Starting phenix.real_space_refine on Sat Aug 3 03:07:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/08_2024/8pb1_17580.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/08_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_17580/08_2024/8pb1_17580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/08_2024/8pb1_17580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/08_2024/8pb1_17580.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb1_17580/08_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-5409/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: 5.62, per 1000 atoms: 0.84 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: 3.09 Conformation dependent library (CDL) restraints added in 1.1 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: 0.88 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: 1.77 Time building geometry restraints manager: 2.86 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 3.040 nonbonded pdb=" OG1 THR B 61 " pdb=" OG1 THR B 89 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP B 234 " pdb=" OG SER B 258 " model vdw 2.267 3.040 nonbonded pdb=" OE2 GLU B 108 " pdb=" OH TYR C 143 " model vdw 2.290 3.040 nonbonded pdb=" O SER C 171 " pdb=" OG SER C 171 " model vdw 2.300 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 7.030 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.000 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- 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 : 0.788 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: 0.2123 time to fit residues: 35.3858 Evaluate side-chains 100 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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: 7.9990 chunk 61 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** D 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6787 Z= 0.241 Angle : 0.631 9.340 9201 Z= 0.324 Chirality : 0.043 0.269 1060 Planarity : 0.004 0.039 1166 Dihedral : 10.233 77.112 1047 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.45 % Allowed : 9.25 % Favored : 89.30 % 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: -0.71 (0.29), residues: 803 helix: 1.62 (0.55), residues: 96 sheet: 0.36 (0.32), residues: 273 loop : -1.58 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 123 HIS 0.009 0.001 HIS A 196 PHE 0.013 0.001 PHE C 108 TYR 0.015 0.001 TYR A 124 ARG 0.004 0.001 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 115 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8058 (mttt) cc_final: 0.7595 (tttt) REVERT: A 66 ASP cc_start: 0.8343 (m-30) cc_final: 0.8114 (m-30) REVERT: A 72 ARG cc_start: 0.8535 (mmt90) cc_final: 0.8281 (mmt90) REVERT: A 164 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7562 (tp-100) REVERT: B 44 GLU cc_start: 0.6959 (tt0) cc_final: 0.6314 (mp0) REVERT: B 45 THR cc_start: 0.8526 (m) cc_final: 0.8115 (m) REVERT: B 264 SER cc_start: 0.8542 (p) cc_final: 0.8326 (p) REVERT: C 181 ARG cc_start: 0.7292 (ptp-170) cc_final: 0.6552 (ptt-90) REVERT: D 189 ASP cc_start: 0.8524 (p0) cc_final: 0.6828 (p0) REVERT: D 191 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7648 (mtt90) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 0.1916 time to fit residues: 28.6039 Evaluate side-chains 106 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 145 CYS 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: 2.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN D 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6787 Z= 0.210 Angle : 0.600 9.283 9201 Z= 0.302 Chirality : 0.042 0.223 1060 Planarity : 0.004 0.040 1166 Dihedral : 8.479 55.802 1047 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.45 % Allowed : 13.34 % Favored : 85.20 % 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: -0.46 (0.29), residues: 803 helix: 2.00 (0.54), residues: 96 sheet: 0.45 (0.32), residues: 282 loop : -1.44 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 109 HIS 0.006 0.001 HIS A 196 PHE 0.010 0.001 PHE C 108 TYR 0.018 0.001 TYR A 124 ARG 0.004 0.000 ARG A 72 *********************** 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 112 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8744 (tmmt) REVERT: A 66 ASP cc_start: 0.8366 (m-30) cc_final: 0.8063 (m-30) REVERT: A 126 ASP cc_start: 0.8463 (t0) cc_final: 0.8172 (t0) REVERT: A 160 ASP cc_start: 0.8473 (m-30) cc_final: 0.8098 (m-30) REVERT: A 164 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7573 (tp-100) REVERT: B 44 GLU cc_start: 0.7046 (tt0) cc_final: 0.6425 (mp0) REVERT: B 45 THR cc_start: 0.8567 (m) cc_final: 0.8207 (m) REVERT: B 58 ILE cc_start: 0.7967 (mm) cc_final: 0.7411 (mm) REVERT: B 264 SER cc_start: 0.8528 (p) cc_final: 0.8304 (p) REVERT: C 137 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8646 (ptpp) REVERT: C 181 ARG cc_start: 0.7307 (ptp-170) cc_final: 0.6633 (ptt-90) REVERT: D 189 ASP cc_start: 0.8119 (p0) cc_final: 0.7819 (p0) outliers start: 11 outliers final: 7 residues processed: 107 average time/residue: 0.1474 time to fit residues: 22.2560 Evaluate side-chains 106 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 MET Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 145 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6787 Z= 0.301 Angle : 0.625 9.301 9201 Z= 0.316 Chirality : 0.043 0.218 1060 Planarity : 0.004 0.041 1166 Dihedral : 7.519 56.267 1043 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.59 % Allowed : 14.40 % Favored : 84.02 % 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: -0.50 (0.30), residues: 803 helix: 1.97 (0.52), residues: 96 sheet: 0.44 (0.33), residues: 284 loop : -1.49 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 109 HIS 0.005 0.001 HIS A 196 PHE 0.013 0.002 PHE C 180 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 112 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8437 (m-30) cc_final: 0.8108 (m-30) REVERT: A 160 ASP cc_start: 0.8460 (m-30) cc_final: 0.8090 (m-30) REVERT: A 164 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7658 (tp-100) REVERT: B 23 MET cc_start: 0.8058 (tpt) cc_final: 0.7730 (tpt) REVERT: B 44 GLU cc_start: 0.7099 (tt0) cc_final: 0.6647 (mp0) REVERT: B 45 THR cc_start: 0.8562 (m) cc_final: 0.8231 (m) REVERT: B 58 ILE cc_start: 0.8034 (mm) cc_final: 0.7509 (mm) REVERT: B 264 SER cc_start: 0.8554 (p) cc_final: 0.8334 (p) REVERT: D 207 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.5277 (mp) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.1631 time to fit residues: 24.1913 Evaluate side-chains 104 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 50 SER Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN D 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6787 Z= 0.167 Angle : 0.587 9.394 9201 Z= 0.293 Chirality : 0.042 0.225 1060 Planarity : 0.004 0.037 1166 Dihedral : 6.872 55.681 1043 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.11 % Allowed : 15.19 % Favored : 82.69 % 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: 1.98 (0.53), residues: 96 sheet: 0.57 (0.32), residues: 281 loop : -1.43 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 109 HIS 0.005 0.001 HIS A 196 PHE 0.011 0.001 PHE D 212 TYR 0.015 0.001 TYR C 61 ARG 0.003 0.000 ARG A 72 *********************** 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 116 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8387 (m-30) cc_final: 0.8037 (m-30) REVERT: A 164 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7634 (tp-100) REVERT: B 23 MET cc_start: 0.8140 (tpt) cc_final: 0.7893 (tpt) REVERT: B 44 GLU cc_start: 0.7046 (tt0) cc_final: 0.6607 (mp0) REVERT: B 58 ILE cc_start: 0.8004 (mm) cc_final: 0.7698 (mm) REVERT: B 264 SER cc_start: 0.8541 (p) cc_final: 0.8337 (p) REVERT: C 67 TYR cc_start: 0.7383 (t80) cc_final: 0.6536 (t80) REVERT: C 181 ARG cc_start: 0.7259 (ptp-170) cc_final: 0.6615 (ptt-90) REVERT: D 207 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5244 (mp) outliers start: 16 outliers final: 9 residues processed: 111 average time/residue: 0.1492 time to fit residues: 23.1650 Evaluate side-chains 105 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 310 VAL 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 D residue 50 SER 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 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.1202 > 50: distance: 34 - 38: 17.645 distance: 38 - 39: 9.064 distance: 39 - 40: 35.779 distance: 40 - 41: 49.257 distance: 40 - 42: 19.443 distance: 42 - 43: 25.119 distance: 43 - 44: 16.885 distance: 43 - 46: 12.121 distance: 44 - 45: 13.771 distance: 44 - 50: 16.536 distance: 46 - 47: 28.697 distance: 46 - 48: 26.520 distance: 47 - 49: 24.474 distance: 50 - 51: 18.103 distance: 51 - 52: 18.132 distance: 51 - 54: 13.418 distance: 52 - 53: 24.941 distance: 52 - 58: 26.574 distance: 54 - 55: 12.506 distance: 55 - 56: 10.246 distance: 58 - 59: 37.643 distance: 59 - 60: 16.232 distance: 59 - 62: 16.674 distance: 60 - 61: 38.196 distance: 60 - 66: 30.450 distance: 62 - 63: 16.023 distance: 63 - 64: 21.471 distance: 63 - 65: 18.896 distance: 66 - 67: 16.230 distance: 67 - 68: 26.921 distance: 67 - 70: 27.318 distance: 68 - 69: 35.872 distance: 68 - 72: 15.338 distance: 70 - 71: 47.997 distance: 72 - 73: 11.689 distance: 72 - 78: 15.774 distance: 73 - 74: 9.331 distance: 73 - 76: 30.841 distance: 74 - 75: 13.403 distance: 74 - 79: 23.690 distance: 76 - 77: 22.137 distance: 77 - 78: 21.021 distance: 79 - 80: 13.258 distance: 80 - 81: 12.647 distance: 80 - 83: 31.964 distance: 81 - 82: 16.426 distance: 81 - 87: 23.254 distance: 83 - 84: 29.988 distance: 84 - 85: 12.031 distance: 84 - 86: 16.119 distance: 87 - 88: 27.187 distance: 88 - 89: 10.734 distance: 88 - 91: 25.531 distance: 89 - 90: 41.661 distance: 89 - 95: 38.418 distance: 91 - 92: 21.071 distance: 92 - 93: 24.577 distance: 92 - 94: 12.990 distance: 95 - 96: 18.619 distance: 96 - 97: 12.391 distance: 96 - 99: 25.655 distance: 97 - 98: 29.637 distance: 97 - 100: 8.606 distance: 100 - 101: 10.680 distance: 101 - 102: 6.691 distance: 101 - 104: 9.605 distance: 102 - 103: 9.632 distance: 102 - 109: 3.840 distance: 104 - 105: 15.415 distance: 105 - 106: 8.532 distance: 106 - 107: 7.344