Starting phenix.real_space_refine on Fri Aug 22 23:44:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzq_41766/08_2025/8tzq_41766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzq_41766/08_2025/8tzq_41766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tzq_41766/08_2025/8tzq_41766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzq_41766/08_2025/8tzq_41766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tzq_41766/08_2025/8tzq_41766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzq_41766/08_2025/8tzq_41766.map" } resolution = 3.2 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= 0.012 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 62 5.16 5 C 5501 2.51 5 N 1443 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 8618 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1749 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 419 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2135 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.27 Number of scatterers: 8618 At special positions: 0 Unit cell: (90.896, 121.486, 132.848, 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 62 16.00 O 1612 8.00 N 1443 7.00 C 5501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " 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 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 513.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.9% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.520A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.770A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 26 removed outlier: 3.615A pdb=" N CYS A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.706A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 41 through 61 removed outlier: 3.982A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 87 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 103 through 138 Processing helix chain 'R' and resid 138 through 143 Processing helix chain 'R' and resid 146 through 168 Processing helix chain 'R' and resid 169 through 172 removed outlier: 3.638A pdb=" N PHE R 172 " --> pdb=" O PRO R 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 169 through 172' Processing helix chain 'R' and resid 186 through 198 removed outlier: 3.980A pdb=" N TYR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 224 Processing helix chain 'R' and resid 362 through 399 removed outlier: 3.591A pdb=" N GLN R 366 " --> pdb=" O LYS R 362 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 3.890A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 428 Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 441 Processing helix chain 'B' and resid 6 through 32 removed outlier: 4.129A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.706A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.415A pdb=" N ASP B 232 " --> pdb=" O SER B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.800A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.092A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AA4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.020A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 51 removed outlier: 5.470A pdb=" N THR A 47 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN A 340 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 49 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 63 removed outlier: 6.857A pdb=" N ALA A 73 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET A 61 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 71 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP A 63 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A 69 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP A 83 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS A 89 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.878A pdb=" N GLY A 115 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS A 103 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 113 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR A 105 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR A 111 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY A 116 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS A 121 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU A 138 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 123 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 134 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 146 through 151 removed outlier: 3.646A pdb=" N CYS A 148 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS A 166 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR A 179 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 168 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 175 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 187 through 192 removed outlier: 6.989A pdb=" N GLY A 202 " --> pdb=" O MET A 188 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 190 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 200 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 192 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 198 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 229 through 234 removed outlier: 4.585A pdb=" N THR A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP A 254 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU A 260 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.763A pdb=" N SER A 275 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP A 298 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 304 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.774A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1293 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: 1.44 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2771 1.34 - 1.46: 1875 1.46 - 1.58: 4058 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 8793 Sorted by residual: bond pdb=" N PHE A 234 " pdb=" CA PHE A 234 " ideal model delta sigma weight residual 1.455 1.484 -0.028 1.23e-02 6.61e+03 5.32e+00 bond pdb=" N HIS R 393 " pdb=" CA HIS R 393 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.05e+00 bond pdb=" N ARG R 151 " pdb=" CA ARG R 151 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.53e+00 bond pdb=" N ARG R 218 " pdb=" CA ARG R 218 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.19e-02 7.06e+03 3.45e+00 bond pdb=" CG HIS R 393 " pdb=" CD2 HIS R 393 " ideal model delta sigma weight residual 1.354 1.337 0.017 1.10e-02 8.26e+03 2.26e+00 ... (remaining 8788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 11563 1.34 - 2.67: 309 2.67 - 4.01: 59 4.01 - 5.34: 7 5.34 - 6.68: 4 Bond angle restraints: 11942 Sorted by residual: angle pdb=" C GLN R 179 " pdb=" CA GLN R 179 " pdb=" CB GLN R 179 " ideal model delta sigma weight residual 117.23 110.55 6.68 1.36e+00 5.41e-01 2.41e+01 angle pdb=" CA GLN R 179 " pdb=" C GLN R 179 " pdb=" N ASN R 180 " ideal model delta sigma weight residual 119.98 117.12 2.86 8.50e-01 1.38e+00 1.13e+01 angle pdb=" OG1 THR R 205 " pdb=" CB THR R 205 " pdb=" CG2 THR R 205 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.91e+00 angle pdb=" C LYS B 193 " pdb=" CA LYS B 193 " pdb=" CB LYS B 193 " ideal model delta sigma weight residual 110.42 116.08 -5.66 1.99e+00 2.53e-01 8.09e+00 angle pdb=" C CYS R 385 " pdb=" N TRP R 386 " pdb=" CA TRP R 386 " ideal model delta sigma weight residual 122.58 116.80 5.78 2.07e+00 2.33e-01 7.79e+00 ... (remaining 11937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 5002 17.49 - 34.99: 169 34.99 - 52.48: 19 52.48 - 69.97: 2 69.97 - 87.46: 4 Dihedral angle restraints: 5196 sinusoidal: 1950 harmonic: 3246 Sorted by residual: dihedral pdb=" CD ARG R 151 " pdb=" NE ARG R 151 " pdb=" CZ ARG R 151 " pdb=" NH1 ARG R 151 " ideal model delta sinusoidal sigma weight residual 0.00 -63.05 63.05 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CD ARG R 218 " pdb=" NE ARG R 218 " pdb=" CZ ARG R 218 " pdb=" NH1 ARG R 218 " ideal model delta sinusoidal sigma weight residual 0.00 -47.27 47.27 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CA LYS A 78 " pdb=" C LYS A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 912 0.033 - 0.067: 341 0.067 - 0.100: 89 0.100 - 0.134: 44 0.134 - 0.167: 3 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CB THR R 205 " pdb=" CA THR R 205 " pdb=" OG1 THR R 205 " pdb=" CG2 THR R 205 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA ARG R 151 " pdb=" N ARG R 151 " pdb=" C ARG R 151 " pdb=" CB ARG R 151 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ARG R 218 " pdb=" N ARG R 218 " pdb=" C ARG R 218 " pdb=" CB ARG R 218 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1386 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 151 " -0.981 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG R 151 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG R 151 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG R 151 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 151 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 218 " 0.805 9.50e-02 1.11e+02 3.61e-01 7.91e+01 pdb=" NE ARG R 218 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG R 218 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG R 218 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 218 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 50 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C PHE R 50 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE R 50 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY R 51 " 0.010 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1301 2.76 - 3.30: 8224 3.30 - 3.83: 14188 3.83 - 4.37: 16661 4.37 - 4.90: 29435 Nonbonded interactions: 69809 Sorted by model distance: nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 274 " pdb=" O VAL A 315 " model vdw 2.247 3.040 nonbonded pdb=" O THR R 39 " pdb=" OG1 THR R 42 " model vdw 2.248 3.040 nonbonded pdb=" O ILE R 424 " pdb=" OG1 THR R 428 " model vdw 2.267 3.040 nonbonded pdb=" OG SER A 331 " pdb=" OD1 ASP A 333 " model vdw 2.296 3.040 ... (remaining 69804 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 0.029 8794 Z= 0.146 Angle : 0.546 6.675 11944 Z= 0.339 Chirality : 0.041 0.167 1389 Planarity : 0.015 0.440 1504 Dihedral : 9.079 87.464 3099 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.43 % Allowed : 3.12 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.04 (0.25), residues: 1101 helix: 1.99 (0.27), residues: 389 sheet: 0.27 (0.29), residues: 286 loop : -0.15 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 218 TYR 0.009 0.001 TYR E 102 PHE 0.016 0.001 PHE R 382 TRP 0.015 0.001 TRP A 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8793) covalent geometry : angle 0.54587 (11942) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.82447 ( 2) hydrogen bonds : bond 0.13634 ( 458) hydrogen bonds : angle 5.49130 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 266 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8709 (tttt) cc_final: 0.8437 (tttm) REVERT: E 57 THR cc_start: 0.9120 (p) cc_final: 0.8789 (p) REVERT: A 280 LYS cc_start: 0.8861 (tttt) cc_final: 0.8272 (tttm) REVERT: C 21 MET cc_start: 0.8643 (ttm) cc_final: 0.8270 (tpp) REVERT: C 27 ARG cc_start: 0.8412 (mtt90) cc_final: 0.8069 (mtm-85) REVERT: C 48 ASP cc_start: 0.8787 (t0) cc_final: 0.8390 (t0) REVERT: B 231 TYR cc_start: 0.7274 (p90) cc_final: 0.6529 (p90) REVERT: B 262 ASP cc_start: 0.7773 (p0) cc_final: 0.7558 (p0) REVERT: B 333 GLN cc_start: 0.8159 (tp40) cc_final: 0.7742 (tm-30) REVERT: B 337 ASP cc_start: 0.8337 (m-30) cc_final: 0.7781 (m-30) outliers start: 4 outliers final: 2 residues processed: 269 average time/residue: 0.1249 time to fit residues: 43.4514 Evaluate side-chains 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN R 66 GLN B 189 HIS B 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.090420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067570 restraints weight = 22908.884| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.46 r_work: 0.3029 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8794 Z= 0.267 Angle : 0.656 11.789 11944 Z= 0.350 Chirality : 0.045 0.140 1389 Planarity : 0.004 0.039 1504 Dihedral : 4.805 56.164 1208 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.34 % Allowed : 11.96 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.75 (0.25), residues: 1101 helix: 1.81 (0.26), residues: 399 sheet: 0.18 (0.30), residues: 276 loop : -0.48 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.014 0.001 TYR E 235 PHE 0.024 0.002 PHE A 253 TRP 0.014 0.002 TRP A 82 HIS 0.005 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 8793) covalent geometry : angle 0.65594 (11942) SS BOND : bond 0.00292 ( 1) SS BOND : angle 1.11907 ( 2) hydrogen bonds : bond 0.04870 ( 458) hydrogen bonds : angle 4.88037 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8711 (tttt) cc_final: 0.8396 (tttp) REVERT: E 57 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8811 (p) REVERT: E 83 MET cc_start: 0.8092 (mtm) cc_final: 0.7889 (mtp) REVERT: E 90 ASP cc_start: 0.7578 (m-30) cc_final: 0.7307 (m-30) REVERT: E 93 MET cc_start: 0.8029 (ttt) cc_final: 0.7730 (tpp) REVERT: E 219 LEU cc_start: 0.9117 (tp) cc_final: 0.8863 (tp) REVERT: E 220 GLU cc_start: 0.7759 (mp0) cc_final: 0.7336 (mp0) REVERT: A 215 GLU cc_start: 0.8931 (mp0) cc_final: 0.8729 (mp0) REVERT: A 262 MET cc_start: 0.8485 (tpp) cc_final: 0.8002 (tpp) REVERT: C 21 MET cc_start: 0.9059 (ttm) cc_final: 0.8396 (tpp) REVERT: C 22 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7985 (tm-30) REVERT: C 47 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7833 (tm-30) REVERT: R 62 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7120 (tm-30) REVERT: R 413 TRP cc_start: 0.8724 (m100) cc_final: 0.8173 (m100) REVERT: B 262 ASP cc_start: 0.8557 (p0) cc_final: 0.8197 (p0) REVERT: B 333 GLN cc_start: 0.8585 (tp40) cc_final: 0.8233 (tp40) outliers start: 31 outliers final: 23 residues processed: 185 average time/residue: 0.1049 time to fit residues: 26.4048 Evaluate side-chains 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 75 GLN A 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.068758 restraints weight = 22726.653| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.45 r_work: 0.3055 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8794 Z= 0.140 Angle : 0.571 10.163 11944 Z= 0.303 Chirality : 0.042 0.139 1389 Planarity : 0.003 0.040 1504 Dihedral : 4.656 56.530 1208 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.37 % Allowed : 13.25 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.25), residues: 1101 helix: 1.98 (0.27), residues: 392 sheet: 0.20 (0.30), residues: 274 loop : -0.52 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.016 0.001 TYR E 190 PHE 0.015 0.001 PHE R 429 TRP 0.016 0.001 TRP A 82 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8793) covalent geometry : angle 0.57112 (11942) SS BOND : bond 0.00171 ( 1) SS BOND : angle 1.12914 ( 2) hydrogen bonds : bond 0.04255 ( 458) hydrogen bonds : angle 4.59371 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8720 (tttt) cc_final: 0.8422 (ttmm) REVERT: E 57 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8897 (p) REVERT: E 62 ASP cc_start: 0.8619 (m-30) cc_final: 0.7879 (t0) REVERT: E 90 ASP cc_start: 0.7494 (m-30) cc_final: 0.7241 (m-30) REVERT: E 219 LEU cc_start: 0.9115 (tp) cc_final: 0.8870 (tp) REVERT: E 220 GLU cc_start: 0.7846 (mp0) cc_final: 0.7341 (mp0) REVERT: E 246 GLU cc_start: 0.7583 (pm20) cc_final: 0.7223 (pm20) REVERT: A 23 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9351 (mmmm) REVERT: C 21 MET cc_start: 0.9063 (ttm) cc_final: 0.8483 (tpp) REVERT: C 22 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8105 (tm-30) REVERT: R 62 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7645 (tm-30) REVERT: R 108 ASP cc_start: 0.8731 (m-30) cc_final: 0.7835 (t0) REVERT: R 117 MET cc_start: 0.7944 (mmt) cc_final: 0.7300 (mmt) REVERT: R 168 CYS cc_start: 0.8672 (m) cc_final: 0.8288 (m) REVERT: R 413 TRP cc_start: 0.8605 (m100) cc_final: 0.8213 (m100) REVERT: B 50 VAL cc_start: 0.8687 (p) cc_final: 0.8425 (m) REVERT: B 189 HIS cc_start: 0.8174 (m170) cc_final: 0.7940 (m170) REVERT: B 262 ASP cc_start: 0.8568 (p0) cc_final: 0.8232 (p0) REVERT: B 333 GLN cc_start: 0.8605 (tp40) cc_final: 0.8227 (tp40) outliers start: 22 outliers final: 13 residues processed: 165 average time/residue: 0.0971 time to fit residues: 22.2056 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.9990 chunk 102 optimal weight: 0.0670 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.091107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.068345 restraints weight = 22777.349| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.45 r_work: 0.3054 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8794 Z= 0.141 Angle : 0.553 8.445 11944 Z= 0.293 Chirality : 0.042 0.137 1389 Planarity : 0.003 0.040 1504 Dihedral : 4.556 56.597 1206 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.77 % Allowed : 12.28 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.87 (0.25), residues: 1101 helix: 2.10 (0.27), residues: 390 sheet: 0.17 (0.30), residues: 275 loop : -0.50 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 198 TYR 0.015 0.001 TYR B 354 PHE 0.014 0.001 PHE A 253 TRP 0.017 0.001 TRP R 100 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8793) covalent geometry : angle 0.55211 (11942) SS BOND : bond 0.00937 ( 1) SS BOND : angle 1.69580 ( 2) hydrogen bonds : bond 0.04071 ( 458) hydrogen bonds : angle 4.53055 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8717 (tttt) cc_final: 0.8434 (ttmm) REVERT: E 57 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8933 (p) REVERT: E 62 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7868 (t0) REVERT: E 219 LEU cc_start: 0.9165 (tp) cc_final: 0.8950 (tp) REVERT: E 220 GLU cc_start: 0.7921 (mp0) cc_final: 0.7153 (mp0) REVERT: E 246 GLU cc_start: 0.7638 (pm20) cc_final: 0.7301 (pm20) REVERT: A 8 ARG cc_start: 0.9359 (ptp90) cc_final: 0.8891 (ptp-170) REVERT: A 23 LYS cc_start: 0.9598 (mmmm) cc_final: 0.9350 (mmmm) REVERT: C 13 ARG cc_start: 0.9330 (mtm-85) cc_final: 0.9020 (mtm-85) REVERT: C 21 MET cc_start: 0.9116 (ttm) cc_final: 0.8531 (tpp) REVERT: C 22 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8119 (tm-30) REVERT: R 62 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7573 (tm-30) REVERT: R 108 ASP cc_start: 0.8380 (m-30) cc_final: 0.7664 (t0) REVERT: R 116 MET cc_start: 0.7432 (ttp) cc_final: 0.6946 (ttp) REVERT: R 117 MET cc_start: 0.8018 (mmt) cc_final: 0.7545 (mmt) REVERT: R 119 THR cc_start: 0.8790 (m) cc_final: 0.8295 (p) REVERT: R 168 CYS cc_start: 0.8774 (m) cc_final: 0.8354 (m) REVERT: R 413 TRP cc_start: 0.8600 (m100) cc_final: 0.8149 (m100) REVERT: B 187 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 262 ASP cc_start: 0.8572 (p0) cc_final: 0.8246 (p0) REVERT: B 333 GLN cc_start: 0.8707 (tp40) cc_final: 0.8355 (tp40) outliers start: 35 outliers final: 22 residues processed: 167 average time/residue: 0.1005 time to fit residues: 23.0742 Evaluate side-chains 166 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 100 TRP Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 29 optimal weight: 0.0000 chunk 100 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066882 restraints weight = 23089.460| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.39 r_work: 0.3023 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8794 Z= 0.189 Angle : 0.576 7.422 11944 Z= 0.308 Chirality : 0.042 0.138 1389 Planarity : 0.003 0.042 1504 Dihedral : 4.618 57.272 1206 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.66 % Allowed : 13.79 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.84 (0.25), residues: 1101 helix: 2.14 (0.27), residues: 391 sheet: 0.09 (0.30), residues: 273 loop : -0.54 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.019 0.001 TYR E 235 PHE 0.020 0.002 PHE A 253 TRP 0.013 0.001 TRP A 82 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8793) covalent geometry : angle 0.57541 (11942) SS BOND : bond 0.00956 ( 1) SS BOND : angle 1.64459 ( 2) hydrogen bonds : bond 0.04201 ( 458) hydrogen bonds : angle 4.59015 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8690 (tttt) cc_final: 0.8393 (tttp) REVERT: E 62 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7929 (t0) REVERT: E 220 GLU cc_start: 0.8240 (mp0) cc_final: 0.7622 (mp0) REVERT: E 246 GLU cc_start: 0.7739 (pm20) cc_final: 0.7393 (pm20) REVERT: A 20 ASP cc_start: 0.9323 (m-30) cc_final: 0.8925 (p0) REVERT: A 23 LYS cc_start: 0.9612 (mmmm) cc_final: 0.9353 (mmmm) REVERT: A 215 GLU cc_start: 0.8966 (mp0) cc_final: 0.8649 (mp0) REVERT: C 21 MET cc_start: 0.9133 (ttm) cc_final: 0.8543 (tpp) REVERT: C 22 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8097 (tm-30) REVERT: R 62 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7485 (tm-30) REVERT: R 108 ASP cc_start: 0.8362 (m-30) cc_final: 0.7697 (t0) REVERT: R 117 MET cc_start: 0.7967 (mmt) cc_final: 0.7616 (mmt) REVERT: R 168 CYS cc_start: 0.8861 (m) cc_final: 0.8482 (m) REVERT: R 413 TRP cc_start: 0.8666 (m100) cc_final: 0.8223 (m100) REVERT: B 187 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8140 (tt0) REVERT: B 189 HIS cc_start: 0.8022 (m170) cc_final: 0.7631 (m170) REVERT: B 262 ASP cc_start: 0.8577 (p0) cc_final: 0.8258 (p0) REVERT: B 333 GLN cc_start: 0.8864 (tp40) cc_final: 0.8487 (tp40) outliers start: 34 outliers final: 23 residues processed: 158 average time/residue: 0.0987 time to fit residues: 21.4918 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** B 52 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 = 0.3615 r_free = 0.3615 target = 0.089584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067054 restraints weight = 23805.766| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.45 r_work: 0.3011 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8794 Z= 0.196 Angle : 0.595 12.242 11944 Z= 0.314 Chirality : 0.042 0.134 1389 Planarity : 0.003 0.042 1504 Dihedral : 4.603 57.339 1206 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.77 % Allowed : 13.79 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.85 (0.25), residues: 1101 helix: 2.17 (0.27), residues: 391 sheet: 0.02 (0.30), residues: 273 loop : -0.51 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.016 0.001 TYR E 235 PHE 0.018 0.001 PHE A 253 TRP 0.015 0.002 TRP A 82 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8793) covalent geometry : angle 0.59520 (11942) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.83451 ( 2) hydrogen bonds : bond 0.04218 ( 458) hydrogen bonds : angle 4.59117 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8684 (tttt) cc_final: 0.8388 (tttp) REVERT: E 62 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7974 (t0) REVERT: E 93 MET cc_start: 0.7996 (ttt) cc_final: 0.7542 (tpp) REVERT: E 220 GLU cc_start: 0.8230 (mp0) cc_final: 0.7701 (mp0) REVERT: E 230 MET cc_start: 0.8956 (ttp) cc_final: 0.8743 (ttt) REVERT: E 246 GLU cc_start: 0.7790 (pm20) cc_final: 0.7465 (pm20) REVERT: A 17 GLN cc_start: 0.9347 (tp40) cc_final: 0.8800 (tp-100) REVERT: A 20 ASP cc_start: 0.9315 (m-30) cc_final: 0.8948 (p0) REVERT: A 23 LYS cc_start: 0.9620 (mmmm) cc_final: 0.9347 (mmmm) REVERT: C 13 ARG cc_start: 0.9341 (mtm-85) cc_final: 0.9124 (mtm-85) REVERT: C 21 MET cc_start: 0.9136 (ttm) cc_final: 0.8536 (tpp) REVERT: C 22 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8085 (tm-30) REVERT: R 62 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7730 (tm-30) REVERT: R 108 ASP cc_start: 0.8320 (m-30) cc_final: 0.7661 (t0) REVERT: R 116 MET cc_start: 0.7474 (ttp) cc_final: 0.6736 (ppp) REVERT: R 119 THR cc_start: 0.8875 (m) cc_final: 0.8372 (p) REVERT: R 168 CYS cc_start: 0.8942 (m) cc_final: 0.8549 (m) REVERT: R 413 TRP cc_start: 0.8640 (m100) cc_final: 0.8252 (m100) REVERT: B 187 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8240 (tt0) REVERT: B 262 ASP cc_start: 0.8550 (p0) cc_final: 0.8220 (p0) outliers start: 35 outliers final: 26 residues processed: 161 average time/residue: 0.0996 time to fit residues: 22.0575 Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** B 52 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 = 0.3638 r_free = 0.3638 target = 0.090907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.068600 restraints weight = 23587.921| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.37 r_work: 0.3054 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8794 Z= 0.137 Angle : 0.566 13.096 11944 Z= 0.299 Chirality : 0.041 0.135 1389 Planarity : 0.003 0.041 1504 Dihedral : 4.573 56.952 1206 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.59 % Allowed : 16.27 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.90 (0.25), residues: 1101 helix: 2.14 (0.27), residues: 391 sheet: 0.10 (0.30), residues: 271 loop : -0.45 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 222 TYR 0.015 0.001 TYR E 190 PHE 0.014 0.001 PHE R 50 TRP 0.019 0.001 TRP A 82 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8793) covalent geometry : angle 0.56507 (11942) SS BOND : bond 0.00289 ( 1) SS BOND : angle 2.01065 ( 2) hydrogen bonds : bond 0.03951 ( 458) hydrogen bonds : angle 4.45751 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.7905 (t0) REVERT: E 93 MET cc_start: 0.7987 (ttt) cc_final: 0.7559 (tpp) REVERT: E 220 GLU cc_start: 0.8378 (mp0) cc_final: 0.7806 (mp0) REVERT: E 244 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8022 (tttp) REVERT: E 246 GLU cc_start: 0.7796 (pm20) cc_final: 0.7485 (pm20) REVERT: A 17 GLN cc_start: 0.9389 (tp40) cc_final: 0.8812 (tp-100) REVERT: A 20 ASP cc_start: 0.9316 (m-30) cc_final: 0.8950 (p0) REVERT: A 23 LYS cc_start: 0.9617 (mmmm) cc_final: 0.9330 (mmmm) REVERT: A 188 MET cc_start: 0.9248 (mmm) cc_final: 0.8953 (mmm) REVERT: C 21 MET cc_start: 0.9130 (ttm) cc_final: 0.8518 (tpp) REVERT: C 22 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8039 (tm-30) REVERT: R 62 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7859 (tm-30) REVERT: R 108 ASP cc_start: 0.8267 (m-30) cc_final: 0.7430 (t70) REVERT: R 116 MET cc_start: 0.7298 (ttp) cc_final: 0.7060 (ppp) REVERT: R 168 CYS cc_start: 0.8956 (m) cc_final: 0.8517 (m) REVERT: R 413 TRP cc_start: 0.8583 (m100) cc_final: 0.8267 (m100) REVERT: B 189 HIS cc_start: 0.8013 (m170) cc_final: 0.7767 (m170) REVERT: B 217 GLU cc_start: 0.8837 (tp30) cc_final: 0.8633 (mm-30) REVERT: B 262 ASP cc_start: 0.8585 (p0) cc_final: 0.8246 (p0) outliers start: 24 outliers final: 20 residues processed: 156 average time/residue: 0.1052 time to fit residues: 22.3572 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** B 52 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 = 0.3597 r_free = 0.3597 target = 0.088984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066029 restraints weight = 23495.547| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.44 r_work: 0.2976 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8794 Z= 0.275 Angle : 0.677 13.319 11944 Z= 0.352 Chirality : 0.044 0.143 1389 Planarity : 0.004 0.043 1504 Dihedral : 4.810 57.617 1206 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.23 % Allowed : 16.81 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1101 helix: 2.04 (0.26), residues: 390 sheet: -0.10 (0.30), residues: 273 loop : -0.57 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 13 TYR 0.023 0.002 TYR E 235 PHE 0.023 0.002 PHE A 253 TRP 0.023 0.002 TRP R 100 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00634 ( 8793) covalent geometry : angle 0.67672 (11942) SS BOND : bond 0.00323 ( 1) SS BOND : angle 1.60092 ( 2) hydrogen bonds : bond 0.04571 ( 458) hydrogen bonds : angle 4.70692 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8094 (t0) REVERT: E 220 GLU cc_start: 0.8439 (mp0) cc_final: 0.7795 (mp0) REVERT: E 246 GLU cc_start: 0.7755 (pm20) cc_final: 0.7429 (pm20) REVERT: A 17 GLN cc_start: 0.9413 (tp40) cc_final: 0.8847 (tp-100) REVERT: A 20 ASP cc_start: 0.9312 (m-30) cc_final: 0.8993 (p0) REVERT: A 23 LYS cc_start: 0.9633 (mmmm) cc_final: 0.9320 (mmmm) REVERT: A 101 MET cc_start: 0.9399 (mtp) cc_final: 0.9104 (mtp) REVERT: C 21 MET cc_start: 0.9151 (ttm) cc_final: 0.8532 (tpp) REVERT: C 22 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8048 (tm-30) REVERT: R 62 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7797 (tm-30) REVERT: R 108 ASP cc_start: 0.8294 (m-30) cc_final: 0.7459 (t70) REVERT: R 116 MET cc_start: 0.7107 (ttp) cc_final: 0.6828 (ppp) REVERT: R 168 CYS cc_start: 0.9045 (m) cc_final: 0.8640 (m) REVERT: R 413 TRP cc_start: 0.8700 (m100) cc_final: 0.8280 (m100) REVERT: B 249 MET cc_start: 0.8636 (tpp) cc_final: 0.8376 (tpp) REVERT: B 262 ASP cc_start: 0.8669 (p0) cc_final: 0.8310 (p0) outliers start: 30 outliers final: 24 residues processed: 152 average time/residue: 0.1034 time to fit residues: 21.6361 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.091333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069004 restraints weight = 23340.153| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.41 r_work: 0.3041 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8794 Z= 0.135 Angle : 0.604 13.968 11944 Z= 0.316 Chirality : 0.042 0.166 1389 Planarity : 0.004 0.052 1504 Dihedral : 4.621 56.992 1206 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.16 % Allowed : 18.21 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.88 (0.25), residues: 1101 helix: 2.16 (0.27), residues: 390 sheet: 0.11 (0.30), residues: 265 loop : -0.49 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 13 TYR 0.016 0.001 TYR E 235 PHE 0.017 0.001 PHE R 50 TRP 0.032 0.002 TRP R 100 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8793) covalent geometry : angle 0.60385 (11942) SS BOND : bond 0.00225 ( 1) SS BOND : angle 1.31819 ( 2) hydrogen bonds : bond 0.04000 ( 458) hydrogen bonds : angle 4.52012 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.7958 (t0) REVERT: E 93 MET cc_start: 0.8028 (ttt) cc_final: 0.7521 (tpp) REVERT: E 220 GLU cc_start: 0.8460 (mp0) cc_final: 0.7758 (mp0) REVERT: E 244 LYS cc_start: 0.8484 (ttmm) cc_final: 0.8060 (tttp) REVERT: E 246 GLU cc_start: 0.7795 (pm20) cc_final: 0.7498 (pm20) REVERT: A 17 GLN cc_start: 0.9404 (tp40) cc_final: 0.8826 (tp-100) REVERT: A 20 ASP cc_start: 0.9317 (m-30) cc_final: 0.8977 (p0) REVERT: A 23 LYS cc_start: 0.9633 (mmmm) cc_final: 0.9310 (mmmm) REVERT: C 21 MET cc_start: 0.9165 (ttm) cc_final: 0.8537 (tpp) REVERT: C 22 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8083 (tm-30) REVERT: R 62 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7881 (tm-30) REVERT: R 108 ASP cc_start: 0.8267 (m-30) cc_final: 0.7447 (t70) REVERT: R 116 MET cc_start: 0.7100 (ttp) cc_final: 0.6826 (tmm) REVERT: R 168 CYS cc_start: 0.9029 (m) cc_final: 0.8559 (m) REVERT: R 413 TRP cc_start: 0.8596 (m100) cc_final: 0.8276 (m100) REVERT: B 217 GLU cc_start: 0.9046 (tp30) cc_final: 0.8794 (tp30) REVERT: B 249 MET cc_start: 0.8614 (tpp) cc_final: 0.8354 (tpp) REVERT: B 262 ASP cc_start: 0.8666 (p0) cc_final: 0.8315 (p0) outliers start: 20 outliers final: 18 residues processed: 150 average time/residue: 0.0950 time to fit residues: 19.5054 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.0060 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.091318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.068613 restraints weight = 23493.031| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.46 r_work: 0.3047 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8794 Z= 0.134 Angle : 0.634 19.133 11944 Z= 0.328 Chirality : 0.044 0.567 1389 Planarity : 0.004 0.049 1504 Dihedral : 4.617 56.994 1206 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.05 % Allowed : 18.53 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.91 (0.26), residues: 1101 helix: 2.12 (0.27), residues: 392 sheet: 0.17 (0.30), residues: 265 loop : -0.46 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 198 TYR 0.016 0.001 TYR E 190 PHE 0.017 0.001 PHE R 50 TRP 0.037 0.002 TRP R 100 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8793) covalent geometry : angle 0.63377 (11942) SS BOND : bond 0.00156 ( 1) SS BOND : angle 1.11349 ( 2) hydrogen bonds : bond 0.04012 ( 458) hydrogen bonds : angle 4.58693 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7928 (t0) REVERT: E 93 MET cc_start: 0.7911 (ttt) cc_final: 0.7505 (tpp) REVERT: E 220 GLU cc_start: 0.8460 (mp0) cc_final: 0.7800 (mp0) REVERT: E 244 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8149 (tttp) REVERT: E 246 GLU cc_start: 0.7856 (pm20) cc_final: 0.7565 (pm20) REVERT: A 17 GLN cc_start: 0.9390 (tp40) cc_final: 0.8807 (tp-100) REVERT: A 20 ASP cc_start: 0.9302 (m-30) cc_final: 0.8958 (p0) REVERT: A 23 LYS cc_start: 0.9624 (mmmm) cc_final: 0.9303 (mmmm) REVERT: C 21 MET cc_start: 0.9158 (ttm) cc_final: 0.8516 (tpp) REVERT: C 22 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8105 (tm-30) REVERT: R 62 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7949 (tm-30) REVERT: R 108 ASP cc_start: 0.8181 (m-30) cc_final: 0.7342 (t70) REVERT: R 113 LEU cc_start: 0.8701 (mm) cc_final: 0.8422 (mt) REVERT: R 168 CYS cc_start: 0.9056 (m) cc_final: 0.8604 (m) REVERT: R 413 TRP cc_start: 0.8580 (m100) cc_final: 0.8298 (m100) REVERT: B 33 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7612 (t70) REVERT: B 217 GLU cc_start: 0.9023 (tp30) cc_final: 0.8773 (tp30) REVERT: B 249 MET cc_start: 0.8615 (tpp) cc_final: 0.8355 (tpp) REVERT: B 262 ASP cc_start: 0.8641 (p0) cc_final: 0.8296 (p0) outliers start: 19 outliers final: 15 residues processed: 144 average time/residue: 0.0976 time to fit residues: 19.1487 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 142 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 = 0.3646 r_free = 0.3646 target = 0.090411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.067632 restraints weight = 23222.448| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.36 r_work: 0.3054 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 8794 Z= 0.174 Angle : 0.926 59.194 11944 Z= 0.526 Chirality : 0.043 0.365 1389 Planarity : 0.004 0.047 1504 Dihedral : 4.618 57.066 1206 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.72 % Allowed : 18.75 % Favored : 79.53 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % 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: 0.89 (0.26), residues: 1101 helix: 2.09 (0.27), residues: 392 sheet: 0.18 (0.30), residues: 265 loop : -0.46 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 198 TYR 0.015 0.001 TYR E 190 PHE 0.017 0.001 PHE R 102 TRP 0.019 0.002 TRP A 82 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8793) covalent geometry : angle 0.92554 (11942) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.98408 ( 2) hydrogen bonds : bond 0.04010 ( 458) hydrogen bonds : angle 4.56500 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.32 seconds wall clock time: 43 minutes 12.34 seconds (2592.34 seconds total)