Starting phenix.real_space_refine on Fri Aug 22 20:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hc6_34653/08_2025/8hc6_34653.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc6_34653/08_2025/8hc6_34653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hc6_34653/08_2025/8hc6_34653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc6_34653/08_2025/8hc6_34653.map" model { file = "/net/cci-nas-00/data/ceres_data/8hc6_34653/08_2025/8hc6_34653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc6_34653/08_2025/8hc6_34653.cif" } resolution = 4.69 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.058 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 27 5.16 5 C 4704 2.51 5 N 1226 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7377 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2134 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain: "H" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "B" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1929 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 13, 'TRANS': 223} Chain breaks: 5 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.67, per 1000 atoms: 0.23 Number of scatterers: 7377 At special positions: 0 Unit cell: (112.2, 84.15, 158.4, 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 27 16.00 O 1420 8.00 N 1226 7.00 C 4704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 NAG-ASN " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG C 601 " - " ASN C 331 " " NAG C 602 " - " ASN C 343 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 393.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 20 sheets defined 4.3% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.666A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.769A pdb=" N LEU C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 188 through 192 removed outlier: 3.531A pdb=" N SER H 191 " --> pdb=" O PRO H 188 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 192 " --> pdb=" O SER H 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 188 through 192' Processing helix chain 'L' and resid 184 through 188 removed outlier: 4.126A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.619A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'C' and resid 541 through 543 removed outlier: 3.667A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.538A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR H 77 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.979A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.979A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 123 through 126 removed outlier: 3.538A pdb=" N LYS H 146 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 123 through 126 removed outlier: 3.538A pdb=" N LYS H 146 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.755A pdb=" N THR H 154 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN H 202 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL H 201 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL H 210 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.790A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.548A pdb=" N VAL L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.949A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN L 38 " --> pdb=" O SER L 85 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN L 90 " --> pdb=" O THR L 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.761A pdb=" N PHE L 117 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU L 136 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 131 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 133 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR L 179 " --> pdb=" O GLN L 161 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 149 through 151 removed outlier: 4.273A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 192 through 193 removed outlier: 3.622A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.628A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.843A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 141 removed outlier: 4.519A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) 147 hydrogen bonds defined for protein. 375 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: 0.71 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2336 1.35 - 1.46: 1912 1.46 - 1.58: 3276 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 7555 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 7550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 9927 1.40 - 2.80: 282 2.80 - 4.20: 47 4.20 - 5.60: 10 5.60 - 7.00: 6 Bond angle restraints: 10272 Sorted by residual: angle pdb=" C ARG L 109 " pdb=" N THR L 110 " pdb=" CA THR L 110 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C SER H 206 " pdb=" N ASN H 207 " pdb=" CA ASN H 207 " ideal model delta sigma weight residual 121.54 127.10 -5.56 1.91e+00 2.74e-01 8.49e+00 angle pdb=" N VAL B 159 " pdb=" CA VAL B 159 " pdb=" C VAL B 159 " ideal model delta sigma weight residual 113.53 110.68 2.85 9.80e-01 1.04e+00 8.47e+00 angle pdb=" C GLY H 100 " pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.00e+00 angle pdb=" N CYS H 219 " pdb=" CA CYS H 219 " pdb=" C CYS H 219 " ideal model delta sigma weight residual 114.04 110.59 3.45 1.24e+00 6.50e-01 7.75e+00 ... (remaining 10267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 4057 15.92 - 31.83: 407 31.83 - 47.75: 81 47.75 - 63.67: 16 63.67 - 79.58: 15 Dihedral angle restraints: 4576 sinusoidal: 1868 harmonic: 2708 Sorted by residual: dihedral pdb=" CB CYS H 143 " pdb=" SG CYS H 143 " pdb=" SG CYS H 199 " pdb=" CB CYS H 199 " ideal model delta sinusoidal sigma weight residual 93.00 168.38 -75.38 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 141.82 -48.82 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 138.26 -45.26 1 1.00e+01 1.00e-02 2.84e+01 ... (remaining 4573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1009 0.065 - 0.130: 150 0.130 - 0.196: 5 0.196 - 0.261: 2 0.261 - 0.326: 1 Chirality restraints: 1167 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL L 147 " pdb=" CA VAL L 147 " pdb=" CG1 VAL L 147 " pdb=" CG2 VAL L 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1164 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 524 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C VAL C 524 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL C 524 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS C 525 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 235 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C ILE B 235 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE B 235 " 0.009 2.00e-02 2.50e+03 pdb=" N THR B 236 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO C 330 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.019 5.00e-02 4.00e+02 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2188 2.82 - 3.34: 5884 3.34 - 3.86: 11654 3.86 - 4.38: 12475 4.38 - 4.90: 21939 Nonbonded interactions: 54140 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.296 3.040 nonbonded pdb=" O PRO H 126 " pdb=" OG SER L 122 " model vdw 2.339 3.040 nonbonded pdb=" OH TYR C 501 " pdb=" O GLY L 30 " model vdw 2.346 3.040 nonbonded pdb=" O LYS B 278 " pdb=" OG1 THR B 286 " model vdw 2.352 3.040 nonbonded pdb=" O LEU C 455 " pdb=" OH TYR H 33 " model vdw 2.353 3.040 ... (remaining 54135 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.003 0.043 7572 Z= 0.141 Angle : 0.586 11.147 10313 Z= 0.289 Chirality : 0.045 0.326 1167 Planarity : 0.004 0.034 1310 Dihedral : 13.451 79.582 2806 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.12 % Allowed : 0.49 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.27), residues: 913 helix: -3.66 (0.60), residues: 24 sheet: 0.99 (0.34), residues: 235 loop : -1.05 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 212 TYR 0.008 0.001 TYR H 93 PHE 0.014 0.001 PHE L 140 TRP 0.004 0.001 TRP L 32 HIS 0.003 0.000 HIS H 203 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7555) covalent geometry : angle 0.56566 (10272) SS BOND : bond 0.00271 ( 10) SS BOND : angle 0.84249 ( 20) hydrogen bonds : bond 0.30925 ( 131) hydrogen bonds : angle 12.18200 ( 375) link_NAG-ASN : bond 0.00861 ( 7) link_NAG-ASN : angle 3.35360 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8591 (tpt) cc_final: 0.8215 (tpp) REVERT: H 35 HIS cc_start: 0.8593 (m90) cc_final: 0.8238 (m170) REVERT: H 82 MET cc_start: 0.6132 (tmm) cc_final: 0.5096 (tmm) REVERT: H 101 ASP cc_start: 0.7600 (t0) cc_final: 0.7335 (t0) REVERT: L 62 PHE cc_start: 0.8011 (m-80) cc_final: 0.7776 (m-80) REVERT: B 42 VAL cc_start: 0.8923 (t) cc_final: 0.8481 (t) REVERT: B 55 PHE cc_start: 0.7434 (m-80) cc_final: 0.6410 (m-10) REVERT: B 80 ASP cc_start: 0.7432 (m-30) cc_final: 0.7149 (m-30) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.0660 time to fit residues: 5.7858 Evaluate side-chains 37 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.0270 chunk 74 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS B 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.083971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.068392 restraints weight = 47991.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.069818 restraints weight = 26138.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.070504 restraints weight = 19750.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.070656 restraints weight = 17017.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.070811 restraints weight = 15227.980| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7572 Z= 0.104 Angle : 0.507 10.116 10313 Z= 0.262 Chirality : 0.043 0.355 1167 Planarity : 0.003 0.030 1310 Dihedral : 4.928 49.335 1151 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.27), residues: 913 helix: -3.04 (0.58), residues: 26 sheet: 0.75 (0.34), residues: 248 loop : -0.89 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.014 0.001 TYR L 49 PHE 0.009 0.001 PHE C 562 TRP 0.007 0.001 TRP L 35 HIS 0.003 0.001 HIS H 203 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7555) covalent geometry : angle 0.48964 (10272) SS BOND : bond 0.00365 ( 10) SS BOND : angle 0.73737 ( 20) hydrogen bonds : bond 0.05672 ( 131) hydrogen bonds : angle 7.97196 ( 375) link_NAG-ASN : bond 0.00660 ( 7) link_NAG-ASN : angle 2.89101 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: H 35 HIS cc_start: 0.8768 (m-70) cc_final: 0.7752 (m-70) REVERT: H 82 MET cc_start: 0.6426 (tmm) cc_final: 0.5306 (tmm) REVERT: H 101 ASP cc_start: 0.7776 (t0) cc_final: 0.7391 (t0) REVERT: L 118 ILE cc_start: 0.7057 (pt) cc_final: 0.6767 (mp) REVERT: B 42 VAL cc_start: 0.8952 (t) cc_final: 0.8510 (t) REVERT: B 55 PHE cc_start: 0.6849 (m-80) cc_final: 0.6183 (m-10) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0659 time to fit residues: 6.0849 Evaluate side-chains 42 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 0.0980 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.073638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.056472 restraints weight = 46903.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.056917 restraints weight = 29050.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057278 restraints weight = 23364.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057467 restraints weight = 21144.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.057588 restraints weight = 19251.701| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 7572 Z= 0.324 Angle : 0.799 11.253 10313 Z= 0.413 Chirality : 0.049 0.312 1167 Planarity : 0.005 0.044 1310 Dihedral : 5.806 53.299 1151 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.27), residues: 913 helix: -2.65 (0.74), residues: 30 sheet: -0.01 (0.33), residues: 249 loop : -1.26 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 273 TYR 0.024 0.003 TYR C 421 PHE 0.023 0.003 PHE B 58 TRP 0.020 0.002 TRP L 35 HIS 0.009 0.003 HIS H 203 Details of bonding type rmsd covalent geometry : bond 0.00702 ( 7555) covalent geometry : angle 0.79025 (10272) SS BOND : bond 0.00874 ( 10) SS BOND : angle 1.01424 ( 20) hydrogen bonds : bond 0.05420 ( 131) hydrogen bonds : angle 7.66681 ( 375) link_NAG-ASN : bond 0.00397 ( 7) link_NAG-ASN : angle 2.61135 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8629 (mmp) cc_final: 0.7971 (mmm) REVERT: H 82 MET cc_start: 0.7695 (tmm) cc_final: 0.6732 (tmm) REVERT: L 118 ILE cc_start: 0.7963 (pt) cc_final: 0.7588 (mt) REVERT: B 40 ASP cc_start: 0.9234 (p0) cc_final: 0.8977 (p0) REVERT: B 42 VAL cc_start: 0.9069 (t) cc_final: 0.8783 (t) REVERT: B 49 HIS cc_start: 0.8196 (t70) cc_final: 0.7647 (t-170) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0678 time to fit residues: 4.2974 Evaluate side-chains 24 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 71 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN L 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.076626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.060347 restraints weight = 46724.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.061278 restraints weight = 36816.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061959 restraints weight = 26270.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.062098 restraints weight = 22578.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.062366 restraints weight = 20193.414| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7572 Z= 0.115 Angle : 0.555 10.607 10313 Z= 0.280 Chirality : 0.045 0.330 1167 Planarity : 0.004 0.039 1310 Dihedral : 5.178 58.785 1151 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.27), residues: 913 helix: -2.56 (0.72), residues: 31 sheet: 0.26 (0.33), residues: 249 loop : -1.13 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.007 0.001 TYR H 79 PHE 0.012 0.001 PHE H 125 TRP 0.015 0.001 TRP C 436 HIS 0.004 0.001 HIS H 203 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7555) covalent geometry : angle 0.53461 (10272) SS BOND : bond 0.00318 ( 10) SS BOND : angle 0.70381 ( 20) hydrogen bonds : bond 0.03863 ( 131) hydrogen bonds : angle 6.74146 ( 375) link_NAG-ASN : bond 0.00683 ( 7) link_NAG-ASN : angle 3.28582 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8356 (mmp) cc_final: 0.7696 (mmm) REVERT: H 82 MET cc_start: 0.7113 (tmm) cc_final: 0.6336 (tmm) REVERT: L 62 PHE cc_start: 0.8178 (m-80) cc_final: 0.7902 (m-80) REVERT: L 83 PHE cc_start: 0.8382 (m-80) cc_final: 0.7841 (m-80) REVERT: L 118 ILE cc_start: 0.7524 (pt) cc_final: 0.7284 (mt) REVERT: B 18 LEU cc_start: 0.3817 (mm) cc_final: 0.3439 (mm) REVERT: B 49 HIS cc_start: 0.8281 (t70) cc_final: 0.8079 (t-170) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0618 time to fit residues: 4.2304 Evaluate side-chains 27 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 = 0.3591 r_free = 0.3591 target = 0.069217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052358 restraints weight = 49569.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052600 restraints weight = 30197.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053235 restraints weight = 24222.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053365 restraints weight = 20159.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.053450 restraints weight = 19084.900| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 7572 Z= 0.394 Angle : 0.944 14.669 10313 Z= 0.479 Chirality : 0.053 0.308 1167 Planarity : 0.007 0.056 1310 Dihedral : 6.905 54.641 1151 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.27), residues: 913 helix: -2.73 (0.79), residues: 30 sheet: -0.23 (0.32), residues: 247 loop : -1.62 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 237 TYR 0.031 0.003 TYR L 187 PHE 0.024 0.003 PHE H 58 TRP 0.029 0.004 TRP H 157 HIS 0.013 0.004 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00846 ( 7555) covalent geometry : angle 0.93195 (10272) SS BOND : bond 0.00983 ( 10) SS BOND : angle 1.24438 ( 20) hydrogen bonds : bond 0.05664 ( 131) hydrogen bonds : angle 7.68929 ( 375) link_NAG-ASN : bond 0.00553 ( 7) link_NAG-ASN : angle 3.34621 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8888 (mmp) cc_final: 0.8268 (mmm) REVERT: H 82 MET cc_start: 0.7955 (tmm) cc_final: 0.7138 (tmm) REVERT: L 118 ILE cc_start: 0.8138 (pt) cc_final: 0.7730 (tp) REVERT: B 191 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8460 (mt-10) REVERT: B 198 ASP cc_start: 0.9163 (t0) cc_final: 0.8927 (t0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0680 time to fit residues: 3.6025 Evaluate side-chains 19 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 = 0.3604 r_free = 0.3604 target = 0.070071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053466 restraints weight = 49470.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053639 restraints weight = 28706.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.054196 restraints weight = 23681.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054365 restraints weight = 19219.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.054588 restraints weight = 18535.648| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7572 Z= 0.267 Angle : 0.721 13.826 10313 Z= 0.370 Chirality : 0.048 0.328 1167 Planarity : 0.005 0.060 1310 Dihedral : 6.070 38.422 1151 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.27), residues: 913 helix: -3.02 (0.69), residues: 36 sheet: -0.40 (0.32), residues: 254 loop : -1.52 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 44 TYR 0.021 0.002 TYR L 187 PHE 0.018 0.002 PHE B 43 TRP 0.012 0.002 TRP H 157 HIS 0.013 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 7555) covalent geometry : angle 0.70780 (10272) SS BOND : bond 0.00660 ( 10) SS BOND : angle 1.04886 ( 20) hydrogen bonds : bond 0.04376 ( 131) hydrogen bonds : angle 7.16782 ( 375) link_NAG-ASN : bond 0.00527 ( 7) link_NAG-ASN : angle 3.05849 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8798 (mmp) cc_final: 0.8183 (mmm) REVERT: H 82 MET cc_start: 0.7507 (tmm) cc_final: 0.6815 (tmm) REVERT: L 62 PHE cc_start: 0.8218 (m-80) cc_final: 0.7937 (m-80) REVERT: L 118 ILE cc_start: 0.8001 (pt) cc_final: 0.7669 (mt) REVERT: B 40 ASP cc_start: 0.9354 (p0) cc_final: 0.8821 (p0) REVERT: B 42 VAL cc_start: 0.9268 (t) cc_final: 0.8860 (p) REVERT: B 50 SER cc_start: 0.8823 (t) cc_final: 0.8577 (m) REVERT: B 198 ASP cc_start: 0.9101 (t0) cc_final: 0.8855 (t0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0537 time to fit residues: 2.8797 Evaluate side-chains 22 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 50 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.071108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.053234 restraints weight = 47299.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054090 restraints weight = 25208.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054494 restraints weight = 19623.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054862 restraints weight = 16507.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054962 restraints weight = 14854.991| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7572 Z= 0.157 Angle : 0.607 11.437 10313 Z= 0.311 Chirality : 0.045 0.323 1167 Planarity : 0.004 0.045 1310 Dihedral : 5.473 34.256 1151 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.27), residues: 913 helix: -3.05 (0.73), residues: 36 sheet: -0.35 (0.32), residues: 248 loop : -1.37 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 44 TYR 0.016 0.002 TYR B 279 PHE 0.012 0.001 PHE H 58 TRP 0.010 0.001 TRP H 47 HIS 0.010 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7555) covalent geometry : angle 0.59248 (10272) SS BOND : bond 0.00590 ( 10) SS BOND : angle 1.03013 ( 20) hydrogen bonds : bond 0.03700 ( 131) hydrogen bonds : angle 6.71447 ( 375) link_NAG-ASN : bond 0.00511 ( 7) link_NAG-ASN : angle 2.82105 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8639 (mmp) cc_final: 0.7973 (mmm) REVERT: H 82 MET cc_start: 0.7451 (tmm) cc_final: 0.6741 (tmm) REVERT: L 62 PHE cc_start: 0.8411 (m-80) cc_final: 0.8102 (m-80) REVERT: B 40 ASP cc_start: 0.9353 (p0) cc_final: 0.8822 (p0) REVERT: B 42 VAL cc_start: 0.9335 (t) cc_final: 0.8940 (p) REVERT: B 198 ASP cc_start: 0.9086 (t0) cc_final: 0.8814 (t0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0523 time to fit residues: 3.1254 Evaluate side-chains 21 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.069393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052555 restraints weight = 48678.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.053038 restraints weight = 27619.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053609 restraints weight = 22244.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053868 restraints weight = 17619.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053966 restraints weight = 16587.003| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 7572 Z= 0.251 Angle : 0.722 12.765 10313 Z= 0.371 Chirality : 0.048 0.315 1167 Planarity : 0.005 0.051 1310 Dihedral : 5.946 37.277 1151 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.27), residues: 913 helix: -3.37 (0.63), residues: 38 sheet: -0.68 (0.30), residues: 274 loop : -1.39 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 44 TYR 0.025 0.002 TYR C 369 PHE 0.024 0.002 PHE B 275 TRP 0.017 0.002 TRP H 157 HIS 0.015 0.003 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 7555) covalent geometry : angle 0.71038 (10272) SS BOND : bond 0.00511 ( 10) SS BOND : angle 1.14861 ( 20) hydrogen bonds : bond 0.04238 ( 131) hydrogen bonds : angle 6.96116 ( 375) link_NAG-ASN : bond 0.00463 ( 7) link_NAG-ASN : angle 2.87056 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8778 (mmp) cc_final: 0.8097 (mmm) REVERT: H 82 MET cc_start: 0.7568 (tmm) cc_final: 0.6907 (tmm) REVERT: L 4 MET cc_start: 0.8172 (mmp) cc_final: 0.7555 (ptp) REVERT: L 187 TYR cc_start: 0.2315 (t80) cc_final: 0.2099 (t80) REVERT: B 40 ASP cc_start: 0.9385 (p0) cc_final: 0.8887 (p0) REVERT: B 42 VAL cc_start: 0.9191 (t) cc_final: 0.8800 (p) REVERT: B 198 ASP cc_start: 0.9119 (t0) cc_final: 0.8843 (t0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0604 time to fit residues: 3.1325 Evaluate side-chains 19 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 60 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 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 = 0.3624 r_free = 0.3624 target = 0.071036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.054533 restraints weight = 48578.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054873 restraints weight = 27922.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055415 restraints weight = 22285.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055634 restraints weight = 18339.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055699 restraints weight = 17380.521| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7572 Z= 0.141 Angle : 0.619 10.919 10313 Z= 0.314 Chirality : 0.046 0.323 1167 Planarity : 0.004 0.046 1310 Dihedral : 5.615 37.021 1151 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.27), residues: 913 helix: -3.33 (0.64), residues: 38 sheet: -0.54 (0.30), residues: 271 loop : -1.33 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 44 TYR 0.026 0.001 TYR C 369 PHE 0.010 0.001 PHE B 86 TRP 0.009 0.001 TRP H 47 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7555) covalent geometry : angle 0.59915 (10272) SS BOND : bond 0.00452 ( 10) SS BOND : angle 0.90508 ( 20) hydrogen bonds : bond 0.03579 ( 131) hydrogen bonds : angle 6.59852 ( 375) link_NAG-ASN : bond 0.00496 ( 7) link_NAG-ASN : angle 3.45471 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8708 (mmp) cc_final: 0.8041 (mmm) REVERT: H 82 MET cc_start: 0.7524 (tmm) cc_final: 0.6849 (tmm) REVERT: L 4 MET cc_start: 0.8017 (mmp) cc_final: 0.7568 (ptp) REVERT: L 62 PHE cc_start: 0.8188 (m-80) cc_final: 0.7934 (m-80) REVERT: B 40 ASP cc_start: 0.9391 (p0) cc_final: 0.8895 (p0) REVERT: B 42 VAL cc_start: 0.9292 (t) cc_final: 0.8911 (p) REVERT: B 53 ASP cc_start: 0.8381 (m-30) cc_final: 0.8120 (m-30) REVERT: B 191 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 198 ASP cc_start: 0.9076 (t0) cc_final: 0.8795 (t0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0549 time to fit residues: 3.1978 Evaluate side-chains 24 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.070006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053121 restraints weight = 48360.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053281 restraints weight = 26993.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053762 restraints weight = 23467.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053969 restraints weight = 19509.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054306 restraints weight = 17449.585| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7572 Z= 0.169 Angle : 0.633 11.456 10313 Z= 0.323 Chirality : 0.045 0.318 1167 Planarity : 0.005 0.059 1310 Dihedral : 5.541 37.008 1151 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.27), residues: 913 helix: -3.31 (0.63), residues: 38 sheet: -0.57 (0.30), residues: 274 loop : -1.31 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 44 TYR 0.023 0.002 TYR C 369 PHE 0.014 0.001 PHE B 65 TRP 0.009 0.002 TRP H 157 HIS 0.011 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7555) covalent geometry : angle 0.61741 (10272) SS BOND : bond 0.00434 ( 10) SS BOND : angle 0.83156 ( 20) hydrogen bonds : bond 0.03614 ( 131) hydrogen bonds : angle 6.57807 ( 375) link_NAG-ASN : bond 0.00448 ( 7) link_NAG-ASN : angle 3.14095 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8804 (mmp) cc_final: 0.8087 (mmm) REVERT: H 82 MET cc_start: 0.7550 (tmm) cc_final: 0.6891 (tmm) REVERT: L 4 MET cc_start: 0.7765 (mmp) cc_final: 0.7530 (ptp) REVERT: L 62 PHE cc_start: 0.8403 (m-80) cc_final: 0.8079 (m-80) REVERT: B 40 ASP cc_start: 0.9373 (p0) cc_final: 0.8886 (p0) REVERT: B 42 VAL cc_start: 0.9295 (t) cc_final: 0.8911 (p) REVERT: B 53 ASP cc_start: 0.8383 (m-30) cc_final: 0.8092 (m-30) REVERT: B 80 ASP cc_start: 0.7899 (m-30) cc_final: 0.7632 (m-30) REVERT: B 191 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 198 ASP cc_start: 0.9142 (t0) cc_final: 0.8872 (t0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0579 time to fit residues: 3.2539 Evaluate side-chains 23 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 67 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 0.0070 chunk 10 optimal weight: 5.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.072708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.057681 restraints weight = 46915.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058465 restraints weight = 37861.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.058958 restraints weight = 31776.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.059494 restraints weight = 22932.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.059922 restraints weight = 20417.252| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7572 Z= 0.117 Angle : 0.581 9.977 10313 Z= 0.295 Chirality : 0.045 0.323 1167 Planarity : 0.004 0.042 1310 Dihedral : 5.189 35.260 1151 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.27), residues: 913 helix: -3.27 (0.66), residues: 38 sheet: -0.34 (0.30), residues: 276 loop : -1.28 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 44 TYR 0.023 0.001 TYR C 369 PHE 0.011 0.001 PHE B 238 TRP 0.008 0.001 TRP H 157 HIS 0.007 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7555) covalent geometry : angle 0.56477 (10272) SS BOND : bond 0.00471 ( 10) SS BOND : angle 0.84433 ( 20) hydrogen bonds : bond 0.03265 ( 131) hydrogen bonds : angle 6.30016 ( 375) link_NAG-ASN : bond 0.00519 ( 7) link_NAG-ASN : angle 2.98326 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 997.99 seconds wall clock time: 18 minutes 0.69 seconds (1080.69 seconds total)