Starting phenix.real_space_refine on Sun Dec 10 05:25:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/12_2023/8ty1_41710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/12_2023/8ty1_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_41710/12_2023/8ty1_41710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/12_2023/8ty1_41710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/12_2023/8ty1_41710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ty1_41710/12_2023/8ty1_41710.pdb" } 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-1.21rc1-5172/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: 6 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: 6 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: 6 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.99, per 1000 atoms: 0.52 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: 5.22 Conformation dependent library (CDL) restraints added in 2.3 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: 1.63 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: 5.90 Time building geometry restraints manager: 5.62 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 - 23.40: 7403 23.40 - 46.80: 702 46.80 - 70.21: 100 70.21 - 93.61: 26 93.61 - 117.01: 2 Dihedral angle restraints: 8233 sinusoidal: 3359 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 8230 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: 8.380 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: 32.550 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 38.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.050 ------------------------------------------------------------------------------- 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 : 17.592 117.011 5072 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 : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 167 average time/residue: 0.2577 time to fit residues: 64.3805 Evaluate side-chains 150 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.538 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1473 time to fit residues: 3.1779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2091 GLN A2231 GLN C 64 ASN C 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13869 Z= 0.199 Angle : 0.687 10.132 18816 Z= 0.344 Chirality : 0.047 0.242 2071 Planarity : 0.005 0.107 2379 Dihedral : 7.683 98.609 1953 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.59 % Favored : 90.99 % Rotamer: Outliers : 3.89 % Allowed : 25.38 % Favored : 70.74 % 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: -2.42 (0.20), residues: 1653 helix: -1.44 (0.55), residues: 75 sheet: -1.20 (0.22), residues: 487 loop : -1.89 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 127 HIS 0.006 0.001 HIS C 37 PHE 0.023 0.001 PHE A1785 TYR 0.022 0.001 TYR B 92 ARG 0.006 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 207 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 150 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 27 residues processed: 197 average time/residue: 0.2493 time to fit residues: 74.3078 Evaluate side-chains 165 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1469 time to fit residues: 9.1341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1867 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1957 HIS ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 ASN ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 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: 0.5919 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13869 Z= 0.363 Angle : 0.770 10.337 18816 Z= 0.393 Chirality : 0.049 0.254 2071 Planarity : 0.006 0.081 2379 Dihedral : 7.662 84.614 1953 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.43 % Favored : 88.08 % Rotamer: Outliers : 3.96 % Allowed : 26.40 % Favored : 69.65 % 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: -2.61 (0.20), residues: 1653 helix: -1.52 (0.56), residues: 75 sheet: -1.32 (0.23), residues: 476 loop : -2.04 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 57 HIS 0.019 0.002 HIS A2005 PHE 0.036 0.002 PHE A1785 TYR 0.025 0.002 TYR A 137 ARG 0.005 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 204 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 146 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 27 residues processed: 193 average time/residue: 0.2499 time to fit residues: 73.3250 Evaluate side-chains 162 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1367 time to fit residues: 8.9602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 160 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.1586 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= 0.233 Angle : 0.701 10.743 18816 Z= 0.354 Chirality : 0.046 0.253 2071 Planarity : 0.005 0.073 2379 Dihedral : 7.094 69.546 1953 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.92 % Favored : 89.66 % Rotamer: Outliers : 3.41 % Allowed : 28.10 % Favored : 68.49 % 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: -2.54 (0.20), residues: 1653 helix: -1.68 (0.54), residues: 81 sheet: -1.27 (0.23), residues: 477 loop : -1.97 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 57 HIS 0.010 0.001 HIS A2005 PHE 0.027 0.002 PHE A1785 TYR 0.024 0.002 TYR A 159 ARG 0.008 0.000 ARG C 60 *********************** 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 194 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 144 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 19 residues processed: 187 average time/residue: 0.2504 time to fit residues: 71.4459 Evaluate side-chains 156 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1347 time to fit residues: 6.8671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 66 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** A2113 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 13869 Z= 0.465 Angle : 0.853 11.153 18816 Z= 0.437 Chirality : 0.051 0.261 2071 Planarity : 0.006 0.100 2379 Dihedral : 7.187 55.923 1953 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 29.29 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.31 % Favored : 86.33 % Rotamer: Outliers : 4.57 % Allowed : 27.83 % Favored : 67.60 % 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: -2.91 (0.20), residues: 1653 helix: -2.13 (0.52), residues: 81 sheet: -1.46 (0.23), residues: 480 loop : -2.26 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 57 HIS 0.015 0.002 HIS A2005 PHE 0.044 0.003 PHE A1785 TYR 0.035 0.003 TYR A 159 ARG 0.006 0.001 ARG C 48 *********************** 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 207 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 140 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 38 residues processed: 191 average time/residue: 0.2516 time to fit residues: 72.0833 Evaluate side-chains 168 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1364 time to fit residues: 11.6472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 154 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1915 ASN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.2222 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= 0.215 Angle : 0.717 11.190 18816 Z= 0.358 Chirality : 0.047 0.260 2071 Planarity : 0.005 0.073 2379 Dihedral : 6.442 56.548 1953 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.13 % Favored : 90.44 % Rotamer: Outliers : 1.98 % Allowed : 29.47 % Favored : 68.55 % 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: -2.69 (0.20), residues: 1653 helix: -1.97 (0.49), residues: 94 sheet: -1.38 (0.22), residues: 474 loop : -2.06 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 57 HIS 0.006 0.001 HIS C 37 PHE 0.019 0.002 PHE A1785 TYR 0.025 0.002 TYR A 476 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 178 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 174 average time/residue: 0.2658 time to fit residues: 69.6391 Evaluate side-chains 154 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2057 time to fit residues: 7.1209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 0.1980 chunk 89 optimal weight: 0.6980 chunk 159 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13869 Z= 0.215 Angle : 0.704 12.089 18816 Z= 0.351 Chirality : 0.046 0.249 2071 Planarity : 0.005 0.077 2379 Dihedral : 6.225 55.682 1953 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.04 % Favored : 89.59 % Rotamer: Outliers : 1.98 % Allowed : 30.42 % Favored : 67.60 % 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: -2.61 (0.20), residues: 1653 helix: -1.95 (0.49), residues: 93 sheet: -1.28 (0.23), residues: 475 loop : -2.03 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 209 HIS 0.006 0.001 HIS A2005 PHE 0.023 0.001 PHE A1785 TYR 0.038 0.002 TYR A 159 ARG 0.005 0.000 ARG A2220 *********************** 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 169 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.731 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 159 average time/residue: 0.2410 time to fit residues: 58.7362 Evaluate side-chains 147 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1716 time to fit residues: 4.9500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13869 Z= 0.200 Angle : 0.696 10.973 18816 Z= 0.346 Chirality : 0.046 0.252 2071 Planarity : 0.005 0.079 2379 Dihedral : 6.116 55.964 1953 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.68 % Favored : 89.96 % Rotamer: Outliers : 1.57 % Allowed : 30.56 % Favored : 67.87 % 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: -2.53 (0.20), residues: 1653 helix: -1.91 (0.48), residues: 93 sheet: -1.25 (0.22), residues: 496 loop : -1.95 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 209 HIS 0.009 0.001 HIS A2005 PHE 0.020 0.001 PHE A1785 TYR 0.045 0.002 TYR A 159 ARG 0.006 0.000 ARG A 531 *********************** 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 158 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.545 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 153 average time/residue: 0.2487 time to fit residues: 58.7242 Evaluate side-chains 148 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1776 time to fit residues: 6.3828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0.5870 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13869 Z= 0.282 Angle : 0.735 10.949 18816 Z= 0.370 Chirality : 0.048 0.244 2071 Planarity : 0.005 0.082 2379 Dihedral : 6.331 57.820 1953 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.13 % Favored : 88.57 % Rotamer: Outliers : 1.30 % Allowed : 30.76 % Favored : 67.94 % 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: -2.63 (0.20), residues: 1653 helix: -1.94 (0.48), residues: 93 sheet: -1.28 (0.23), residues: 488 loop : -2.04 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 139 HIS 0.014 0.001 HIS A2005 PHE 0.033 0.002 PHE A1785 TYR 0.053 0.002 TYR A 159 ARG 0.004 0.000 ARG A 4 *********************** 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 155 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.645 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 151 average time/residue: 0.2448 time to fit residues: 57.0684 Evaluate side-chains 139 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.556 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1352 time to fit residues: 4.4059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13869 Z= 0.234 Angle : 0.735 12.272 18816 Z= 0.367 Chirality : 0.048 0.358 2071 Planarity : 0.005 0.084 2379 Dihedral : 6.262 58.884 1953 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.10 % Favored : 89.59 % Rotamer: Outliers : 0.55 % Allowed : 31.51 % Favored : 67.94 % 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: -2.55 (0.20), residues: 1653 helix: -1.86 (0.49), residues: 93 sheet: -1.23 (0.22), residues: 503 loop : -1.99 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 209 HIS 0.011 0.001 HIS A2005 PHE 0.025 0.002 PHE A1785 TYR 0.048 0.002 TYR A 159 ARG 0.004 0.000 ARG A 4 ********************** 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 140 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.610 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 137 average time/residue: 0.2598 time to fit residues: 54.7647 Evaluate side-chains 135 residues out of total 1467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1399 time to fit residues: 3.3753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 115 optimal weight: 0.0270 overall best weight: 1.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** 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 C 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.191422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.148595 restraints weight = 23261.586| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 3.70 r_work: 0.4162 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13869 Z= 0.396 Angle : 0.834 13.483 18816 Z= 0.423 Chirality : 0.052 0.436 2071 Planarity : 0.006 0.087 2379 Dihedral : 6.807 57.594 1953 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.52 % Favored : 87.11 % Rotamer: Outliers : 0.75 % Allowed : 31.99 % Favored : 67.26 % 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: -2.82 (0.20), residues: 1653 helix: -1.98 (0.50), residues: 86 sheet: -1.38 (0.23), residues: 494 loop : -2.21 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 209 HIS 0.018 0.002 HIS A2005 PHE 0.044 0.003 PHE A1785 TYR 0.059 0.003 TYR A 159 ARG 0.009 0.001 ARG A 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3506.65 seconds wall clock time: 65 minutes 9.04 seconds (3909.04 seconds total)