Starting phenix.real_space_refine on Sun Jul 21 09:16:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/07_2024/8ty1_41710.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/07_2024/8ty1_41710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/07_2024/8ty1_41710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/07_2024/8ty1_41710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/07_2024/8ty1_41710.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/07_2024/8ty1_41710.cif" } resolution = 3.46 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= 0.007 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 65 5.16 5 C 8618 2.51 5 N 2290 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 1766": "OE1" <-> "OE2" Residue "A ASP 1794": "OD1" <-> "OD2" Residue "A PHE 1838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1844": "OE1" <-> "OE2" Residue "A PHE 1983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13508 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1236, 10004 Classifications: {'peptide': 1236} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 59, 'TRANS': 1176} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1570 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1784 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 223} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.80, per 1000 atoms: 0.73 Number of scatterers: 13508 At special positions: 0 Unit cell: (81.164, 123.716, 178.088, 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 65 16.00 O 2535 8.00 N 2290 7.00 C 8618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.03 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 220 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG D 1 " - " ASN A 240 " " NAG E 1 " - " ASN A1810 " " NAG F 1 " - " ASN C 28 " Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.4 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 33 sheets defined 9.3% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 120 through 128 removed outlier: 4.426A pdb=" N GLU A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 128 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.733A pdb=" N GLU A 195 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 538 through 546 removed outlier: 4.228A pdb=" N ALA A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 694 through 700 removed outlier: 4.156A pdb=" N ASN A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1755 removed outlier: 3.551A pdb=" N ASN A1753 " --> pdb=" O GLY A1750 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS A1755 " --> pdb=" O LEU A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1824 Processing helix chain 'A' and resid 1842 through 1847 removed outlier: 3.514A pdb=" N ASP A1846 " --> pdb=" O ASP A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1891 through 1895 removed outlier: 3.618A pdb=" N VAL A1895 " --> pdb=" O THR A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1915 Processing helix chain 'A' and resid 2002 through 2007 Processing helix chain 'A' and resid 2047 through 2051 removed outlier: 4.084A pdb=" N LEU A2050 " --> pdb=" O ALA A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2190 Processing helix chain 'A' and resid 2204 through 2208 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.572A pdb=" N ALA B 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 184 through 191 removed outlier: 4.429A pdb=" N HIS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 removed outlier: 4.056A pdb=" N GLN C 75 " --> pdb=" O HIS C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.970A pdb=" N THR C 101 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 removed outlier: 4.108A pdb=" N THR C 155 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.596A pdb=" N TYR A 6 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 90 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.596A pdb=" N TYR A 6 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 5.763A pdb=" N ILE A 77 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 180 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 198 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248 removed outlier: 5.617A pdb=" N LEU A 246 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 422 through 429 Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 477 removed outlier: 3.905A pdb=" N TYR A 476 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 534 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.901A pdb=" N ILE A 574 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 658 through 659 removed outlier: 3.700A pdb=" N PHE A 658 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 665 " --> pdb=" O PHE A 658 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1695 through 1697 Processing sheet with id=AB3, first strand: chain 'A' and resid 1701 through 1707 Processing sheet with id=AB4, first strand: chain 'A' and resid 1763 through 1765 removed outlier: 6.421A pdb=" N ILE A1763 " --> pdb=" O LEU A1856 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N CYS A1858 " --> pdb=" O ILE A1763 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A1765 " --> pdb=" O CYS A1858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1917 through 1921 Processing sheet with id=AB6, first strand: chain 'A' and resid 1933 through 1935 removed outlier: 3.629A pdb=" N TYR A2017 " --> pdb=" O MET A1934 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A2016 " --> pdb=" O GLY A1994 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1975 through 1976 Processing sheet with id=AB8, first strand: chain 'A' and resid 1963 through 1965 Processing sheet with id=AB9, first strand: chain 'A' and resid 2062 through 2064 removed outlier: 6.953A pdb=" N CYS A2169 " --> pdb=" O ILE A2081 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE A2081 " --> pdb=" O CYS A2169 " (cutoff:3.500A) removed outlier: 13.348A pdb=" N ILE A2071 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N THR A2154 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 12.503A pdb=" N VAL A2073 " --> pdb=" O HIS A2152 " (cutoff:3.500A) removed outlier: 11.960A pdb=" N HIS A2152 " --> pdb=" O VAL A2073 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N LEU A2075 " --> pdb=" O ARG A2150 " (cutoff:3.500A) removed outlier: 11.952A pdb=" N ARG A2150 " --> pdb=" O LEU A2075 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ALA A2077 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR A2148 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR A2156 " --> pdb=" O ILE A2098 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A2098 " --> pdb=" O TYR A2156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2089 through 2091 Processing sheet with id=AC2, first strand: chain 'A' and resid 2191 through 2192 removed outlier: 3.948A pdb=" N THR A2272 " --> pdb=" O SER A2264 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2293 through 2296 removed outlier: 4.969A pdb=" N VAL A2240 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N CYS A2326 " --> pdb=" O VAL A2240 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2248 through 2250 Processing sheet with id=AC5, first strand: chain 'B' and resid 5 through 7 removed outlier: 12.177A pdb=" N CYS B 23 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 11.253A pdb=" N THR B 75 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N ALA B 25 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 11.974A pdb=" N THR B 73 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N GLN B 27 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP B 71 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.547A pdb=" N LEU B 11 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.547A pdb=" N LEU B 11 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 91 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 99 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AC9, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.371A pdb=" N TRP B 150 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLU C 10 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 109 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER C 43 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 44 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG C 60 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP C 46 " --> pdb=" O MET C 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 58 " --> pdb=" O TRP C 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLU C 10 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N CYS C 106 " --> pdb=" O TRP C 127 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP C 127 " --> pdb=" O CYS C 106 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG C 108 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 125 " --> pdb=" O ARG C 108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.033A pdb=" N SER C 144 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR C 200 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.033A pdb=" N SER C 144 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR C 200 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 174 through 177 340 hydrogen bonds defined for protein. 822 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: 5.40 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4283 1.34 - 1.46: 3586 1.46 - 1.59: 5896 1.59 - 1.71: 1 1.71 - 1.83: 103 Bond restraints: 13869 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.70e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.453 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 13864 not shown) Histogram of bond angle deviations from ideal: 94.83 - 102.70: 75 102.70 - 110.57: 4090 110.57 - 118.43: 6589 118.43 - 126.30: 7792 126.30 - 134.17: 270 Bond angle restraints: 18816 Sorted by residual: angle pdb=" CA PRO C 209 " pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 112.00 101.99 10.01 1.40e+00 5.10e-01 5.12e+01 angle pdb=" C ASN A1805 " pdb=" CA ASN A1805 " pdb=" CB ASN A1805 " ideal model delta sigma weight residual 116.54 110.18 6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C HIS A2315 " pdb=" N GLN A2316 " pdb=" CA GLN A2316 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" N GLN A2316 " pdb=" CA GLN A2316 " pdb=" CB GLN A2316 " ideal model delta sigma weight residual 110.49 118.97 -8.48 1.69e+00 3.50e-01 2.52e+01 angle pdb=" C VAL A2314 " pdb=" N HIS A2315 " pdb=" CA HIS A2315 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 18811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 7469 23.52 - 47.03: 713 47.03 - 70.55: 105 70.55 - 94.06: 42 94.06 - 117.58: 18 Dihedral angle restraints: 8347 sinusoidal: 3473 harmonic: 4874 Sorted by residual: dihedral pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.96 -61.96 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" CB CYS C 164 " pdb=" SG CYS C 164 " pdb=" SG CYS C 220 " pdb=" CB CYS C 220 " ideal model delta sinusoidal sigma weight residual 93.00 151.99 -58.99 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CA CYS A 180 " pdb=" C CYS A 180 " pdb=" N ARG A 181 " pdb=" CA ARG A 181 " ideal model delta harmonic sigma weight residual -180.00 -148.81 -31.19 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1598 0.055 - 0.110: 384 0.110 - 0.164: 81 0.164 - 0.219: 5 0.219 - 0.274: 3 Chirality restraints: 2071 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2068 not shown) Planarity restraints: 2382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 208 " 0.119 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO C 209 " -0.299 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 127 " -0.018 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP C 127 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 127 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 127 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 127 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 127 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP C 127 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.025 2.00e-02 2.50e+03 2.40e-02 1.45e+01 pdb=" CG TRP A 139 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.006 2.00e-02 2.50e+03 ... (remaining 2379 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 222 2.58 - 3.16: 11640 3.16 - 3.74: 21330 3.74 - 4.32: 29351 4.32 - 4.90: 47611 Nonbonded interactions: 110154 Sorted by model distance: nonbonded pdb=" OE2 GLU A 111 " pdb=" OH TYR A 115 " model vdw 2.005 2.440 nonbonded pdb=" O ALA A1877 " pdb=" ND2 ASN A1922 " model vdw 2.124 2.520 nonbonded pdb=" OE1 GLN A 135 " pdb=" OH TYR A 137 " model vdw 2.136 2.440 nonbonded pdb=" OG SER A 628 " pdb=" O LYS A 707 " model vdw 2.138 2.440 nonbonded pdb=" OE2 GLU A 389 " pdb=" NH2 ARG A 439 " model vdw 2.139 2.520 ... (remaining 110149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 40.970 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 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 : 0.005 0.119 13869 Z= 0.349 Angle : 0.887 11.625 18816 Z= 0.452 Chirality : 0.050 0.274 2071 Planarity : 0.006 0.173 2379 Dihedral : 19.173 117.576 5186 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.53 % Favored : 88.99 % Rotamer: Outliers : 0.68 % Allowed : 27.90 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.57 (0.20), residues: 1653 helix: -1.71 (0.52), residues: 74 sheet: -1.19 (0.22), residues: 491 loop : -2.05 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP C 127 HIS 0.009 0.002 HIS A2005 PHE 0.033 0.002 PHE A1785 TYR 0.025 0.002 TYR B 88 ARG 0.010 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 MET cc_start: 0.7284 (ppp) cc_final: 0.6583 (ttt) REVERT: A 625 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 666 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6903 (t0) REVERT: A 683 GLU cc_start: 0.6371 (mm-30) cc_final: 0.6127 (mm-30) REVERT: A 1711 MET cc_start: 0.3602 (mpp) cc_final: 0.3044 (mpp) REVERT: A 1794 ASP cc_start: 0.5830 (t0) cc_final: 0.4916 (p0) REVERT: A 1797 GLU cc_start: 0.4601 (tp30) cc_final: 0.4215 (tp30) REVERT: A 2180 MET cc_start: 0.7767 (tpt) cc_final: 0.7433 (tpt) REVERT: A 2313 TRP cc_start: 0.4492 (p90) cc_final: 0.4154 (p90) REVERT: C 42 TYR cc_start: 0.4728 (p90) cc_final: 0.4482 (p90) outliers start: 10 outliers final: 4 residues processed: 167 average time/residue: 0.2500 time to fit residues: 62.1626 Evaluate side-chains 154 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 0.0050 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 ASN A1957 HIS ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2091 GLN A2231 GLN C 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13869 Z= 0.198 Angle : 0.688 10.025 18816 Z= 0.344 Chirality : 0.047 0.231 2071 Planarity : 0.005 0.107 2379 Dihedral : 12.520 114.717 2078 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.41 % Favored : 91.17 % Rotamer: Outliers : 4.37 % Allowed : 25.38 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.39 (0.20), residues: 1653 helix: -1.43 (0.55), residues: 75 sheet: -1.19 (0.22), residues: 487 loop : -1.87 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 127 HIS 0.005 0.001 HIS C 37 PHE 0.022 0.001 PHE A1785 TYR 0.022 0.001 TYR B 92 ARG 0.004 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 151 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5003 (mp) REVERT: A 293 THR cc_start: 0.7941 (m) cc_final: 0.7682 (m) REVERT: A 313 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7089 (mt) REVERT: A 321 MET cc_start: 0.6395 (ttp) cc_final: 0.6150 (mtp) REVERT: A 658 PHE cc_start: 0.5022 (OUTLIER) cc_final: 0.3856 (p90) REVERT: A 665 GLU cc_start: 0.7979 (mp0) cc_final: 0.7706 (mp0) REVERT: A 683 GLU cc_start: 0.6455 (mm-30) cc_final: 0.6245 (mm-30) REVERT: A 1711 MET cc_start: 0.3482 (mpp) cc_final: 0.2872 (mpp) REVERT: A 1756 LEU cc_start: 0.7697 (mm) cc_final: 0.7476 (mp) REVERT: A 1794 ASP cc_start: 0.5885 (t0) cc_final: 0.4993 (p0) REVERT: A 1797 GLU cc_start: 0.4642 (tp30) cc_final: 0.4395 (tp30) REVERT: A 1818 LYS cc_start: 0.8152 (tptt) cc_final: 0.7924 (tptt) REVERT: A 2010 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7506 (mpp) REVERT: A 2167 MET cc_start: 0.5787 (mmt) cc_final: 0.5243 (mmt) REVERT: A 2180 MET cc_start: 0.7814 (tpt) cc_final: 0.7270 (tpt) REVERT: A 2238 MET cc_start: 0.4476 (mmm) cc_final: 0.4206 (mmm) REVERT: A 2313 TRP cc_start: 0.4388 (p90) cc_final: 0.4170 (p90) REVERT: A 2324 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6760 (mt) REVERT: B 88 TYR cc_start: 0.5878 (m-80) cc_final: 0.5614 (m-80) REVERT: C 57 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7275 (t60) outliers start: 64 outliers final: 26 residues processed: 203 average time/residue: 0.2374 time to fit residues: 74.2026 Evaluate side-chains 173 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2010 MET Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1778 GLN A1867 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.150 13869 Z= 0.598 Angle : 0.964 13.824 18816 Z= 0.499 Chirality : 0.056 0.305 2071 Planarity : 0.007 0.083 2379 Dihedral : 11.744 114.941 2071 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 33.08 Ramachandran Plot: Outliers : 1.03 % Allowed : 12.83 % Favored : 86.15 % Rotamer: Outliers : 7.37 % Allowed : 25.38 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.03 (0.19), residues: 1653 helix: -2.00 (0.53), residues: 75 sheet: -1.46 (0.23), residues: 479 loop : -2.40 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 209 HIS 0.023 0.002 HIS A2005 PHE 0.052 0.004 PHE A1785 TYR 0.034 0.003 TYR A 137 ARG 0.008 0.001 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 148 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4453 (OUTLIER) cc_final: 0.4095 (m-80) REVERT: A 124 LYS cc_start: 0.7065 (tptp) cc_final: 0.6233 (tmmt) REVERT: A 137 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.5306 (m-10) REVERT: A 232 MET cc_start: 0.5489 (mmt) cc_final: 0.5203 (mmt) REVERT: A 261 MET cc_start: 0.8447 (tmm) cc_final: 0.8150 (tmm) REVERT: A 292 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.5798 (mp) REVERT: A 407 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.5429 (t80) REVERT: A 625 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7879 (mp) REVERT: A 666 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6962 (t0) REVERT: A 683 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6449 (mm-30) REVERT: A 1711 MET cc_start: 0.3801 (mpp) cc_final: 0.3163 (mpp) REVERT: A 1958 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.4335 (m-80) REVERT: A 2010 MET cc_start: 0.8109 (tpp) cc_final: 0.7761 (mpp) REVERT: A 2167 MET cc_start: 0.5878 (mmt) cc_final: 0.5260 (mmt) REVERT: A 2180 MET cc_start: 0.7726 (tpt) cc_final: 0.7057 (tpt) REVERT: A 2219 TRP cc_start: 0.4932 (t60) cc_final: 0.4225 (p-90) REVERT: A 2238 MET cc_start: 0.5770 (mmm) cc_final: 0.4888 (tpp) REVERT: B 88 TYR cc_start: 0.5865 (m-80) cc_final: 0.5444 (m-80) REVERT: C 57 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.7351 (t60) outliers start: 108 outliers final: 66 residues processed: 238 average time/residue: 0.2451 time to fit residues: 86.8959 Evaluate side-chains 213 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 139 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1873 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1958 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1986 VAL Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2129 ASN Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13869 Z= 0.242 Angle : 0.724 10.328 18816 Z= 0.367 Chirality : 0.048 0.258 2071 Planarity : 0.005 0.075 2379 Dihedral : 10.548 114.755 2071 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.22 % Favored : 89.41 % Rotamer: Outliers : 5.53 % Allowed : 27.76 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.79 (0.20), residues: 1653 helix: -2.10 (0.49), residues: 88 sheet: -1.38 (0.22), residues: 476 loop : -2.15 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 209 HIS 0.008 0.001 HIS A2005 PHE 0.025 0.002 PHE A1785 TYR 0.021 0.002 TYR B 92 ARG 0.005 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 150 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.6706 (tptp) cc_final: 0.5892 (tppt) REVERT: A 261 MET cc_start: 0.8411 (tmm) cc_final: 0.7916 (tmm) REVERT: A 275 HIS cc_start: 0.3471 (OUTLIER) cc_final: 0.2666 (t-170) REVERT: A 292 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5399 (mp) REVERT: A 302 MET cc_start: 0.4668 (tpt) cc_final: 0.4451 (tpt) REVERT: A 313 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7238 (mt) REVERT: A 324 HIS cc_start: 0.5768 (m-70) cc_final: 0.5270 (m-70) REVERT: A 407 TYR cc_start: 0.6076 (OUTLIER) cc_final: 0.5447 (t80) REVERT: A 665 GLU cc_start: 0.8108 (mp0) cc_final: 0.7808 (mp0) REVERT: A 1711 MET cc_start: 0.3718 (mpp) cc_final: 0.3046 (mpp) REVERT: A 1768 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5623 (tt0) REVERT: A 1794 ASP cc_start: 0.5716 (t0) cc_final: 0.4949 (p0) REVERT: A 2010 MET cc_start: 0.8037 (tpp) cc_final: 0.7254 (mpp) REVERT: A 2167 MET cc_start: 0.5812 (mmt) cc_final: 0.5127 (mmt) REVERT: A 2180 MET cc_start: 0.7507 (tpt) cc_final: 0.7248 (tpt) REVERT: A 2219 TRP cc_start: 0.4842 (t60) cc_final: 0.3879 (p-90) REVERT: A 2238 MET cc_start: 0.5996 (mmm) cc_final: 0.5428 (tpp) REVERT: B 86 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7734 (t) REVERT: B 88 TYR cc_start: 0.5812 (m-80) cc_final: 0.5330 (m-80) REVERT: B 138 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8678 (pp) REVERT: B 141 PHE cc_start: 0.4476 (p90) cc_final: 0.3896 (p90) REVERT: C 57 TRP cc_start: 0.8295 (OUTLIER) cc_final: 0.7314 (t60) REVERT: C 103 MET cc_start: 0.6071 (tpp) cc_final: 0.5780 (tpp) outliers start: 81 outliers final: 45 residues processed: 213 average time/residue: 0.2294 time to fit residues: 74.1545 Evaluate side-chains 192 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 139 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1915 ASN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 13869 Z= 0.488 Angle : 0.876 12.679 18816 Z= 0.450 Chirality : 0.053 0.247 2071 Planarity : 0.006 0.078 2379 Dihedral : 10.348 111.912 2071 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 32.97 Ramachandran Plot: Outliers : 0.54 % Allowed : 13.49 % Favored : 85.96 % Rotamer: Outliers : 9.14 % Allowed : 26.06 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.11 (0.19), residues: 1653 helix: -2.34 (0.49), residues: 84 sheet: -1.55 (0.22), residues: 481 loop : -2.42 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 209 HIS 0.015 0.002 HIS A2005 PHE 0.046 0.003 PHE A1785 TYR 0.033 0.003 TYR A 137 ARG 0.006 0.001 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 139 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4527 (OUTLIER) cc_final: 0.4148 (m-80) REVERT: A 137 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.5215 (m-10) REVERT: A 261 MET cc_start: 0.8432 (tmm) cc_final: 0.8072 (tmm) REVERT: A 275 HIS cc_start: 0.3617 (OUTLIER) cc_final: 0.2686 (t-170) REVERT: A 292 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.5847 (mp) REVERT: A 313 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7114 (mp) REVERT: A 324 HIS cc_start: 0.5988 (m-70) cc_final: 0.5406 (m-70) REVERT: A 407 TYR cc_start: 0.6416 (OUTLIER) cc_final: 0.5749 (t80) REVERT: A 622 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6260 (m-10) REVERT: A 625 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7785 (mp) REVERT: A 666 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6993 (t0) REVERT: A 1711 MET cc_start: 0.3868 (mpp) cc_final: 0.3307 (mpp) REVERT: A 1768 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5771 (tt0) REVERT: A 1785 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.5476 (t80) REVERT: A 1801 GLU cc_start: 0.4921 (OUTLIER) cc_final: 0.4503 (pm20) REVERT: A 1958 PHE cc_start: 0.4978 (OUTLIER) cc_final: 0.4442 (m-80) REVERT: A 2002 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 2033 ARG cc_start: 0.7549 (ptt90) cc_final: 0.7016 (mtm110) REVERT: A 2180 MET cc_start: 0.7674 (tpt) cc_final: 0.6442 (tpt) REVERT: A 2238 MET cc_start: 0.6262 (mmm) cc_final: 0.5622 (tpp) REVERT: B 86 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7651 (t) REVERT: B 88 TYR cc_start: 0.5695 (m-80) cc_final: 0.5283 (m-80) REVERT: B 138 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8718 (pp) REVERT: B 141 PHE cc_start: 0.4556 (p90) cc_final: 0.3932 (p90) REVERT: C 57 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7334 (t60) REVERT: C 127 TRP cc_start: 0.4753 (OUTLIER) cc_final: 0.4529 (m-10) outliers start: 134 outliers final: 86 residues processed: 253 average time/residue: 0.2469 time to fit residues: 93.0255 Evaluate side-chains 238 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 134 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 622 PHE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1815 TYR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1952 ASN Chi-restraints excluded: chain A residue 1958 PHE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2002 ILE Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2129 ASN Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 127 TRP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1915 ASN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13869 Z= 0.358 Angle : 0.782 10.537 18816 Z= 0.400 Chirality : 0.049 0.255 2071 Planarity : 0.006 0.069 2379 Dihedral : 9.929 110.026 2071 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.49 % Favored : 88.14 % Rotamer: Outliers : 7.50 % Allowed : 27.63 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.06 (0.19), residues: 1653 helix: -2.30 (0.50), residues: 82 sheet: -1.63 (0.22), residues: 483 loop : -2.32 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A2219 HIS 0.009 0.001 HIS A2005 PHE 0.037 0.002 PHE A1785 TYR 0.026 0.002 TYR A 159 ARG 0.005 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 145 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4566 (OUTLIER) cc_final: 0.4183 (m-80) REVERT: A 209 TRP cc_start: 0.7609 (t-100) cc_final: 0.7151 (t-100) REVERT: A 261 MET cc_start: 0.8427 (tmm) cc_final: 0.7997 (tmm) REVERT: A 275 HIS cc_start: 0.3563 (OUTLIER) cc_final: 0.2672 (t-170) REVERT: A 292 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5586 (mp) REVERT: A 313 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7182 (mp) REVERT: A 321 MET cc_start: 0.6494 (ttp) cc_final: 0.6163 (mtp) REVERT: A 324 HIS cc_start: 0.5893 (m-70) cc_final: 0.5345 (m-70) REVERT: A 407 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.5734 (t80) REVERT: A 622 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6265 (m-10) REVERT: A 666 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6929 (t0) REVERT: A 1711 MET cc_start: 0.3812 (mpp) cc_final: 0.3249 (mpp) REVERT: A 1768 GLU cc_start: 0.6175 (OUTLIER) cc_final: 0.5729 (tt0) REVERT: A 1785 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.5372 (t80) REVERT: A 1801 GLU cc_start: 0.4867 (OUTLIER) cc_final: 0.4447 (pm20) REVERT: A 2002 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 2238 MET cc_start: 0.6219 (mmm) cc_final: 0.5541 (tpp) REVERT: B 86 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7614 (t) REVERT: B 88 TYR cc_start: 0.5571 (m-80) cc_final: 0.5161 (m-80) REVERT: B 138 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8687 (pp) REVERT: B 141 PHE cc_start: 0.4574 (p90) cc_final: 0.3989 (p90) REVERT: C 57 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.7267 (t60) REVERT: C 103 MET cc_start: 0.5989 (tpp) cc_final: 0.5394 (mtp) outliers start: 110 outliers final: 75 residues processed: 237 average time/residue: 0.2280 time to fit residues: 82.6918 Evaluate side-chains 227 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 138 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 622 PHE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 1747 SER Chi-restraints excluded: chain A residue 1758 LEU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1785 PHE Chi-restraints excluded: chain A residue 1787 SER Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1956 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1986 VAL Chi-restraints excluded: chain A residue 2002 ILE Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 100 optimal weight: 0.0020 chunk 97 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13869 Z= 0.199 Angle : 0.699 9.918 18816 Z= 0.351 Chirality : 0.047 0.251 2071 Planarity : 0.005 0.077 2379 Dihedral : 9.189 107.592 2071 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.44 % Favored : 90.14 % Rotamer: Outliers : 5.87 % Allowed : 29.47 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.77 (0.20), residues: 1653 helix: -1.89 (0.55), residues: 75 sheet: -1.46 (0.22), residues: 493 loop : -2.11 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A2219 HIS 0.006 0.001 HIS C 37 PHE 0.021 0.001 PHE A1785 TYR 0.027 0.002 TYR A 159 ARG 0.007 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 150 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.6732 (tptp) cc_final: 0.5750 (tppt) REVERT: A 209 TRP cc_start: 0.7341 (t-100) cc_final: 0.6934 (t-100) REVERT: A 261 MET cc_start: 0.8347 (tmm) cc_final: 0.7851 (tmm) REVERT: A 275 HIS cc_start: 0.3350 (OUTLIER) cc_final: 0.2572 (t-170) REVERT: A 292 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5806 (mp) REVERT: A 313 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7205 (mt) REVERT: A 321 MET cc_start: 0.6365 (ttp) cc_final: 0.6098 (mtp) REVERT: A 324 HIS cc_start: 0.5590 (m-70) cc_final: 0.5090 (m-70) REVERT: A 407 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.5603 (t80) REVERT: A 605 ASP cc_start: 0.6192 (OUTLIER) cc_final: 0.5990 (p0) REVERT: A 658 PHE cc_start: 0.5111 (OUTLIER) cc_final: 0.3788 (p90) REVERT: A 665 GLU cc_start: 0.8042 (mp0) cc_final: 0.7518 (mp0) REVERT: A 1711 MET cc_start: 0.3725 (mpp) cc_final: 0.3091 (mpp) REVERT: A 2167 MET cc_start: 0.5810 (mmt) cc_final: 0.5042 (mmt) REVERT: A 2219 TRP cc_start: 0.2476 (t60) cc_final: 0.2259 (t60) REVERT: A 2238 MET cc_start: 0.5878 (mmm) cc_final: 0.5235 (tpp) REVERT: A 2321 MET cc_start: 0.6059 (mmm) cc_final: 0.5699 (mpp) REVERT: B 86 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7573 (t) REVERT: B 88 TYR cc_start: 0.5739 (m-80) cc_final: 0.5290 (m-80) REVERT: B 138 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8632 (pp) REVERT: B 141 PHE cc_start: 0.4722 (p90) cc_final: 0.4158 (p90) REVERT: C 57 TRP cc_start: 0.8153 (OUTLIER) cc_final: 0.7200 (t60) REVERT: C 103 MET cc_start: 0.5765 (tpp) cc_final: 0.5489 (tpp) outliers start: 86 outliers final: 54 residues processed: 222 average time/residue: 0.2438 time to fit residues: 82.6188 Evaluate side-chains 209 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 146 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2180 MET Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 125 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13869 Z= 0.247 Angle : 0.712 11.338 18816 Z= 0.358 Chirality : 0.047 0.246 2071 Planarity : 0.005 0.081 2379 Dihedral : 8.879 104.722 2069 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.53 % Favored : 89.05 % Rotamer: Outliers : 6.21 % Allowed : 28.51 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.72 (0.20), residues: 1653 helix: -1.76 (0.57), residues: 74 sheet: -1.44 (0.22), residues: 497 loop : -2.09 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2219 HIS 0.011 0.001 HIS A2005 PHE 0.027 0.002 PHE A1785 TYR 0.051 0.002 TYR A 159 ARG 0.004 0.000 ARG A1694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 144 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.3619 (OUTLIER) cc_final: 0.1902 (t70) REVERT: A 137 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.4676 (m-10) REVERT: A 209 TRP cc_start: 0.7347 (t-100) cc_final: 0.6977 (t-100) REVERT: A 261 MET cc_start: 0.8392 (tmm) cc_final: 0.7856 (tmm) REVERT: A 275 HIS cc_start: 0.3323 (OUTLIER) cc_final: 0.2551 (t-170) REVERT: A 292 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.5761 (mp) REVERT: A 313 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7183 (mp) REVERT: A 324 HIS cc_start: 0.5622 (m-70) cc_final: 0.5102 (m-70) REVERT: A 407 TYR cc_start: 0.6363 (OUTLIER) cc_final: 0.5629 (t80) REVERT: A 552 LEU cc_start: 0.7864 (tp) cc_final: 0.7659 (mm) REVERT: A 658 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.3855 (p90) REVERT: A 1711 MET cc_start: 0.3656 (mpp) cc_final: 0.2955 (mpp) REVERT: A 1768 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5648 (tt0) REVERT: A 2010 MET cc_start: 0.8008 (tpp) cc_final: 0.7513 (mpp) REVERT: A 2219 TRP cc_start: 0.2348 (t60) cc_final: 0.2025 (t60) REVERT: A 2238 MET cc_start: 0.6217 (mmm) cc_final: 0.5948 (mmm) REVERT: A 2321 MET cc_start: 0.5869 (mmm) cc_final: 0.5612 (mpp) REVERT: B 86 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7572 (t) REVERT: B 88 TYR cc_start: 0.5720 (m-80) cc_final: 0.5297 (m-80) REVERT: B 138 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8695 (pp) REVERT: B 141 PHE cc_start: 0.4718 (p90) cc_final: 0.4175 (p90) REVERT: C 57 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7284 (t60) REVERT: C 103 MET cc_start: 0.5821 (tpp) cc_final: 0.5564 (tpp) outliers start: 91 outliers final: 68 residues processed: 220 average time/residue: 0.2458 time to fit residues: 81.3070 Evaluate side-chains 216 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 137 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1787 SER Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2180 MET Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13869 Z= 0.279 Angle : 0.732 11.504 18816 Z= 0.368 Chirality : 0.048 0.251 2071 Planarity : 0.005 0.083 2379 Dihedral : 8.736 101.851 2069 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.01 % Favored : 88.63 % Rotamer: Outliers : 6.07 % Allowed : 28.85 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.76 (0.20), residues: 1653 helix: -1.78 (0.56), residues: 73 sheet: -1.42 (0.22), residues: 498 loop : -2.14 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 139 HIS 0.013 0.001 HIS A2005 PHE 0.032 0.002 PHE A1785 TYR 0.053 0.002 TYR A 159 ARG 0.004 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 138 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4138 (OUTLIER) cc_final: 0.2968 (m-80) REVERT: A 137 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.4728 (m-10) REVERT: A 209 TRP cc_start: 0.7390 (t-100) cc_final: 0.7067 (t-100) REVERT: A 261 MET cc_start: 0.8408 (tmm) cc_final: 0.7857 (tmm) REVERT: A 275 HIS cc_start: 0.3305 (OUTLIER) cc_final: 0.2513 (t-170) REVERT: A 292 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.5673 (mp) REVERT: A 313 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7193 (mp) REVERT: A 321 MET cc_start: 0.6477 (ttp) cc_final: 0.6217 (mtp) REVERT: A 324 HIS cc_start: 0.5736 (m-70) cc_final: 0.5216 (m-70) REVERT: A 407 TYR cc_start: 0.6412 (OUTLIER) cc_final: 0.5682 (t80) REVERT: A 552 LEU cc_start: 0.7599 (tp) cc_final: 0.7166 (mm) REVERT: A 553 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6654 (mm) REVERT: A 658 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.3871 (p90) REVERT: A 1711 MET cc_start: 0.3791 (mpp) cc_final: 0.3163 (mpp) REVERT: A 1768 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5645 (tt0) REVERT: A 1801 GLU cc_start: 0.4853 (OUTLIER) cc_final: 0.4448 (pm20) REVERT: A 2033 ARG cc_start: 0.7324 (ptt90) cc_final: 0.6831 (mtm110) REVERT: A 2238 MET cc_start: 0.6120 (mmm) cc_final: 0.5571 (mmp) REVERT: B 86 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7536 (t) REVERT: B 88 TYR cc_start: 0.5563 (m-80) cc_final: 0.5179 (m-80) REVERT: B 138 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8622 (pp) REVERT: B 141 PHE cc_start: 0.4771 (p90) cc_final: 0.4200 (p90) REVERT: C 57 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.7334 (t60) REVERT: C 103 MET cc_start: 0.5867 (tpp) cc_final: 0.5608 (tpp) outliers start: 89 outliers final: 71 residues processed: 212 average time/residue: 0.2363 time to fit residues: 75.7575 Evaluate side-chains 216 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 132 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1787 SER Chi-restraints excluded: chain A residue 1801 GLU Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1952 ASN Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2129 ASN Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 165 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13869 Z= 0.212 Angle : 0.709 11.276 18816 Z= 0.353 Chirality : 0.047 0.253 2071 Planarity : 0.005 0.083 2379 Dihedral : 8.327 98.689 2069 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.56 % Favored : 90.08 % Rotamer: Outliers : 5.53 % Allowed : 29.47 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.62 (0.20), residues: 1653 helix: -1.55 (0.58), residues: 67 sheet: -1.37 (0.22), residues: 500 loop : -2.03 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2219 HIS 0.010 0.001 HIS A2005 PHE 0.021 0.001 PHE A1785 TYR 0.046 0.002 TYR A 159 ARG 0.004 0.000 ARG A 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 139 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 TRP cc_start: 0.7275 (t-100) cc_final: 0.6973 (t-100) REVERT: A 261 MET cc_start: 0.8334 (tmm) cc_final: 0.7816 (tmm) REVERT: A 275 HIS cc_start: 0.3255 (OUTLIER) cc_final: 0.2480 (t-170) REVERT: A 292 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5731 (mp) REVERT: A 313 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7223 (mp) REVERT: A 321 MET cc_start: 0.6382 (ttp) cc_final: 0.6106 (mtp) REVERT: A 407 TYR cc_start: 0.6353 (OUTLIER) cc_final: 0.5661 (t80) REVERT: A 553 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7169 (mm) REVERT: A 636 TYR cc_start: 0.5140 (m-80) cc_final: 0.4537 (m-80) REVERT: A 658 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.3707 (p90) REVERT: A 665 GLU cc_start: 0.8011 (mp0) cc_final: 0.7518 (mp0) REVERT: A 1711 MET cc_start: 0.3683 (mpp) cc_final: 0.3030 (mpp) REVERT: A 1768 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5566 (tt0) REVERT: A 2033 ARG cc_start: 0.7191 (ptt90) cc_final: 0.6289 (ptp-110) REVERT: A 2167 MET cc_start: 0.5654 (mmt) cc_final: 0.5048 (mmt) REVERT: A 2238 MET cc_start: 0.6066 (mmm) cc_final: 0.5545 (mmp) REVERT: A 2321 MET cc_start: 0.6032 (mmm) cc_final: 0.5678 (mpp) REVERT: B 86 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7519 (t) REVERT: B 88 TYR cc_start: 0.5651 (m-80) cc_final: 0.5244 (m-80) REVERT: B 138 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8592 (pp) REVERT: B 141 PHE cc_start: 0.4839 (p90) cc_final: 0.4282 (p90) REVERT: C 57 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.7244 (t60) REVERT: C 103 MET cc_start: 0.5788 (tpp) cc_final: 0.5534 (tpp) outliers start: 81 outliers final: 61 residues processed: 206 average time/residue: 0.2332 time to fit residues: 73.3168 Evaluate side-chains 208 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 137 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1787 SER Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2129 ASN Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.0010 chunk 131 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 115 optimal weight: 0.0020 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1861 ASN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2087 GLN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.191671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.149011 restraints weight = 23896.872| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 3.81 r_work: 0.4133 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13869 Z= 0.370 Angle : 0.795 11.520 18816 Z= 0.402 Chirality : 0.050 0.237 2071 Planarity : 0.006 0.086 2379 Dihedral : 8.379 93.855 2069 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.34 % Favored : 87.30 % Rotamer: Outliers : 6.14 % Allowed : 29.26 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.84 (0.20), residues: 1653 helix: -1.78 (0.57), residues: 67 sheet: -1.35 (0.22), residues: 494 loop : -2.27 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2062 HIS 0.016 0.001 HIS A2005 PHE 0.040 0.002 PHE A1785 TYR 0.045 0.002 TYR A 159 ARG 0.004 0.001 ARG A 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3664.77 seconds wall clock time: 66 minutes 33.45 seconds (3993.45 seconds total)