Starting phenix.real_space_refine on Fri Jul 19 06:12:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/07_2024/8pb1_17580.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/07_2024/8pb1_17580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/07_2024/8pb1_17580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/07_2024/8pb1_17580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/07_2024/8pb1_17580.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/07_2024/8pb1_17580.cif" } resolution = 3.5 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 56 5.16 5 C 4160 2.51 5 N 1137 2.21 5 O 1299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6652 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1247 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 152} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2336 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1542 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 15, 'TRANS': 174} Chain breaks: 2 Chain: "D" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1420 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 176} Chain breaks: 3 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.90, per 1000 atoms: 0.89 Number of scatterers: 6652 At special positions: 0 Unit cell: (88.335, 131.37, 129.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1299 8.00 N 1137 7.00 C 4160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 328 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 144 " " NAG D 801 " - " ASN D 224 " " NAG D 802 " - " ASN D 48 " " NAG E 1 " - " ASN B 220 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 18 sheets defined 13.9% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 32 through 55 removed outlier: 4.329A pdb=" N GLN A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 114 through 143 removed outlier: 4.153A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.230A pdb=" N LEU A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 214 removed outlier: 3.777A pdb=" N MET A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.586A pdb=" N ALA B 85 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 92 Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 27 removed outlier: 7.025A pdb=" N VAL B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N CYS B 90 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N HIS B 99 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR B 88 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS B 101 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY B 86 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 70 " --> pdb=" O TRP B 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 27 removed outlier: 7.025A pdb=" N VAL B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.261A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.261A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 185 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG B 182 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 177 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR B 184 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 175 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS B 186 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 54 removed outlier: 6.495A pdb=" N ASP C 68 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN C 50 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN C 66 " --> pdb=" O ASN C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 101 removed outlier: 6.038A pdb=" N HIS C 76 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 126 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET C 133 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 101 removed outlier: 6.038A pdb=" N HIS C 76 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.574A pdb=" N TRP C 168 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 214 " --> pdb=" O TRP C 168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 190 through 193 removed outlier: 3.529A pdb=" N GLN C 179 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG C 230 " --> pdb=" O GLN C 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.708A pdb=" N GLN D 36 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN D 48 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 40 through 42 removed outlier: 6.194A pdb=" N ILE D 41 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N CYS D 127 " --> pdb=" O CYS D 111 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU D 70 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN D 81 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS D 72 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 196 through 198 removed outlier: 4.445A pdb=" N THR D 153 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 148 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN D 159 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN D 142 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N ILE D 239 " --> pdb=" O CYS D 145 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLN D 147 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 180 through 188 removed outlier: 3.568A pdb=" N GLY D 223 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 180 through 188 282 hydrogen bonds defined for protein. 738 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: 1.85 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2013 1.34 - 1.46: 1370 1.46 - 1.58: 3328 1.58 - 1.70: 1 1.70 - 1.82: 75 Bond restraints: 6787 Sorted by residual: bond pdb=" N VAL D 146 " pdb=" CA VAL D 146 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.14e-02 7.69e+03 1.17e+01 bond pdb=" N SER D 144 " pdb=" CA SER D 144 " ideal model delta sigma weight residual 1.454 1.495 -0.040 1.23e-02 6.61e+03 1.08e+01 bond pdb=" N VAL B 249 " pdb=" CA VAL B 249 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.05e+01 bond pdb=" N CYS B 311 " pdb=" CA CYS B 311 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.83e+00 bond pdb=" N ILE D 237 " pdb=" CA ILE D 237 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.63e+00 ... (remaining 6782 not shown) Histogram of bond angle deviations from ideal: 96.10 - 103.75: 112 103.75 - 111.41: 2932 111.41 - 119.07: 2694 119.07 - 126.72: 3336 126.72 - 134.38: 127 Bond angle restraints: 9201 Sorted by residual: angle pdb=" N ALA B 327 " pdb=" CA ALA B 327 " pdb=" C ALA B 327 " ideal model delta sigma weight residual 109.85 100.66 9.19 1.58e+00 4.01e-01 3.38e+01 angle pdb=" CA ALA B 327 " pdb=" C ALA B 327 " pdb=" O ALA B 327 " ideal model delta sigma weight residual 121.46 116.48 4.98 1.17e+00 7.31e-01 1.81e+01 angle pdb=" C GLN B 248 " pdb=" CA GLN B 248 " pdb=" CB GLN B 248 " ideal model delta sigma weight residual 109.37 117.13 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C ASN B 238 " pdb=" N LEU B 239 " pdb=" CA LEU B 239 " ideal model delta sigma weight residual 120.95 115.48 5.47 1.40e+00 5.10e-01 1.53e+01 angle pdb=" CA ASN B 246 " pdb=" C ASN B 246 " pdb=" O ASN B 246 " ideal model delta sigma weight residual 121.28 116.77 4.51 1.19e+00 7.06e-01 1.44e+01 ... (remaining 9196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 3903 21.34 - 42.69: 296 42.69 - 64.03: 44 64.03 - 85.38: 13 85.38 - 106.72: 8 Dihedral angle restraints: 4264 sinusoidal: 1848 harmonic: 2416 Sorted by residual: dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 159.40 -66.40 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS B 305 " pdb=" SG CYS B 305 " pdb=" SG CYS B 331 " pdb=" CB CYS B 331 " ideal model delta sinusoidal sigma weight residual -86.00 -144.02 58.02 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS C 194 " pdb=" SG CYS C 194 " pdb=" SG CYS C 216 " pdb=" CB CYS C 216 " ideal model delta sinusoidal sigma weight residual 93.00 146.74 -53.74 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 4261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1006 0.111 - 0.221: 46 0.221 - 0.332: 6 0.332 - 0.442: 1 0.442 - 0.553: 1 Chirality restraints: 1060 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 220 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA GLN B 240 " pdb=" N GLN B 240 " pdb=" C GLN B 240 " pdb=" CB GLN B 240 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA ILE D 237 " pdb=" N ILE D 237 " pdb=" C ILE D 237 " pdb=" CB ILE D 237 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1057 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 324 " -0.025 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C SER B 324 " 0.086 2.00e-02 2.50e+03 pdb=" O SER B 324 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS B 325 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 108 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO A 109 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 325 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C LYS B 325 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS B 325 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP B 326 " -0.014 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1325 2.78 - 3.31: 5767 3.31 - 3.84: 10280 3.84 - 4.37: 11344 4.37 - 4.90: 20260 Nonbonded interactions: 48976 Sorted by model distance: nonbonded pdb=" OG1 THR D 171 " pdb=" OE1 GLN D 185 " model vdw 2.253 2.440 nonbonded pdb=" OG1 THR B 61 " pdb=" OG1 THR B 89 " model vdw 2.257 2.440 nonbonded pdb=" OD2 ASP B 234 " pdb=" OG SER B 258 " model vdw 2.267 2.440 nonbonded pdb=" OE2 GLU B 108 " pdb=" OH TYR C 143 " model vdw 2.290 2.440 nonbonded pdb=" O SER C 171 " pdb=" OG SER C 171 " model vdw 2.300 2.440 ... (remaining 48971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 9.780 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 24.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 0.088 6787 Z= 0.305 Angle : 0.862 9.187 9201 Z= 0.484 Chirality : 0.059 0.553 1060 Planarity : 0.006 0.068 1166 Dihedral : 15.489 106.722 2640 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.26 % Allowed : 1.19 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.29), residues: 803 helix: 0.91 (0.54), residues: 96 sheet: 0.23 (0.32), residues: 275 loop : -1.67 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 123 HIS 0.003 0.001 HIS A 144 PHE 0.009 0.001 PHE C 108 TYR 0.009 0.001 TYR A 130 ARG 0.010 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7422 (ptmm) cc_final: 0.7108 (ptpp) REVERT: A 66 ASP cc_start: 0.8261 (m-30) cc_final: 0.8024 (m-30) REVERT: A 164 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7572 (tp-100) REVERT: B 44 GLU cc_start: 0.6883 (tt0) cc_final: 0.6321 (mp0) REVERT: B 45 THR cc_start: 0.8499 (m) cc_final: 0.8161 (m) REVERT: B 264 SER cc_start: 0.8575 (p) cc_final: 0.8363 (p) REVERT: C 181 ARG cc_start: 0.7242 (ptp-170) cc_final: 0.6651 (ptt-90) REVERT: D 191 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7707 (mtt90) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.2109 time to fit residues: 35.0505 Evaluate side-chains 100 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain D residue 191 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 34 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.0270 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN C 179 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6787 Z= 0.164 Angle : 0.584 9.476 9201 Z= 0.298 Chirality : 0.043 0.272 1060 Planarity : 0.004 0.039 1166 Dihedral : 9.888 75.339 1047 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.32 % Allowed : 9.51 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.29), residues: 803 helix: 1.62 (0.55), residues: 96 sheet: 0.35 (0.31), residues: 282 loop : -1.52 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 123 HIS 0.009 0.001 HIS A 196 PHE 0.013 0.001 PHE D 109 TYR 0.015 0.001 TYR A 124 ARG 0.005 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7991 (mttt) cc_final: 0.7457 (tttt) REVERT: A 56 LYS cc_start: 0.7409 (ptmm) cc_final: 0.7082 (ptpp) REVERT: A 66 ASP cc_start: 0.8293 (m-30) cc_final: 0.8065 (m-30) REVERT: A 164 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7556 (tp-100) REVERT: B 44 GLU cc_start: 0.6954 (tt0) cc_final: 0.6297 (mp0) REVERT: B 45 THR cc_start: 0.8493 (m) cc_final: 0.8094 (m) REVERT: B 264 SER cc_start: 0.8511 (p) cc_final: 0.8304 (p) REVERT: C 181 ARG cc_start: 0.7141 (ptp-170) cc_final: 0.6577 (ptt-90) REVERT: C 223 MET cc_start: 0.6480 (ptp) cc_final: 0.6027 (ptp) REVERT: D 191 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7750 (mtt90) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 0.2030 time to fit residues: 28.8395 Evaluate side-chains 108 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 0.0070 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6787 Z= 0.177 Angle : 0.570 9.336 9201 Z= 0.283 Chirality : 0.042 0.242 1060 Planarity : 0.004 0.037 1166 Dihedral : 8.471 56.025 1047 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.98 % Allowed : 11.49 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 803 helix: 2.03 (0.54), residues: 96 sheet: 0.52 (0.32), residues: 282 loop : -1.45 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 109 HIS 0.006 0.001 HIS A 196 PHE 0.009 0.001 PHE C 108 TYR 0.016 0.001 TYR A 124 ARG 0.002 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8862 (ttpp) cc_final: 0.8653 (tmmt) REVERT: A 66 ASP cc_start: 0.8354 (m-30) cc_final: 0.8086 (m-30) REVERT: A 160 ASP cc_start: 0.8475 (m-30) cc_final: 0.8215 (m-30) REVERT: A 164 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7615 (tp-100) REVERT: B 44 GLU cc_start: 0.6960 (tt0) cc_final: 0.6312 (mp0) REVERT: B 58 ILE cc_start: 0.7808 (mm) cc_final: 0.7322 (mm) REVERT: B 264 SER cc_start: 0.8495 (p) cc_final: 0.8286 (p) REVERT: C 137 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8613 (ptpp) REVERT: C 181 ARG cc_start: 0.7266 (ptp-170) cc_final: 0.6702 (ptt-90) REVERT: C 223 MET cc_start: 0.6481 (ptp) cc_final: 0.6011 (ptp) REVERT: D 191 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7741 (mtt90) REVERT: D 207 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.5612 (mp) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.1670 time to fit residues: 25.6162 Evaluate side-chains 111 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 213 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6787 Z= 0.252 Angle : 0.586 9.349 9201 Z= 0.295 Chirality : 0.042 0.221 1060 Planarity : 0.004 0.035 1166 Dihedral : 7.433 56.238 1047 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.64 % Allowed : 12.95 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.30), residues: 803 helix: 2.08 (0.53), residues: 96 sheet: 0.54 (0.32), residues: 284 loop : -1.44 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 109 HIS 0.005 0.001 HIS A 196 PHE 0.013 0.001 PHE C 108 TYR 0.014 0.001 TYR C 61 ARG 0.004 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8389 (m-30) cc_final: 0.8088 (m-30) REVERT: A 164 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7662 (tp-100) REVERT: B 23 MET cc_start: 0.7274 (tpt) cc_final: 0.7046 (tpp) REVERT: B 44 GLU cc_start: 0.7004 (tt0) cc_final: 0.6319 (mp0) REVERT: B 58 ILE cc_start: 0.7954 (mm) cc_final: 0.7538 (mm) REVERT: B 264 SER cc_start: 0.8516 (p) cc_final: 0.8299 (p) REVERT: C 137 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8746 (mmtm) REVERT: D 187 PHE cc_start: 0.8487 (m-80) cc_final: 0.8249 (m-80) REVERT: D 191 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7817 (mtt90) REVERT: D 192 GLN cc_start: 0.7695 (tt0) cc_final: 0.7454 (tt0) REVERT: D 207 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5538 (mp) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 0.1681 time to fit residues: 25.4681 Evaluate side-chains 108 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 213 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6787 Z= 0.249 Angle : 0.589 9.310 9201 Z= 0.295 Chirality : 0.042 0.219 1060 Planarity : 0.004 0.034 1166 Dihedral : 6.987 56.480 1047 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.91 % Allowed : 15.19 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.30), residues: 803 helix: 2.01 (0.53), residues: 96 sheet: 0.47 (0.32), residues: 287 loop : -1.40 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 109 HIS 0.004 0.001 HIS A 196 PHE 0.012 0.001 PHE C 108 TYR 0.015 0.001 TYR C 61 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8396 (m-30) cc_final: 0.8044 (m-30) REVERT: A 164 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7663 (tp-100) REVERT: B 44 GLU cc_start: 0.7027 (tt0) cc_final: 0.6336 (mp0) REVERT: B 58 ILE cc_start: 0.7997 (mm) cc_final: 0.7598 (mm) REVERT: B 264 SER cc_start: 0.8526 (p) cc_final: 0.8311 (p) REVERT: C 181 ARG cc_start: 0.7291 (ptp-170) cc_final: 0.6311 (ptt-90) REVERT: D 187 PHE cc_start: 0.8473 (m-80) cc_final: 0.8234 (m-80) REVERT: D 191 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7718 (mtt90) REVERT: D 192 GLN cc_start: 0.7720 (tt0) cc_final: 0.7479 (tt0) REVERT: D 207 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.5633 (mp) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.1854 time to fit residues: 27.6247 Evaluate side-chains 113 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 213 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6787 Z= 0.179 Angle : 0.564 9.340 9201 Z= 0.282 Chirality : 0.041 0.223 1060 Planarity : 0.004 0.033 1166 Dihedral : 6.683 55.656 1047 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.64 % Allowed : 16.12 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.30), residues: 803 helix: 2.03 (0.54), residues: 96 sheet: 0.52 (0.33), residues: 287 loop : -1.38 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 109 HIS 0.004 0.001 HIS A 196 PHE 0.009 0.001 PHE B 266 TYR 0.015 0.001 TYR C 61 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7653 (tttt) cc_final: 0.7445 (tttt) REVERT: A 66 ASP cc_start: 0.8363 (m-30) cc_final: 0.8012 (m-30) REVERT: A 153 LYS cc_start: 0.8815 (mppt) cc_final: 0.8484 (mmmt) REVERT: A 160 ASP cc_start: 0.8514 (m-30) cc_final: 0.8215 (m-30) REVERT: A 164 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7865 (tp-100) REVERT: B 44 GLU cc_start: 0.6960 (tt0) cc_final: 0.6485 (mp0) REVERT: B 58 ILE cc_start: 0.8000 (mm) cc_final: 0.7606 (mm) REVERT: B 264 SER cc_start: 0.8505 (p) cc_final: 0.8302 (p) REVERT: C 67 TYR cc_start: 0.7355 (t80) cc_final: 0.6517 (t80) REVERT: C 181 ARG cc_start: 0.7273 (ptp-170) cc_final: 0.6383 (ptt-90) REVERT: D 187 PHE cc_start: 0.8454 (m-80) cc_final: 0.8243 (m-80) REVERT: D 191 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7742 (mtt90) REVERT: D 192 GLN cc_start: 0.7731 (tt0) cc_final: 0.7494 (tt0) REVERT: D 207 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.5615 (mp) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 0.1696 time to fit residues: 25.7901 Evaluate side-chains 111 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 123 TRP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.0470 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 46 optimal weight: 0.0270 chunk 23 optimal weight: 0.8980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS B 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6787 Z= 0.146 Angle : 0.561 9.410 9201 Z= 0.278 Chirality : 0.041 0.228 1060 Planarity : 0.004 0.042 1166 Dihedral : 6.426 55.736 1047 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.38 % Allowed : 16.64 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.30), residues: 803 helix: 2.11 (0.54), residues: 96 sheet: 0.59 (0.33), residues: 287 loop : -1.37 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 24 HIS 0.004 0.000 HIS A 196 PHE 0.008 0.001 PHE B 266 TYR 0.015 0.001 TYR C 61 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7651 (tttt) cc_final: 0.7364 (tttt) REVERT: A 66 ASP cc_start: 0.8306 (m-30) cc_final: 0.7944 (m-30) REVERT: A 160 ASP cc_start: 0.8525 (m-30) cc_final: 0.8240 (m-30) REVERT: A 164 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7862 (tp-100) REVERT: B 23 MET cc_start: 0.6555 (tpp) cc_final: 0.6313 (tpt) REVERT: B 44 GLU cc_start: 0.6910 (tt0) cc_final: 0.6571 (mp0) REVERT: B 58 ILE cc_start: 0.8002 (mm) cc_final: 0.7611 (mm) REVERT: C 67 TYR cc_start: 0.7329 (t80) cc_final: 0.6509 (t80) REVERT: C 181 ARG cc_start: 0.7315 (ptp-170) cc_final: 0.6385 (ptt-90) REVERT: C 223 MET cc_start: 0.6431 (ptp) cc_final: 0.5965 (ptp) REVERT: D 147 GLN cc_start: 0.4993 (tm-30) cc_final: 0.4597 (tm-30) REVERT: D 187 PHE cc_start: 0.8460 (m-80) cc_final: 0.8255 (m-80) REVERT: D 191 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7747 (mtt90) REVERT: D 192 GLN cc_start: 0.7723 (tt0) cc_final: 0.7488 (tt0) REVERT: D 207 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6110 (pp) outliers start: 18 outliers final: 13 residues processed: 106 average time/residue: 0.1604 time to fit residues: 23.7008 Evaluate side-chains 104 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 123 TRP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 0.0050 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 74 optimal weight: 0.0270 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 6787 Z= 0.162 Angle : 0.556 9.422 9201 Z= 0.276 Chirality : 0.044 0.533 1060 Planarity : 0.003 0.039 1166 Dihedral : 6.362 55.754 1047 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.25 % Allowed : 18.10 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.30), residues: 803 helix: 2.03 (0.54), residues: 96 sheet: 0.62 (0.32), residues: 287 loop : -1.36 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 24 HIS 0.003 0.000 HIS A 144 PHE 0.008 0.001 PHE C 108 TYR 0.014 0.001 TYR C 61 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8303 (m-30) cc_final: 0.7924 (m-30) REVERT: A 160 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: A 164 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7852 (tp-100) REVERT: B 23 MET cc_start: 0.6685 (tpp) cc_final: 0.6461 (tpt) REVERT: B 44 GLU cc_start: 0.7007 (tt0) cc_final: 0.6616 (mp0) REVERT: B 58 ILE cc_start: 0.7980 (mm) cc_final: 0.7513 (mm) REVERT: C 67 TYR cc_start: 0.7335 (t80) cc_final: 0.6510 (t80) REVERT: C 181 ARG cc_start: 0.7373 (ptp-170) cc_final: 0.6442 (ptt-90) REVERT: D 147 GLN cc_start: 0.5007 (tm-30) cc_final: 0.4614 (tm-30) REVERT: D 191 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7755 (mtt90) REVERT: D 192 GLN cc_start: 0.7727 (tt0) cc_final: 0.7500 (tt0) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.1659 time to fit residues: 23.1318 Evaluate side-chains 104 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 123 TRP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6787 Z= 0.261 Angle : 0.594 9.324 9201 Z= 0.299 Chirality : 0.044 0.499 1060 Planarity : 0.004 0.040 1166 Dihedral : 6.547 57.232 1047 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.25 % Allowed : 18.49 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.30), residues: 803 helix: 1.88 (0.53), residues: 96 sheet: 0.52 (0.33), residues: 288 loop : -1.39 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 109 HIS 0.003 0.001 HIS A 144 PHE 0.012 0.001 PHE C 108 TYR 0.011 0.001 TYR C 61 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8094 (tptm) cc_final: 0.7449 (tttm) REVERT: A 66 ASP cc_start: 0.8359 (m-30) cc_final: 0.7969 (m-30) REVERT: A 164 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7895 (tp-100) REVERT: B 44 GLU cc_start: 0.7013 (tt0) cc_final: 0.6671 (mp0) REVERT: B 58 ILE cc_start: 0.8030 (mm) cc_final: 0.7575 (mm) REVERT: C 67 TYR cc_start: 0.7390 (t80) cc_final: 0.6473 (t80) REVERT: C 181 ARG cc_start: 0.7356 (ptp-170) cc_final: 0.6364 (ptt-90) REVERT: D 147 GLN cc_start: 0.5008 (tm-30) cc_final: 0.4629 (tm-30) REVERT: D 191 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7726 (mtt90) REVERT: D 192 GLN cc_start: 0.7751 (tt0) cc_final: 0.7514 (tt0) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 0.1769 time to fit residues: 24.5580 Evaluate side-chains 103 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 191 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 19 optimal weight: 0.0870 chunk 59 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6787 Z= 0.252 Angle : 0.607 9.932 9201 Z= 0.301 Chirality : 0.044 0.463 1060 Planarity : 0.004 0.041 1166 Dihedral : 6.606 58.798 1047 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.98 % Allowed : 18.63 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.30), residues: 803 helix: 1.84 (0.53), residues: 96 sheet: 0.54 (0.32), residues: 293 loop : -1.39 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 109 HIS 0.003 0.001 HIS A 144 PHE 0.012 0.001 PHE C 108 TYR 0.013 0.001 TYR C 61 ARG 0.003 0.000 ARG C 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8375 (m-30) cc_final: 0.7991 (m-30) REVERT: A 164 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7862 (tp-100) REVERT: B 44 GLU cc_start: 0.6994 (tt0) cc_final: 0.6684 (mp0) REVERT: B 58 ILE cc_start: 0.8049 (mm) cc_final: 0.7587 (mm) REVERT: C 67 TYR cc_start: 0.7406 (t80) cc_final: 0.6507 (t80) REVERT: C 181 ARG cc_start: 0.7348 (ptp-170) cc_final: 0.6366 (ptt-90) REVERT: D 147 GLN cc_start: 0.5056 (tm-30) cc_final: 0.4667 (tm-30) REVERT: D 192 GLN cc_start: 0.7765 (tt0) cc_final: 0.7541 (tt0) outliers start: 15 outliers final: 14 residues processed: 100 average time/residue: 0.1853 time to fit residues: 25.1572 Evaluate side-chains 102 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.110680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083967 restraints weight = 17308.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.085997 restraints weight = 9400.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086691 restraints weight = 6894.586| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6787 Z= 0.230 Angle : 0.600 9.308 9201 Z= 0.301 Chirality : 0.043 0.445 1060 Planarity : 0.004 0.040 1166 Dihedral : 6.320 55.603 1043 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.98 % Allowed : 18.76 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.30), residues: 803 helix: 1.80 (0.53), residues: 96 sheet: 0.53 (0.32), residues: 293 loop : -1.41 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 109 HIS 0.003 0.001 HIS A 144 PHE 0.011 0.001 PHE C 108 TYR 0.014 0.001 TYR C 61 ARG 0.003 0.000 ARG C 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.04 seconds wall clock time: 34 minutes 22.85 seconds (2062.85 seconds total)