753 CYS cc_start: 0.7287 (m) cc_final: 0.6543 (m) REVERT: A 874 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: A 900 CYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6541 (t) REVERT: A 1059 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6560 (tpt-90) REVERT: C 92 ASN cc_start: 0.8692 (t0) cc_final: 0.8444 (t0) REVERT: C 146 ASP cc_start: 0.7521 (m-30) cc_final: 0.7220 (m-30) REVERT: C 315 ILE cc_start: 0.7926 (pt) cc_final: 0.7716 (pt) outliers start: 43 outliers final: 26 residues processed: 132 average time/residue: 0.2356 time to fit residues: 44.7196 Evaluate side-chains 121 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 682 HIS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS 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: 2.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 682 HIS C 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10826 Z= 0.195 Angle : 0.583 8.231 14696 Z= 0.299 Chirality : 0.043 0.173 1682 Planarity : 0.004 0.042 1836 Dihedral : 6.340 58.221 1595 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.30 % Allowed : 16.15 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -1.22 (0.23), residues: 1302 helix: 0.10 (0.22), residues: 595 sheet: -0.61 (0.39), residues: 181 loop : -1.92 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.016 0.001 HIS A 682 PHE 0.013 0.001 PHE A 968 TYR 0.014 0.001 TYR C 122 ARG 0.003 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 94 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 136 GLN cc_start: 0.7235 (mp10) cc_final: 0.6935 (tm-30) REVERT: A 165 ILE cc_start: 0.8502 (mt) cc_final: 0.8246 (mt) REVERT: A 226 ARG cc_start: 0.7268 (ptm-80) cc_final: 0.6498 (ptp-170) REVERT: A 326 LYS cc_start: 0.8742 (mttt) cc_final: 0.8217 (mtmt) REVERT: A 535 THR cc_start: 0.2810 (OUTLIER) cc_final: 0.2419 (t) REVERT: A 599 ILE cc_start: -0.0716 (OUTLIER) cc_final: -0.1404 (tp) REVERT: A 693 MET cc_start: 0.3906 (mpp) cc_final: 0.2924 (ttt) REVERT: A 727 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 742 VAL cc_start: 0.5677 (OUTLIER) cc_final: 0.5437 (t) REVERT: A 753 CYS cc_start: 0.7254 (m) cc_final: 0.6461 (m) REVERT: A 772 MET cc_start: 0.8321 (tmm) cc_final: 0.8110 (tmm) REVERT: A 852 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8220 (mp) REVERT: A 874 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: A 900 CYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6572 (t) REVERT: A 1059 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6585 (tpt-90) REVERT: C 146 ASP cc_start: 0.7478 (m-30) cc_final: 0.7206 (m-30) REVERT: C 223 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8025 (tt) outliers start: 38 outliers final: 18 residues processed: 127 average time/residue: 0.2035 time to fit residues: 38.6406 Evaluate side-chains 117 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 682 HIS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 0.0270 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN A 682 HIS C 92 ASN C 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10826 Z= 0.161 Angle : 0.557 7.692 14696 Z= 0.286 Chirality : 0.043 0.163 1682 Planarity : 0.004 0.042 1836 Dihedral : 5.949 57.761 1595 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.12 % Allowed : 16.58 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -0.82 (0.24), residues: 1302 helix: 0.46 (0.22), residues: 592 sheet: -0.46 (0.39), residues: 182 loop : -1.71 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.014 0.001 HIS A 682 PHE 0.022 0.001 PHE A 368 TYR 0.013 0.001 TYR C 273 ARG 0.004 0.000 ARG A 901 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 136 GLN cc_start: 0.7189 (mp10) cc_final: 0.6859 (tp40) REVERT: A 165 ILE cc_start: 0.8487 (mt) cc_final: 0.8225 (mt) REVERT: A 180 MET cc_start: 0.5700 (mmt) cc_final: 0.4744 (mmt) REVERT: A 226 ARG cc_start: 0.7250 (ptm-80) cc_final: 0.6429 (ptp-170) REVERT: A 326 LYS cc_start: 0.8717 (mttt) cc_final: 0.8192 (mtmt) REVERT: A 535 THR cc_start: 0.2836 (OUTLIER) cc_final: 0.2382 (t) REVERT: A 599 ILE cc_start: -0.0681 (OUTLIER) cc_final: -0.1300 (tp) REVERT: A 693 MET cc_start: 0.3962 (mpp) cc_final: 0.2959 (ttt) REVERT: A 727 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 742 VAL cc_start: 0.5686 (OUTLIER) cc_final: 0.5445 (t) REVERT: A 753 CYS cc_start: 0.7293 (m) cc_final: 0.6494 (m) REVERT: A 852 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8159 (mp) REVERT: A 874 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: A 900 CYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6492 (t) REVERT: A 1059 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6557 (tpt-90) REVERT: C 146 ASP cc_start: 0.7405 (m-30) cc_final: 0.7178 (m-30) REVERT: C 223 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8036 (tt) outliers start: 36 outliers final: 21 residues processed: 126 average time/residue: 0.2036 time to fit residues: 38.3318 Evaluate side-chains 123 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 682 HIS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 104 optimal weight: 0.0980 chunk 58 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10826 Z= 0.177 Angle : 0.555 7.818 14696 Z= 0.285 Chirality : 0.043 0.181 1682 Planarity : 0.004 0.042 1836 Dihedral : 5.792 57.263 1595 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.56 % Allowed : 16.93 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -0.66 (0.24), residues: 1302 helix: 0.59 (0.22), residues: 592 sheet: -0.37 (0.39), residues: 182 loop : -1.63 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 927 HIS 0.005 0.001 HIS A 682 PHE 0.021 0.001 PHE A 368 TYR 0.014 0.001 TYR C 122 ARG 0.004 0.000 ARG A 901 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 99 time to evaluate : 1.093 Fit side-chains REVERT: A 136 GLN cc_start: 0.7193 (mp10) cc_final: 0.6852 (tp40) REVERT: A 165 ILE cc_start: 0.8486 (mt) cc_final: 0.8228 (mt) REVERT: A 180 MET cc_start: 0.5708 (mmt) cc_final: 0.4784 (mmt) REVERT: A 226 ARG cc_start: 0.7260 (ptm-80) cc_final: 0.6414 (ptp-170) REVERT: A 326 LYS cc_start: 0.8701 (mttt) cc_final: 0.8173 (mtmt) REVERT: A 599 ILE cc_start: -0.0747 (OUTLIER) cc_final: -0.1430 (tt) REVERT: A 693 MET cc_start: 0.3982 (mpp) cc_final: 0.2990 (ttt) REVERT: A 727 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 742 VAL cc_start: 0.5827 (OUTLIER) cc_final: 0.5566 (t) REVERT: A 747 LEU cc_start: 0.8499 (mm) cc_final: 0.8269 (mm) REVERT: A 753 CYS cc_start: 0.7352 (m) cc_final: 0.6563 (m) REVERT: A 852 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 874 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: A 900 CYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6395 (t) REVERT: A 1059 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6543 (tpt-90) REVERT: C 146 ASP cc_start: 0.7385 (m-30) cc_final: 0.7143 (m-30) REVERT: C 223 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8087 (tt) outliers start: 41 outliers final: 23 residues processed: 132 average time/residue: 0.1912 time to fit residues: 38.2584 Evaluate side-chains 126 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 900 CYS Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 455 ASN C 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10826 Z= 0.200 Angle : 0.566 10.286 14696 Z= 0.288 Chirality : 0.044 0.172 1682 Planarity : 0.004 0.042 1836 Dihedral : 5.686 56.972 1594 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.73 % Allowed : 17.19 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -0.63 (0.24), residues: 1302 helix: 0.61 (0.22), residues: 599 sheet: -0.29 (0.39), residues: 181 loop : -1.67 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.021 0.001 PHE A 368 TYR 0.015 0.001 TYR C 122 ARG 0.007 0.000 ARG A 743 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 136 GLN cc_start: 0.7173 (mp10) cc_final: 0.6839 (tp40) REVERT: A 165 ILE cc_start: 0.8493 (mt) cc_final: 0.8245 (mt) REVERT: A 180 MET cc_start: 0.5731 (mmt) cc_final: 0.4821 (mmt) REVERT: A 226 ARG cc_start: 0.7266 (ptm-80) cc_final: 0.6414 (ptp-170) REVERT: A 326 LYS cc_start: 0.8705 (mttt) cc_final: 0.8173 (mtmt) REVERT: A 535 THR cc_start: 0.3140 (OUTLIER) cc_final: 0.2650 (t) REVERT: A 599 ILE cc_start: -0.0728 (OUTLIER) cc_final: -0.1424 (tt) REVERT: A 693 MET cc_start: 0.4009 (mpp) cc_final: 0.2989 (ttt) REVERT: A 727 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 742 VAL cc_start: 0.5864 (OUTLIER) cc_final: 0.5593 (t) REVERT: A 747 LEU cc_start: 0.8483 (mm) cc_final: 0.8247 (mm) REVERT: A 753 CYS cc_start: 0.7375 (m) cc_final: 0.6566 (m) REVERT: A 852 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 874 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: A 1059 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6585 (tpt-90) REVERT: C 92 ASN cc_start: 0.8352 (t0) cc_final: 0.8083 (m-40) REVERT: C 223 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8051 (tt) outliers start: 43 outliers final: 27 residues processed: 136 average time/residue: 0.1961 time to fit residues: 39.8809 Evaluate side-chains 132 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 40.0000 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 420 GLN A 682 HIS C 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 10826 Z= 0.542 Angle : 0.740 11.354 14696 Z= 0.375 Chirality : 0.051 0.212 1682 Planarity : 0.005 0.043 1836 Dihedral : 6.398 56.830 1594 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.34 % Allowed : 17.01 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -1.06 (0.23), residues: 1302 helix: 0.13 (0.21), residues: 592 sheet: -0.46 (0.38), residues: 182 loop : -1.71 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 143 HIS 0.006 0.002 HIS A 124 PHE 0.024 0.002 PHE C 179 TYR 0.027 0.002 TYR C 122 ARG 0.006 0.001 ARG A 743 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 104 time to evaluate : 1.223 Fit side-chains REVERT: A 136 GLN cc_start: 0.7238 (mp10) cc_final: 0.6903 (tm-30) REVERT: A 165 ILE cc_start: 0.8630 (mt) cc_final: 0.8387 (mt) REVERT: A 326 LYS cc_start: 0.8783 (mttt) cc_final: 0.8203 (mtmt) REVERT: A 503 LEU cc_start: 0.4649 (OUTLIER) cc_final: 0.4242 (tp) REVERT: A 535 THR cc_start: 0.2861 (OUTLIER) cc_final: 0.2470 (t) REVERT: A 599 ILE cc_start: -0.0729 (OUTLIER) cc_final: -0.1440 (tt) REVERT: A 693 MET cc_start: 0.4211 (mpp) cc_final: 0.3094 (ttt) REVERT: A 727 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7678 (mp) REVERT: A 747 LEU cc_start: 0.8544 (mm) cc_final: 0.8176 (mm) REVERT: A 753 CYS cc_start: 0.7497 (m) cc_final: 0.6767 (m) REVERT: A 776 GLN cc_start: 0.7575 (tp40) cc_final: 0.7166 (tm-30) REVERT: A 852 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 874 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: A 1059 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6439 (tpt170) REVERT: C 223 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8214 (tt) outliers start: 50 outliers final: 31 residues processed: 143 average time/residue: 0.1970 time to fit residues: 42.3783 Evaluate side-chains 139 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 123 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10826 Z= 0.165 Angle : 0.571 8.902 14696 Z= 0.293 Chirality : 0.043 0.165 1682 Planarity : 0.004 0.043 1836 Dihedral : 5.819 57.561 1594 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.86 % Allowed : 18.84 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -0.53 (0.24), residues: 1302 helix: 0.68 (0.22), residues: 588 sheet: -0.32 (0.39), residues: 182 loop : -1.51 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 927 HIS 0.002 0.001 HIS A 323 PHE 0.021 0.001 PHE A 368 TYR 0.018 0.001 TYR C 273 ARG 0.008 0.000 ARG A 743 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.200 Fit side-chains REVERT: A 136 GLN cc_start: 0.7205 (mp10) cc_final: 0.6860 (tm-30) REVERT: A 326 LYS cc_start: 0.8698 (mttt) cc_final: 0.8161 (mtmt) REVERT: A 599 ILE cc_start: -0.0809 (OUTLIER) cc_final: -0.1346 (tt) REVERT: A 693 MET cc_start: 0.4090 (mpp) cc_final: 0.3108 (ttt) REVERT: A 747 LEU cc_start: 0.8488 (mm) cc_final: 0.8201 (mm) REVERT: A 753 CYS cc_start: 0.7426 (m) cc_final: 0.7177 (m) REVERT: A 852 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8175 (mp) REVERT: A 874 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: A 1059 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6535 (tpt-90) REVERT: C 223 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7994 (tt) outliers start: 33 outliers final: 23 residues processed: 124 average time/residue: 0.2172 time to fit residues: 39.7182 Evaluate side-chains 121 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.0670 chunk 58 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10826 Z= 0.173 Angle : 0.564 9.268 14696 Z= 0.287 Chirality : 0.043 0.167 1682 Planarity : 0.004 0.042 1836 Dihedral : 5.501 56.395 1594 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.43 % Allowed : 19.36 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -0.37 (0.24), residues: 1302 helix: 0.84 (0.22), residues: 596 sheet: -0.21 (0.39), residues: 182 loop : -1.52 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.019 0.001 PHE A 368 TYR 0.014 0.001 TYR C 122 ARG 0.008 0.000 ARG A 743 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 1.098 Fit side-chains REVERT: A 136 GLN cc_start: 0.7111 (mp10) cc_final: 0.6762 (tm-30) REVERT: A 180 MET cc_start: 0.5718 (mmt) cc_final: 0.4793 (mmt) REVERT: A 326 LYS cc_start: 0.8695 (mttt) cc_final: 0.8169 (mtmt) REVERT: A 599 ILE cc_start: -0.0650 (OUTLIER) cc_final: -0.1218 (tt) REVERT: A 693 MET cc_start: 0.3902 (mpp) cc_final: 0.2918 (ttt) REVERT: A 747 LEU cc_start: 0.8504 (mm) cc_final: 0.8263 (mm) REVERT: A 753 CYS cc_start: 0.7457 (m) cc_final: 0.7168 (m) REVERT: A 852 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8125 (mp) REVERT: A 874 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: A 1059 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6382 (tpt170) REVERT: C 92 ASN cc_start: 0.8271 (t0) cc_final: 0.7790 (m-40) REVERT: C 223 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8007 (tt) outliers start: 28 outliers final: 20 residues processed: 124 average time/residue: 0.1915 time to fit residues: 36.0380 Evaluate side-chains 122 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 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 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.193522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133306 restraints weight = 10804.721| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.93 r_work: 0.2891 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10826 Z= 0.188 Angle : 0.566 10.758 14696 Z= 0.287 Chirality : 0.043 0.179 1682 Planarity : 0.004 0.042 1836 Dihedral : 5.464 56.499 1594 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.60 % Allowed : 19.27 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -0.28 (0.24), residues: 1302 helix: 0.91 (0.22), residues: 590 sheet: -0.22 (0.39), residues: 182 loop : -1.42 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.021 0.001 PHE A 368 TYR 0.014 0.001 TYR C 122 ARG 0.003 0.000 ARG A 743 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.60 seconds wall clock time: 43 minutes 7.98 seconds (2587.98 seconds total)