Starting phenix.real_space_refine on Sat Dec 28 14:09:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzq_41766/12_2024/8tzq_41766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzq_41766/12_2024/8tzq_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_41766/12_2024/8tzq_41766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzq_41766/12_2024/8tzq_41766.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzq_41766/12_2024/8tzq_41766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzq_41766/12_2024/8tzq_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.69, per 1000 atoms: 0.66 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 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: 0.94 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: 2.43 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2771 1.34 - 1.46: 1875 1.46 - 1.58: 4058 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 8793 Sorted by residual: bond pdb=" N PHE A 234 " pdb=" CA PHE A 234 " ideal model delta sigma weight residual 1.455 1.484 -0.028 1.23e-02 6.61e+03 5.32e+00 bond pdb=" N HIS R 393 " pdb=" CA HIS R 393 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.05e+00 bond pdb=" N ARG R 151 " pdb=" CA ARG R 151 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.53e+00 bond pdb=" N ARG R 218 " pdb=" CA ARG R 218 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.19e-02 7.06e+03 3.45e+00 bond pdb=" CG HIS R 393 " pdb=" CD2 HIS R 393 " ideal model delta sigma weight residual 1.354 1.337 0.017 1.10e-02 8.26e+03 2.26e+00 ... (remaining 8788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 11563 1.34 - 2.67: 309 2.67 - 4.01: 59 4.01 - 5.34: 7 5.34 - 6.68: 4 Bond angle restraints: 11942 Sorted by residual: angle pdb=" C GLN R 179 " pdb=" CA GLN R 179 " pdb=" CB GLN R 179 " ideal model delta sigma weight residual 117.23 110.55 6.68 1.36e+00 5.41e-01 2.41e+01 angle pdb=" CA GLN R 179 " pdb=" C GLN R 179 " pdb=" N ASN R 180 " ideal model delta sigma weight residual 119.98 117.12 2.86 8.50e-01 1.38e+00 1.13e+01 angle pdb=" OG1 THR R 205 " pdb=" CB THR R 205 " pdb=" CG2 THR R 205 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.91e+00 angle pdb=" C LYS B 193 " pdb=" CA LYS B 193 " pdb=" CB LYS B 193 " ideal model delta sigma weight residual 110.42 116.08 -5.66 1.99e+00 2.53e-01 8.09e+00 angle pdb=" C CYS R 385 " pdb=" N TRP R 386 " pdb=" CA TRP R 386 " ideal model delta sigma weight residual 122.58 116.80 5.78 2.07e+00 2.33e-01 7.79e+00 ... (remaining 11937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 5002 17.49 - 34.99: 169 34.99 - 52.48: 19 52.48 - 69.97: 2 69.97 - 87.46: 4 Dihedral angle restraints: 5196 sinusoidal: 1950 harmonic: 3246 Sorted by residual: dihedral pdb=" CD ARG R 151 " pdb=" NE ARG R 151 " pdb=" CZ ARG R 151 " pdb=" NH1 ARG R 151 " ideal model delta sinusoidal sigma weight residual 0.00 -63.05 63.05 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CD ARG R 218 " pdb=" NE ARG R 218 " pdb=" CZ ARG R 218 " pdb=" NH1 ARG R 218 " ideal model delta sinusoidal sigma weight residual 0.00 -47.27 47.27 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CA LYS A 78 " pdb=" C LYS A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 912 0.033 - 0.067: 341 0.067 - 0.100: 89 0.100 - 0.134: 44 0.134 - 0.167: 3 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CB THR R 205 " pdb=" CA THR R 205 " pdb=" OG1 THR R 205 " pdb=" CG2 THR R 205 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA ARG R 151 " pdb=" N ARG R 151 " pdb=" C ARG R 151 " pdb=" CB ARG R 151 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ARG R 218 " pdb=" N ARG R 218 " pdb=" C ARG R 218 " pdb=" CB ARG R 218 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1386 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 151 " -0.981 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG R 151 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG R 151 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG R 151 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 151 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 218 " 0.805 9.50e-02 1.11e+02 3.61e-01 7.91e+01 pdb=" NE ARG R 218 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG R 218 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG R 218 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 218 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 50 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C PHE R 50 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE R 50 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY R 51 " 0.010 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1301 2.76 - 3.30: 8224 3.30 - 3.83: 14188 3.83 - 4.37: 16661 4.37 - 4.90: 29435 Nonbonded interactions: 69809 Sorted by model distance: nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 274 " pdb=" O VAL A 315 " model vdw 2.247 3.040 nonbonded pdb=" O THR R 39 " pdb=" OG1 THR R 42 " model vdw 2.248 3.040 nonbonded pdb=" O ILE R 424 " pdb=" OG1 THR R 428 " model vdw 2.267 3.040 nonbonded pdb=" OG SER A 331 " pdb=" OD1 ASP A 333 " model vdw 2.296 3.040 ... (remaining 69804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- 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 : 1.034 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: 0.2710 time to fit residues: 93.8265 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 : 1.069 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 19 LYS cc_start: 0.8757 (tttt) cc_final: 0.8519 (tttm) REVERT: A 8 ARG cc_start: 0.8984 (ptp-110) cc_final: 0.8675 (ptp-110) REVERT: C 21 MET cc_start: 0.8709 (ttm) cc_final: 0.8395 (tpp) REVERT: C 47 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7608 (tm-30) outliers start: 32 outliers final: 24 residues processed: 183 average time/residue: 0.2311 time to fit residues: 56.7788 Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 75 GLN A 340 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8793 Z= 0.252 Angle : 0.604 10.695 11942 Z= 0.320 Chirality : 0.043 0.143 1389 Planarity : 0.004 0.041 1504 Dihedral : 4.816 56.567 1208 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.02 % Allowed : 13.25 % Favored : 83.73 % 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: 0.71 (0.25), residues: 1101 helix: 1.97 (0.27), residues: 387 sheet: 0.07 (0.30), residues: 275 loop : -0.57 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 82 HIS 0.006 0.001 HIS B 189 PHE 0.015 0.002 PHE R 429 TYR 0.016 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 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.092 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: 0.7941 (m-30) cc_final: 0.7557 (t0) REVERT: C 21 MET cc_start: 0.8678 (ttm) cc_final: 0.8377 (tpp) REVERT: R 45 ILE cc_start: 0.8553 (mp) cc_final: 0.8189 (mm) REVERT: R 108 ASP cc_start: 0.8526 (m-30) cc_final: 0.8213 (t70) REVERT: R 374 MET cc_start: 0.7031 (mmp) cc_final: 0.6774 (mmm) REVERT: B 50 VAL cc_start: 0.9021 (t) cc_final: 0.8711 (p) outliers start: 28 outliers final: 17 residues processed: 170 average time/residue: 0.2314 time to fit residues: 53.4008 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 100 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 107 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8793 Z= 0.265 Angle : 0.604 14.711 11942 Z= 0.317 Chirality : 0.043 0.136 1389 Planarity : 0.003 0.042 1504 Dihedral : 4.777 56.834 1206 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.45 % Allowed : 13.90 % 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: 0.70 (0.25), residues: 1101 helix: 1.93 (0.27), residues: 390 sheet: 0.05 (0.30), residues: 275 loop : -0.54 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 413 HIS 0.004 0.001 HIS B 189 PHE 0.016 0.001 PHE A 253 TYR 0.019 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 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7585 (t0) REVERT: A 8 ARG cc_start: 0.8940 (ptp90) cc_final: 0.8514 (ptp-170) REVERT: C 21 MET cc_start: 0.8687 (ttm) cc_final: 0.8338 (tpp) REVERT: R 88 MET cc_start: 0.7440 (tpp) cc_final: 0.7046 (tpp) REVERT: R 108 ASP cc_start: 0.8490 (m-30) cc_final: 0.8219 (t70) REVERT: R 374 MET cc_start: 0.6936 (mmp) cc_final: 0.6584 (mmm) outliers start: 32 outliers final: 24 residues processed: 157 average time/residue: 0.2189 time to fit residues: 46.9840 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 C residue 57 SER 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 375 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 304 ILE 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 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8793 Z= 0.368 Angle : 0.629 13.358 11942 Z= 0.335 Chirality : 0.044 0.153 1389 Planarity : 0.004 0.044 1504 Dihedral : 4.887 57.721 1206 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.74 % Allowed : 14.87 % Favored : 80.39 % 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: 1.91 (0.26), residues: 390 sheet: -0.01 (0.31), residues: 268 loop : -0.63 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 413 HIS 0.003 0.001 HIS C 44 PHE 0.022 0.002 PHE A 253 TYR 0.019 0.001 TYR E 235 ARG 0.010 0.001 ARG C 13 *********************** 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 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.046 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: 0.7979 (OUTLIER) cc_final: 0.7768 (t0) REVERT: C 21 MET cc_start: 0.8727 (ttm) cc_final: 0.8342 (tpp) REVERT: B 33 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7253 (t70) REVERT: B 50 VAL cc_start: 0.9090 (t) cc_final: 0.8765 (p) outliers start: 44 outliers final: 30 residues processed: 163 average time/residue: 0.2153 time to fit residues: 48.1159 Evaluate side-chains 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 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 262 MET 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 399 CYS Chi-restraints excluded: chain R residue 417 VAL Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8793 Z= 0.235 Angle : 0.595 13.602 11942 Z= 0.316 Chirality : 0.043 0.163 1389 Planarity : 0.004 0.042 1504 Dihedral : 4.750 57.182 1206 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.77 % Allowed : 16.49 % Favored : 79.74 % 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: 0.65 (0.25), residues: 1101 helix: 1.96 (0.26), residues: 392 sheet: -0.09 (0.30), residues: 272 loop : -0.57 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 100 HIS 0.003 0.001 HIS B 189 PHE 0.013 0.001 PHE A 253 TYR 0.015 0.001 TYR E 190 ARG 0.005 0.000 ARG R 222 *********************** 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 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.959 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: E 62 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7616 (t0) REVERT: C 21 MET cc_start: 0.8710 (ttm) cc_final: 0.8265 (tpp) outliers start: 35 outliers final: 24 residues processed: 154 average time/residue: 0.2206 time to fit residues: 46.1851 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 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 262 MET 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 178 ASP 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 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 0.0060 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 HIS E 142 GLN A 91 HIS ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8793 Z= 0.181 Angle : 0.593 13.087 11942 Z= 0.312 Chirality : 0.042 0.142 1389 Planarity : 0.003 0.040 1504 Dihedral : 4.619 56.808 1206 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.59 % Allowed : 18.21 % Favored : 79.20 % 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: 1.99 (0.26), residues: 392 sheet: 0.09 (0.30), residues: 271 loop : -0.50 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 100 HIS 0.004 0.001 HIS B 189 PHE 0.011 0.001 PHE B 190 TYR 0.016 0.001 TYR E 190 ARG 0.005 0.000 ARG C 13 *********************** 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 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.057 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: symmetry clash REVERT: E 62 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7578 (t0) REVERT: C 21 MET cc_start: 0.8705 (ttm) cc_final: 0.8296 (tpp) REVERT: R 119 THR cc_start: 0.9135 (m) cc_final: 0.8862 (p) REVERT: B 33 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6972 (t70) outliers start: 24 outliers final: 17 residues processed: 151 average time/residue: 0.2341 time to fit residues: 47.7968 Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 262 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 57 SER 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 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 399 CYS Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8793 Z= 0.371 Angle : 0.666 11.172 11942 Z= 0.352 Chirality : 0.044 0.157 1389 Planarity : 0.004 0.043 1504 Dihedral : 4.798 57.581 1206 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.34 % Allowed : 17.89 % Favored : 78.77 % 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: 1.96 (0.26), residues: 392 sheet: -0.05 (0.30), residues: 268 loop : -0.56 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 100 HIS 0.005 0.001 HIS B 189 PHE 0.022 0.002 PHE A 253 TYR 0.021 0.001 TYR E 235 ARG 0.004 0.000 ARG C 13 *********************** 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 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.054 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: C 21 MET cc_start: 0.8740 (ttm) cc_final: 0.8308 (tpp) REVERT: B 249 MET cc_start: 0.8287 (tpp) cc_final: 0.8050 (tpp) outliers start: 31 outliers final: 23 residues processed: 147 average time/residue: 0.2244 time to fit residues: 45.2421 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.0870 chunk 64 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 70 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8793 Z= 0.189 Angle : 0.626 11.480 11942 Z= 0.328 Chirality : 0.042 0.162 1389 Planarity : 0.003 0.040 1504 Dihedral : 4.659 56.991 1206 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.94 % Allowed : 18.75 % Favored : 79.31 % 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: 0.74 (0.25), residues: 1101 helix: 1.93 (0.27), residues: 392 sheet: 0.10 (0.30), residues: 265 loop : -0.52 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 100 HIS 0.004 0.001 HIS B 189 PHE 0.013 0.001 PHE R 202 TYR 0.015 0.001 TYR E 190 ARG 0.013 0.001 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 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.035 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: A 23 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8544 (mtmm) REVERT: C 21 MET cc_start: 0.8746 (ttm) cc_final: 0.8281 (tpp) REVERT: B 249 MET cc_start: 0.8229 (tpp) cc_final: 0.7991 (tpp) outliers start: 18 outliers final: 17 residues processed: 145 average time/residue: 0.2360 time to fit residues: 46.7560 Evaluate side-chains 146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain R residue 107 CYS Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 114 ASP Chi-restraints excluded: chain R residue 184 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain 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 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8793 Z= 0.223 Angle : 0.624 10.925 11942 Z= 0.330 Chirality : 0.042 0.158 1389 Planarity : 0.003 0.041 1504 Dihedral : 4.655 57.343 1206 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.83 % Allowed : 18.97 % Favored : 79.20 % 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: 0.71 (0.25), residues: 1101 helix: 1.83 (0.27), residues: 392 sheet: 0.14 (0.30), residues: 265 loop : -0.50 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 100 HIS 0.004 0.001 HIS B 189 PHE 0.017 0.001 PHE B 288 TYR 0.014 0.001 TYR E 190 ARG 0.013 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 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.038 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: A 23 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8536 (mtmm) REVERT: C 21 MET cc_start: 0.8747 (ttm) cc_final: 0.8268 (tpp) REVERT: R 221 LYS cc_start: 0.7219 (pttt) cc_final: 0.6460 (mmtm) REVERT: R 222 ARG cc_start: 0.8420 (mmp-170) cc_final: 0.8172 (mmp80) REVERT: B 249 MET cc_start: 0.8263 (tpp) cc_final: 0.8023 (tpp) outliers start: 17 outliers final: 16 residues processed: 137 average time/residue: 0.2310 time to fit residues: 42.9318 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain C residue 57 SER 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 184 ILE Chi-restraints excluded: chain R residue 207 LEU 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 79 optimal weight: 10.0000 chunk 12 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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** ** B 331 ASN ** 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 = 0.3658 r_free = 0.3658 target = 0.091810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.069671 restraints weight = 23096.903| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.32 r_work: 0.3086 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8793 Z= 0.173 Angle : 0.612 13.582 11942 Z= 0.321 Chirality : 0.041 0.152 1389 Planarity : 0.003 0.040 1504 Dihedral : 4.495 56.529 1206 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.72 % Allowed : 19.18 % Favored : 79.09 % 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: 0.79 (0.25), residues: 1101 helix: 1.86 (0.27), residues: 393 sheet: 0.28 (0.30), residues: 265 loop : -0.48 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 100 HIS 0.004 0.001 HIS B 189 PHE 0.020 0.001 PHE B 288 TYR 0.016 0.001 TYR E 190 ARG 0.012 0.001 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.51 seconds wall clock time: 42 minutes 34.07 seconds (2554.07 seconds total)