Starting phenix.real_space_refine on Thu Feb 13 03:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzq_41766/02_2025/8tzq_41766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzq_41766/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzq_41766/02_2025/8tzq_41766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzq_41766/02_2025/8tzq_41766.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzq_41766/02_2025/8tzq_41766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzq_41766/02_2025/8tzq_41766.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'GLU:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} 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: 5.36, per 1000 atoms: 0.62 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: 2.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.08 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: 2.75 Time building geometry restraints manager: 2.58 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: 0.010 Normalize map: mean=0, sd=1: 2.240 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- 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 8793 Z= 0.172 Angle : 0.546 6.675 11942 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.001 TRP A 82 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE R 382 TYR 0.009 0.001 TYR E 102 ARG 0.002 0.000 ARG R 218 *********************** 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 : 1.071 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: 0.2740 time to fit residues: 94.7473 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 : 0.931 ------------------------------------------------------------------------------- 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 92 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.089679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.066847 restraints weight = 22852.994| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.43 r_work: 0.3015 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 8793 Z= 0.466 Angle : 0.692 12.516 11942 Z= 0.366 Chirality : 0.046 0.155 1389 Planarity : 0.004 0.041 1504 Dihedral : 4.890 56.381 1208 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.45 % Allowed : 11.75 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1101 helix: 1.76 (0.26), residues: 399 sheet: 0.22 (0.30), residues: 271 loop : -0.57 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 36 HIS 0.006 0.001 HIS A 142 PHE 0.027 0.002 PHE A 253 TYR 0.016 0.001 TYR E 235 ARG 0.006 0.001 ARG A 134 *********************** 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 196 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8726 (tttt) cc_final: 0.8313 (tttm) REVERT: E 90 ASP cc_start: 0.7613 (m-30) cc_final: 0.7363 (m-30) REVERT: E 219 LEU cc_start: 0.9133 (tp) cc_final: 0.8881 (tp) REVERT: E 220 GLU cc_start: 0.7789 (mp0) cc_final: 0.7390 (mp0) REVERT: E 230 MET cc_start: 0.9026 (ttp) cc_final: 0.8816 (ttt) REVERT: A 8 ARG cc_start: 0.9338 (ptp-110) cc_final: 0.9102 (ptp-110) REVERT: A 262 MET cc_start: 0.8528 (tpp) cc_final: 0.8129 (tpp) REVERT: C 21 MET cc_start: 0.9071 (ttm) cc_final: 0.8411 (tpp) REVERT: C 22 GLU cc_start: 0.8229 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 47 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7840 (tm-30) REVERT: R 62 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7280 (tm-30) REVERT: R 413 TRP cc_start: 0.8738 (m100) cc_final: 0.8168 (m100) REVERT: B 262 ASP cc_start: 0.8572 (p0) cc_final: 0.8213 (p0) REVERT: B 333 GLN cc_start: 0.8600 (tp40) cc_final: 0.8242 (tp40) outliers start: 32 outliers final: 24 residues processed: 183 average time/residue: 0.2290 time to fit residues: 56.3652 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 : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 159 VAL 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 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.092716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.070086 restraints weight = 23130.585| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.50 r_work: 0.3063 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8793 Z= 0.175 Angle : 0.570 11.669 11942 Z= 0.302 Chirality : 0.042 0.139 1389 Planarity : 0.003 0.040 1504 Dihedral : 4.669 56.272 1208 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.83 % Allowed : 13.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1101 helix: 1.95 (0.27), residues: 392 sheet: 0.27 (0.30), residues: 271 loop : -0.57 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 82 HIS 0.005 0.001 HIS B 189 PHE 0.016 0.001 PHE R 429 TYR 0.017 0.001 TYR E 190 ARG 0.005 0.000 ARG A 134 *********************** 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: 17 poor density : 156 time to evaluate : 1.105 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: 0.8728 (tttt) cc_final: 0.8427 (ttmm) REVERT: E 62 ASP cc_start: 0.8613 (m-30) cc_final: 0.7846 (t0) REVERT: E 90 ASP cc_start: 0.7485 (m-30) cc_final: 0.7256 (m-30) REVERT: E 219 LEU cc_start: 0.9122 (tp) cc_final: 0.8881 (tp) REVERT: E 220 GLU cc_start: 0.7849 (mp0) cc_final: 0.7308 (mp0) REVERT: E 246 GLU cc_start: 0.7601 (pm20) cc_final: 0.7257 (pm20) REVERT: A 217 MET cc_start: 0.8838 (ptt) cc_final: 0.8611 (ptp) REVERT: A 262 MET cc_start: 0.8550 (tpp) cc_final: 0.7936 (tpp) REVERT: C 21 MET cc_start: 0.9072 (ttm) cc_final: 0.8498 (tpp) REVERT: C 22 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7964 (tm-30) REVERT: R 45 ILE cc_start: 0.8441 (mp) cc_final: 0.8017 (mm) REVERT: R 62 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7724 (tm-30) REVERT: R 88 MET cc_start: 0.8331 (mmm) cc_final: 0.8009 (tpp) REVERT: R 108 ASP cc_start: 0.8563 (m-30) cc_final: 0.8150 (t70) REVERT: R 116 MET cc_start: 0.7311 (ttp) cc_final: 0.6908 (ttp) REVERT: R 117 MET cc_start: 0.7907 (mmt) cc_final: 0.7202 (mmt) REVERT: R 119 THR cc_start: 0.8753 (m) cc_final: 0.8265 (p) REVERT: R 168 CYS cc_start: 0.8673 (m) cc_final: 0.8288 (m) REVERT: R 413 TRP cc_start: 0.8568 (m100) cc_final: 0.8229 (m100) REVERT: B 262 ASP cc_start: 0.8589 (p0) cc_final: 0.8259 (p0) REVERT: B 333 GLN cc_start: 0.8594 (tp40) cc_final: 0.8213 (tp40) outliers start: 17 outliers final: 9 residues processed: 171 average time/residue: 0.2179 time to fit residues: 51.0342 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain R residue 107 CYS 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 242 ASN 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 108 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.089748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066981 restraints weight = 22967.253| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.39 r_work: 0.3025 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8793 Z= 0.292 Angle : 0.593 14.869 11942 Z= 0.310 Chirality : 0.043 0.136 1389 Planarity : 0.003 0.041 1504 Dihedral : 4.674 56.863 1206 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.56 % Allowed : 13.79 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1101 helix: 2.09 (0.27), residues: 390 sheet: 0.07 (0.30), residues: 275 loop : -0.54 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 82 HIS 0.004 0.001 HIS B 189 PHE 0.020 0.002 PHE A 253 TYR 0.016 0.001 TYR E 235 ARG 0.004 0.000 ARG A 134 *********************** 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 176 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8716 (tttt) cc_final: 0.8415 (ttmm) REVERT: E 62 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.7920 (t0) REVERT: E 90 ASP cc_start: 0.7506 (m-30) cc_final: 0.7262 (m-30) REVERT: E 219 LEU cc_start: 0.9181 (tp) cc_final: 0.8968 (tp) REVERT: E 220 GLU cc_start: 0.7953 (mp0) cc_final: 0.7153 (mp0) REVERT: E 246 GLU cc_start: 0.7697 (pm20) cc_final: 0.7370 (pm20) REVERT: A 8 ARG cc_start: 0.9410 (ptp90) cc_final: 0.8925 (ptp-170) REVERT: A 217 MET cc_start: 0.8787 (ptt) cc_final: 0.8575 (ptp) REVERT: A 262 MET cc_start: 0.8608 (tpp) cc_final: 0.8313 (tpp) REVERT: C 13 ARG cc_start: 0.9333 (mtm-85) cc_final: 0.9076 (mtm-85) REVERT: C 21 MET cc_start: 0.9121 (ttm) cc_final: 0.8535 (tpp) REVERT: C 22 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8101 (tm-30) REVERT: R 62 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7557 (tm-30) REVERT: R 88 MET cc_start: 0.8302 (mmm) cc_final: 0.7987 (tpp) REVERT: R 108 ASP cc_start: 0.8631 (m-30) cc_final: 0.8213 (t70) REVERT: R 117 MET cc_start: 0.7919 (mmt) cc_final: 0.7601 (mmt) REVERT: R 168 CYS cc_start: 0.8795 (m) cc_final: 0.8423 (m) REVERT: R 413 TRP cc_start: 0.8677 (m100) cc_final: 0.8273 (m100) REVERT: B 50 VAL cc_start: 0.9010 (t) cc_final: 0.8791 (p) REVERT: B 187 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8111 (tt0) REVERT: B 262 ASP cc_start: 0.8565 (p0) cc_final: 0.8234 (p0) REVERT: B 333 GLN cc_start: 0.8797 (tp40) cc_final: 0.8419 (tp40) outliers start: 33 outliers final: 21 residues processed: 164 average time/residue: 0.2228 time to fit residues: 49.9593 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 100 VAL 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 54 VAL Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 107 CYS 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 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 51 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.089444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066937 restraints weight = 22810.297| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.36 r_work: 0.3030 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8793 Z= 0.269 Angle : 0.585 13.981 11942 Z= 0.306 Chirality : 0.042 0.138 1389 Planarity : 0.003 0.041 1504 Dihedral : 4.627 57.213 1206 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.66 % Allowed : 14.33 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1101 helix: 2.13 (0.27), residues: 390 sheet: 0.01 (0.30), residues: 275 loop : -0.49 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 82 HIS 0.005 0.001 HIS B 189 PHE 0.015 0.001 PHE A 253 TYR 0.015 0.001 TYR E 235 ARG 0.004 0.000 ARG R 222 *********************** 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 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7901 (t0) REVERT: E 220 GLU cc_start: 0.8202 (mp0) cc_final: 0.7586 (mp0) REVERT: E 246 GLU cc_start: 0.7726 (pm20) cc_final: 0.7390 (pm20) REVERT: A 23 LYS cc_start: 0.9572 (mtpp) cc_final: 0.9301 (mtmm) REVERT: A 188 MET cc_start: 0.9270 (mmm) cc_final: 0.8939 (mmm) REVERT: A 215 GLU cc_start: 0.8882 (mp0) cc_final: 0.8645 (mp0) REVERT: A 217 MET cc_start: 0.8775 (ptt) cc_final: 0.8571 (ptp) REVERT: A 262 MET cc_start: 0.8628 (tpp) cc_final: 0.8332 (tpp) REVERT: C 13 ARG cc_start: 0.9348 (mtm-85) cc_final: 0.9114 (mtm-85) REVERT: C 21 MET cc_start: 0.9129 (ttm) cc_final: 0.8542 (tpp) REVERT: C 22 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8044 (tm-30) REVERT: R 62 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7619 (tm-30) REVERT: R 88 MET cc_start: 0.8409 (mmm) cc_final: 0.8181 (mmm) REVERT: R 108 ASP cc_start: 0.8601 (m-30) cc_final: 0.8200 (t70) REVERT: R 116 MET cc_start: 0.7400 (ttp) cc_final: 0.6757 (ppp) REVERT: R 119 THR cc_start: 0.8800 (m) cc_final: 0.8304 (p) REVERT: R 168 CYS cc_start: 0.8894 (m) cc_final: 0.8518 (m) REVERT: R 413 TRP cc_start: 0.8658 (m100) cc_final: 0.8289 (m100) REVERT: B 187 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8104 (tt0) REVERT: B 262 ASP cc_start: 0.8575 (p0) cc_final: 0.8258 (p0) REVERT: B 331 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7952 (t0) REVERT: B 333 GLN cc_start: 0.8832 (tp40) cc_final: 0.8456 (tp40) outliers start: 34 outliers final: 23 residues processed: 167 average time/residue: 0.2306 time to fit residues: 52.1748 Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 100 VAL 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 57 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain R residue 107 CYS 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 Chi-restraints excluded: chain B residue 331 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 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 = 0.3626 r_free = 0.3626 target = 0.089428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066878 restraints weight = 23120.993| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.38 r_work: 0.3039 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8793 Z= 0.235 Angle : 0.577 13.754 11942 Z= 0.305 Chirality : 0.042 0.132 1389 Planarity : 0.003 0.041 1504 Dihedral : 4.613 57.031 1206 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.12 % Allowed : 15.19 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1101 helix: 2.06 (0.27), residues: 391 sheet: 0.02 (0.30), residues: 273 loop : -0.48 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 82 HIS 0.006 0.001 HIS B 189 PHE 0.013 0.001 PHE A 253 TYR 0.018 0.001 TYR E 235 ARG 0.003 0.000 ARG A 134 *********************** 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 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.029 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: 0.8502 (OUTLIER) cc_final: 0.7863 (t0) REVERT: E 93 MET cc_start: 0.7965 (ttt) cc_final: 0.7561 (tpp) REVERT: E 220 GLU cc_start: 0.8211 (mp0) cc_final: 0.7717 (mp0) REVERT: E 244 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8058 (tttp) REVERT: E 246 GLU cc_start: 0.7804 (pm20) cc_final: 0.7521 (pm20) REVERT: A 20 ASP cc_start: 0.9359 (m-30) cc_final: 0.8994 (p0) REVERT: A 23 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9332 (mtmm) REVERT: A 215 GLU cc_start: 0.8864 (mp0) cc_final: 0.8644 (mp0) REVERT: A 217 MET cc_start: 0.8812 (ptt) cc_final: 0.8602 (ptp) REVERT: A 262 MET cc_start: 0.8564 (tpp) cc_final: 0.8003 (tpp) REVERT: C 21 MET cc_start: 0.9132 (ttm) cc_final: 0.8536 (tpp) REVERT: C 22 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7947 (tm-30) REVERT: R 62 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7785 (tm-30) REVERT: R 108 ASP cc_start: 0.8530 (m-30) cc_final: 0.8156 (t70) REVERT: R 116 MET cc_start: 0.7455 (ttp) cc_final: 0.6910 (ppp) REVERT: R 168 CYS cc_start: 0.8935 (m) cc_final: 0.8550 (m) REVERT: R 413 TRP cc_start: 0.8614 (m100) cc_final: 0.8308 (m100) REVERT: B 187 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8125 (tt0) REVERT: B 262 ASP cc_start: 0.8499 (p0) cc_final: 0.8167 (p0) REVERT: B 333 GLN cc_start: 0.8855 (tp40) cc_final: 0.8597 (tp40) outliers start: 29 outliers final: 24 residues processed: 158 average time/residue: 0.2341 time to fit residues: 50.5136 Evaluate side-chains 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 82 TRP Chi-restraints excluded: chain A residue 100 VAL 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 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain R residue 107 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3586 r_free = 0.3586 target = 0.088428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.065341 restraints weight = 23696.490| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.46 r_work: 0.2970 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8793 Z= 0.416 Angle : 0.659 12.616 11942 Z= 0.346 Chirality : 0.044 0.144 1389 Planarity : 0.004 0.043 1504 Dihedral : 4.900 57.549 1206 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.88 % Allowed : 15.52 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1101 helix: 1.89 (0.27), residues: 391 sheet: -0.06 (0.31), residues: 268 loop : -0.57 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 100 HIS 0.004 0.001 HIS B 189 PHE 0.023 0.002 PHE A 253 TYR 0.023 0.001 TYR E 235 ARG 0.003 0.000 ARG A 134 *********************** 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 171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.972 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: 0.8616 (OUTLIER) cc_final: 0.8078 (t0) REVERT: E 220 GLU cc_start: 0.8391 (mp0) cc_final: 0.7774 (mp0) REVERT: E 246 GLU cc_start: 0.7746 (pm20) cc_final: 0.7369 (pm20) REVERT: A 20 ASP cc_start: 0.9354 (m-30) cc_final: 0.9040 (p0) REVERT: A 23 LYS cc_start: 0.9610 (mtpp) cc_final: 0.9363 (mtmm) REVERT: A 215 GLU cc_start: 0.8869 (mp0) cc_final: 0.8593 (mp0) REVERT: A 262 MET cc_start: 0.8733 (tpp) cc_final: 0.8301 (tpp) REVERT: C 21 MET cc_start: 0.9145 (ttm) cc_final: 0.8457 (tpp) REVERT: C 22 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7944 (tm-30) REVERT: R 62 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7662 (tm-30) REVERT: R 108 ASP cc_start: 0.8498 (m-30) cc_final: 0.8166 (t70) REVERT: R 116 MET cc_start: 0.7371 (ttp) cc_final: 0.6919 (ppp) REVERT: R 168 CYS cc_start: 0.8959 (m) cc_final: 0.8546 (m) REVERT: R 221 LYS cc_start: 0.7679 (ttpp) cc_final: 0.6895 (mmtm) REVERT: R 222 ARG cc_start: 0.8894 (mmp-170) cc_final: 0.8609 (mmp80) REVERT: R 413 TRP cc_start: 0.8698 (m100) cc_final: 0.8336 (m100) REVERT: B 187 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8194 (tt0) REVERT: B 189 HIS cc_start: 0.8359 (m170) cc_final: 0.7938 (m170) REVERT: B 249 MET cc_start: 0.8641 (tpp) cc_final: 0.8397 (tpp) REVERT: B 262 ASP cc_start: 0.8643 (p0) cc_final: 0.8299 (p0) outliers start: 36 outliers final: 29 residues processed: 155 average time/residue: 0.2145 time to fit residues: 45.5003 Evaluate side-chains 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 100 VAL 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 296 VAL 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 93 TYR Chi-restraints excluded: chain R residue 107 CYS 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 159 VAL 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 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 28 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A 268 ASN R 106 HIS R 175 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066881 restraints weight = 23381.657| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.40 r_work: 0.3025 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8793 Z= 0.209 Angle : 0.592 11.916 11942 Z= 0.312 Chirality : 0.041 0.164 1389 Planarity : 0.003 0.042 1504 Dihedral : 4.685 57.101 1206 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.80 % Allowed : 17.13 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1101 helix: 2.00 (0.27), residues: 391 sheet: 0.04 (0.30), residues: 270 loop : -0.48 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 100 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE E 212 TYR 0.016 0.001 TYR E 235 ARG 0.003 0.000 ARG A 134 *********************** 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 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.031 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: 0.8528 (OUTLIER) cc_final: 0.7965 (t0) REVERT: E 93 MET cc_start: 0.8040 (ttt) cc_final: 0.7532 (tpp) REVERT: E 220 GLU cc_start: 0.8433 (mp0) cc_final: 0.7770 (mp0) REVERT: E 244 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8074 (tttp) REVERT: E 246 GLU cc_start: 0.7730 (pm20) cc_final: 0.7389 (pm20) REVERT: A 17 GLN cc_start: 0.9362 (tp-100) cc_final: 0.8792 (tp-100) REVERT: A 20 ASP cc_start: 0.9357 (m-30) cc_final: 0.9090 (p0) REVERT: A 23 LYS cc_start: 0.9608 (mtpp) cc_final: 0.9348 (mtmm) REVERT: A 215 GLU cc_start: 0.8904 (mp0) cc_final: 0.8656 (mp0) REVERT: C 21 MET cc_start: 0.9139 (ttm) cc_final: 0.8441 (tpp) REVERT: C 22 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7960 (tm-30) REVERT: R 62 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7882 (tm-30) REVERT: R 108 ASP cc_start: 0.8433 (m-30) cc_final: 0.8120 (t70) REVERT: R 168 CYS cc_start: 0.8992 (m) cc_final: 0.8551 (m) REVERT: R 221 LYS cc_start: 0.7681 (ttpp) cc_final: 0.6898 (mmtm) REVERT: R 222 ARG cc_start: 0.8886 (mmp-170) cc_final: 0.8629 (mmp80) REVERT: R 413 TRP cc_start: 0.8635 (m100) cc_final: 0.8255 (m100) REVERT: B 187 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8198 (tt0) REVERT: B 189 HIS cc_start: 0.8310 (m170) cc_final: 0.7977 (m170) REVERT: B 249 MET cc_start: 0.8618 (tpp) cc_final: 0.8370 (tpp) REVERT: B 262 ASP cc_start: 0.8657 (p0) cc_final: 0.8323 (p0) outliers start: 26 outliers final: 23 residues processed: 154 average time/residue: 0.2212 time to fit residues: 46.6600 Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 100 VAL 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 268 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 38 MET 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 93 TYR Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 159 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 0.0020 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 ** 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 = 0.3617 r_free = 0.3617 target = 0.090257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067491 restraints weight = 23525.584| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.45 r_work: 0.3015 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8793 Z= 0.250 Angle : 0.606 11.441 11942 Z= 0.321 Chirality : 0.042 0.162 1389 Planarity : 0.003 0.041 1504 Dihedral : 4.708 57.256 1206 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.12 % Allowed : 17.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1101 helix: 2.02 (0.27), residues: 391 sheet: 0.02 (0.30), residues: 270 loop : -0.49 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 100 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE R 429 TYR 0.018 0.001 TYR E 235 ARG 0.014 0.000 ARG C 13 *********************** 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 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.094 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: 0.8537 (OUTLIER) cc_final: 0.7986 (t0) REVERT: E 93 MET cc_start: 0.8039 (ttt) cc_final: 0.7531 (tpp) REVERT: E 220 GLU cc_start: 0.8447 (mp0) cc_final: 0.7775 (mp0) REVERT: E 246 GLU cc_start: 0.7748 (pm20) cc_final: 0.7392 (pm20) REVERT: A 17 GLN cc_start: 0.9361 (tp-100) cc_final: 0.8762 (tp-100) REVERT: A 20 ASP cc_start: 0.9347 (m-30) cc_final: 0.9075 (p0) REVERT: A 23 LYS cc_start: 0.9605 (mtpp) cc_final: 0.9342 (mtmm) REVERT: A 215 GLU cc_start: 0.8936 (mp0) cc_final: 0.8676 (mp0) REVERT: A 262 MET cc_start: 0.8680 (tpp) cc_final: 0.8185 (tpp) REVERT: C 21 MET cc_start: 0.9166 (ttm) cc_final: 0.8464 (tpp) REVERT: C 22 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7946 (tm-30) REVERT: R 62 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7844 (tm-30) REVERT: R 88 MET cc_start: 0.8682 (mmm) cc_final: 0.8477 (mmm) REVERT: R 108 ASP cc_start: 0.8468 (m-30) cc_final: 0.8160 (t0) REVERT: R 116 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6699 (tmm) REVERT: R 168 CYS cc_start: 0.9026 (m) cc_final: 0.8567 (m) REVERT: R 413 TRP cc_start: 0.8642 (m100) cc_final: 0.8274 (m100) REVERT: B 187 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8199 (tt0) REVERT: B 189 HIS cc_start: 0.8306 (m170) cc_final: 0.7998 (m170) REVERT: B 249 MET cc_start: 0.8636 (tpp) cc_final: 0.8381 (tpp) REVERT: B 262 ASP cc_start: 0.8663 (p0) cc_final: 0.8324 (p0) outliers start: 29 outliers final: 24 residues processed: 153 average time/residue: 0.2236 time to fit residues: 46.8738 Evaluate side-chains 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 100 VAL 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 296 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 116 MET 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 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 61 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3615 r_free = 0.3615 target = 0.089355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.066658 restraints weight = 23106.491| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.37 r_work: 0.3022 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8793 Z= 0.248 Angle : 0.604 10.734 11942 Z= 0.320 Chirality : 0.042 0.160 1389 Planarity : 0.003 0.042 1504 Dihedral : 4.693 57.275 1206 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.02 % Allowed : 16.81 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1101 helix: 2.00 (0.27), residues: 391 sheet: 0.01 (0.30), residues: 270 loop : -0.49 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 100 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE R 382 TYR 0.017 0.001 TYR E 235 ARG 0.009 0.000 ARG C 13 ********************** 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 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.088 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: 0.8522 (OUTLIER) cc_final: 0.8009 (t0) REVERT: E 93 MET cc_start: 0.8038 (ttt) cc_final: 0.7518 (tpp) REVERT: E 220 GLU cc_start: 0.8458 (mp0) cc_final: 0.7748 (mp0) REVERT: E 246 GLU cc_start: 0.7759 (pm20) cc_final: 0.7380 (pm20) REVERT: A 17 GLN cc_start: 0.9365 (tp-100) cc_final: 0.8748 (tp-100) REVERT: A 20 ASP cc_start: 0.9324 (m-30) cc_final: 0.9067 (p0) REVERT: A 23 LYS cc_start: 0.9608 (mtpp) cc_final: 0.9344 (mtmm) REVERT: A 215 GLU cc_start: 0.8919 (mp0) cc_final: 0.8658 (mp0) REVERT: A 262 MET cc_start: 0.8686 (tpp) cc_final: 0.8183 (tpp) REVERT: C 21 MET cc_start: 0.9170 (ttm) cc_final: 0.8464 (tpp) REVERT: C 22 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7997 (tm-30) REVERT: R 62 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7840 (tm-30) REVERT: R 108 ASP cc_start: 0.8393 (m-30) cc_final: 0.8104 (t0) REVERT: R 168 CYS cc_start: 0.9070 (m) cc_final: 0.8620 (m) REVERT: R 221 LYS cc_start: 0.7686 (pttt) cc_final: 0.6893 (mmtm) REVERT: R 222 ARG cc_start: 0.8653 (mmp-170) cc_final: 0.8381 (mmp80) REVERT: R 413 TRP cc_start: 0.8626 (m100) cc_final: 0.8268 (m100) REVERT: B 187 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8198 (tt0) REVERT: B 189 HIS cc_start: 0.8263 (m170) cc_final: 0.7982 (m170) REVERT: B 249 MET cc_start: 0.8635 (tpp) cc_final: 0.8378 (tpp) REVERT: B 262 ASP cc_start: 0.8697 (p0) cc_final: 0.8354 (p0) outliers start: 28 outliers final: 25 residues processed: 149 average time/residue: 0.2207 time to fit residues: 44.8343 Evaluate side-chains 155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 100 VAL 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 296 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain R residue 107 CYS 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 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 53 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.0010 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 ** 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 = 0.3640 r_free = 0.3640 target = 0.090767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.068122 restraints weight = 23165.319| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.39 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: 0.8220 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8793 Z= 0.186 Angle : 0.592 10.937 11942 Z= 0.308 Chirality : 0.041 0.157 1389 Planarity : 0.003 0.041 1504 Dihedral : 4.525 56.814 1206 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.05 % Allowed : 17.78 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1101 helix: 2.08 (0.27), residues: 392 sheet: 0.10 (0.30), residues: 265 loop : -0.44 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 100 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE R 429 TYR 0.016 0.001 TYR E 190 ARG 0.008 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4603.89 seconds wall clock time: 82 minutes 34.61 seconds (4954.61 seconds total)