Starting phenix.real_space_refine on Thu Mar 13 02:36:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yjn_33875/03_2025/7yjn_33875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yjn_33875/03_2025/7yjn_33875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yjn_33875/03_2025/7yjn_33875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yjn_33875/03_2025/7yjn_33875.map" model { file = "/net/cci-nas-00/data/ceres_data/7yjn_33875/03_2025/7yjn_33875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yjn_33875/03_2025/7yjn_33875.cif" } resolution = 3.4 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= 0.101 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 5476 2.51 5 N 1445 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8528 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3230 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "B" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3592 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1122 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 131} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 186 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 383 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.21, per 1000 atoms: 0.61 Number of scatterers: 8528 At special positions: 0 Unit cell: (89.64, 82.08, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 1 15.00 O 1557 8.00 N 1445 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 51.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.857A pdb=" N ASP A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 3.546A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.812A pdb=" N LEU A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.615A pdb=" N THR A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Proline residue: A 187 - end of helix removed outlier: 3.711A pdb=" N CYS A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.552A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.697A pdb=" N ILE A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.777A pdb=" N HIS A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 349 through 365 removed outlier: 3.618A pdb=" N ALA A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 460 through 480 removed outlier: 3.714A pdb=" N LEU A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 36 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.913A pdb=" N ARG B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 169 through 182 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.792A pdb=" N LEU B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.884A pdb=" N GLY B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.682A pdb=" N GLN B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 369 through 389 removed outlier: 3.596A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.553A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 Processing helix chain 'D' and resid 25 through 45 removed outlier: 3.791A pdb=" N MET D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 71 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 99 through 119 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 124 through 141 removed outlier: 3.708A pdb=" N LYS D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 54 removed outlier: 3.563A pdb=" N ARG E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 21 through 47 removed outlier: 3.845A pdb=" N VAL C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 33 " --> pdb=" O ASN C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.648A pdb=" N VAL A 278 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 311 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 280 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ALA A 313 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A 247 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 279 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 249 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP A 281 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA A 251 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 195 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 250 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 392 removed outlier: 3.699A pdb=" N VAL A 435 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 85 removed outlier: 6.147A pdb=" N GLU B 83 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 96 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 85 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.636A pdb=" N ALA B 163 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 304 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 191 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 212 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.501A pdb=" N MET B 401 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 442 " --> pdb=" O MET B 401 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1224 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: 2.18 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: 1.13 - 1.27: 1363 1.27 - 1.40: 2196 1.40 - 1.54: 5003 1.54 - 1.67: 80 1.67 - 1.81: 76 Bond restraints: 8718 Sorted by residual: bond pdb=" CA THR D 64 " pdb=" C THR D 64 " ideal model delta sigma weight residual 1.522 1.396 0.126 1.37e-02 5.33e+03 8.46e+01 bond pdb=" C LEU B 103 " pdb=" N ASN B 104 " ideal model delta sigma weight residual 1.331 1.203 0.129 1.40e-02 5.10e+03 8.43e+01 bond pdb=" C LEU B 103 " pdb=" O LEU B 103 " ideal model delta sigma weight residual 1.234 1.130 0.105 1.15e-02 7.56e+03 8.31e+01 bond pdb=" CA LEU B 103 " pdb=" C LEU B 103 " ideal model delta sigma weight residual 1.520 1.414 0.107 1.20e-02 6.94e+03 7.89e+01 bond pdb=" C CYS B 102 " pdb=" O CYS B 102 " ideal model delta sigma weight residual 1.235 1.133 0.103 1.26e-02 6.30e+03 6.64e+01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 11388 4.26 - 8.51: 367 8.51 - 12.77: 45 12.77 - 17.03: 10 17.03 - 21.28: 6 Bond angle restraints: 11816 Sorted by residual: angle pdb=" N PHE A 189 " pdb=" CA PHE A 189 " pdb=" C PHE A 189 " ideal model delta sigma weight residual 113.16 130.33 -17.17 1.24e+00 6.50e-01 1.92e+02 angle pdb=" C ILE C 8 " pdb=" CA ILE C 8 " pdb=" CB ILE C 8 " ideal model delta sigma weight residual 111.97 98.11 13.86 1.28e+00 6.10e-01 1.17e+02 angle pdb=" C MET D 71 " pdb=" N LYS D 72 " pdb=" CA LYS D 72 " ideal model delta sigma weight residual 122.19 109.66 12.53 1.41e+00 5.03e-01 7.90e+01 angle pdb=" C PHE D 142 " pdb=" N PRO D 143 " pdb=" CA PRO D 143 " ideal model delta sigma weight residual 119.84 130.64 -10.80 1.25e+00 6.40e-01 7.46e+01 angle pdb=" C VAL B 223 " pdb=" CA VAL B 223 " pdb=" CB VAL B 223 " ideal model delta sigma weight residual 112.14 101.03 11.11 1.35e+00 5.49e-01 6.77e+01 ... (remaining 11811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4540 17.95 - 35.89: 499 35.89 - 53.83: 132 53.83 - 71.78: 17 71.78 - 89.72: 4 Dihedral angle restraints: 5192 sinusoidal: 2029 harmonic: 3163 Sorted by residual: dihedral pdb=" C PHE A 183 " pdb=" N PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta harmonic sigma weight residual -122.60 -151.10 28.50 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N PHE A 183 " pdb=" C PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta harmonic sigma weight residual 122.80 150.73 -27.93 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " ideal model delta harmonic sigma weight residual 122.80 143.93 -21.13 0 2.50e+00 1.60e-01 7.14e+01 ... (remaining 5189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1272 0.261 - 0.522: 51 0.522 - 0.782: 14 0.782 - 1.043: 0 1.043 - 1.304: 2 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CA PHE A 183 " pdb=" N PHE A 183 " pdb=" C PHE A 183 " pdb=" CB PHE A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.25e+01 chirality pdb=" CA LEU B 259 " pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CB LEU B 259 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CG LEU D 129 " pdb=" CB LEU D 129 " pdb=" CD1 LEU D 129 " pdb=" CD2 LEU D 129 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 1336 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 186 " -0.145 5.00e-02 4.00e+02 2.18e-01 7.59e+01 pdb=" N PRO A 187 " 0.377 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.121 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.110 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 68 " -0.026 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C PHE D 68 " 0.087 2.00e-02 2.50e+03 pdb=" O PHE D 68 " -0.033 2.00e-02 2.50e+03 pdb=" N HIS D 69 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 229 " -0.023 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C ALA B 229 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA B 229 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU B 230 " -0.028 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 45 2.40 - 3.03: 5810 3.03 - 3.65: 12168 3.65 - 4.28: 17359 4.28 - 4.90: 30608 Nonbonded interactions: 65990 Sorted by model distance: nonbonded pdb=" O GLY B 314 " pdb=" OE1 GLN B 350 " model vdw 1.776 3.040 nonbonded pdb=" OD1 ASP B 27 " pdb=" NH2 ARG B 58 " model vdw 1.869 3.120 nonbonded pdb=" OE1 GLN B 24 " pdb=" CE2 PHE B 54 " model vdw 1.908 3.340 nonbonded pdb=" O ALA B 229 " pdb=" N GLY B 231 " model vdw 1.910 3.120 nonbonded pdb=" O THR D 28 " pdb=" C THR D 29 " model vdw 1.946 3.270 ... (remaining 65985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.980 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.680 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.019 0.149 8718 Z= 1.235 Angle : 1.743 21.282 11816 Z= 1.050 Chirality : 0.133 1.304 1339 Planarity : 0.011 0.218 1486 Dihedral : 15.887 89.725 3162 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 1.94 % Allowed : 11.10 % Favored : 86.96 % Rotamer: Outliers : 8.37 % Allowed : 7.28 % Favored : 84.35 % Cbeta Deviations : 2.07 % Peptide Plane: Cis-proline : 0.00 % 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: -2.39 (0.25), residues: 1081 helix: -0.36 (0.22), residues: 543 sheet: -3.45 (0.48), residues: 80 loop : -2.75 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP D 70 HIS 0.019 0.003 HIS B 61 PHE 0.042 0.004 PHE B 20 TYR 0.029 0.003 TYR B 406 ARG 0.010 0.001 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 126 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6702 (mmt) REVERT: A 368 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7407 (t0) REVERT: A 388 LYS cc_start: 0.7788 (mttp) cc_final: 0.6983 (tttp) REVERT: A 473 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7825 (ttm170) REVERT: B 28 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 90 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.6954 (t0) REVERT: B 94 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8333 (ttpp) REVERT: B 113 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 222 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7122 (ttm170) REVERT: D 24 PRO cc_start: 0.8738 (OUTLIER) cc_final: 0.8500 (Cg_endo) REVERT: D 30 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7677 (t80) REVERT: D 72 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8778 (mttt) REVERT: D 113 TYR cc_start: 0.8295 (t80) cc_final: 0.6948 (t80) REVERT: D 122 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: D 128 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7547 (t80) REVERT: C 2 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.6230 (p0) outliers start: 77 outliers final: 39 residues processed: 191 average time/residue: 0.2247 time to fit residues: 57.7033 Evaluate side-chains 157 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 105 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 24 PRO Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 375 GLN B 61 HIS B 195 HIS B 200 ASN B 214 HIS B 227 GLN B 279 HIS D 84 ASN D 97 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.116246 restraints weight = 12350.472| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.32 r_work: 0.3247 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8718 Z= 0.251 Angle : 0.751 9.946 11816 Z= 0.394 Chirality : 0.047 0.185 1339 Planarity : 0.006 0.061 1486 Dihedral : 9.161 58.991 1296 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.23 % Favored : 91.30 % Rotamer: Outliers : 4.67 % Allowed : 13.37 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.26), residues: 1081 helix: 0.66 (0.22), residues: 561 sheet: -2.95 (0.52), residues: 80 loop : -2.53 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 239 HIS 0.006 0.001 HIS D 124 PHE 0.039 0.002 PHE A 183 TYR 0.019 0.002 TYR B 85 ARG 0.005 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7296 (t-170) REVERT: A 368 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7030 (t0) REVERT: A 473 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8005 (ttp80) REVERT: B 107 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8506 (p) REVERT: B 199 VAL cc_start: 0.8833 (t) cc_final: 0.8556 (p) REVERT: D 30 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7645 (t80) REVERT: D 92 MET cc_start: 0.8278 (mmm) cc_final: 0.7783 (tpt) outliers start: 43 outliers final: 20 residues processed: 158 average time/residue: 0.2130 time to fit residues: 46.1415 Evaluate side-chains 144 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 93 optimal weight: 0.0040 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN B 195 HIS D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121394 restraints weight = 12705.827| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.34 r_work: 0.3311 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8718 Z= 0.213 Angle : 0.652 7.110 11816 Z= 0.344 Chirality : 0.044 0.195 1339 Planarity : 0.005 0.056 1486 Dihedral : 7.328 59.852 1229 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.57 % Favored : 93.06 % Rotamer: Outliers : 3.91 % Allowed : 16.20 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1081 helix: 1.23 (0.22), residues: 560 sheet: -2.66 (0.54), residues: 80 loop : -2.45 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 126 HIS 0.005 0.001 HIS B 214 PHE 0.032 0.001 PHE A 183 TYR 0.016 0.001 TYR D 83 ARG 0.005 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7365 (t-170) REVERT: A 335 GLN cc_start: 0.8411 (tt0) cc_final: 0.8167 (tt0) REVERT: A 368 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7254 (t0) REVERT: A 407 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8079 (mttt) REVERT: A 413 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7662 (tmtt) REVERT: B 199 VAL cc_start: 0.8807 (t) cc_final: 0.8516 (p) REVERT: D 30 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7549 (t80) REVERT: D 97 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7610 (mt0) outliers start: 36 outliers final: 23 residues processed: 146 average time/residue: 0.2101 time to fit residues: 42.1741 Evaluate side-chains 136 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 0.0470 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN B 195 HIS D 84 ASN D 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122522 restraints weight = 12485.754| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.27 r_work: 0.3352 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8718 Z= 0.176 Angle : 0.604 7.690 11816 Z= 0.314 Chirality : 0.043 0.161 1339 Planarity : 0.005 0.053 1486 Dihedral : 6.416 58.492 1217 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Rotamer: Outliers : 3.91 % Allowed : 17.28 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.27), residues: 1081 helix: 1.45 (0.22), residues: 567 sheet: -2.09 (0.50), residues: 105 loop : -2.30 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 239 HIS 0.003 0.001 HIS B 214 PHE 0.028 0.001 PHE A 183 TYR 0.015 0.001 TYR D 83 ARG 0.006 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.7343 (t-170) REVERT: A 182 MET cc_start: 0.8015 (mmm) cc_final: 0.7268 (mmt) REVERT: A 335 GLN cc_start: 0.8417 (tt0) cc_final: 0.8179 (tt0) REVERT: A 388 LYS cc_start: 0.7904 (mttm) cc_final: 0.7074 (tttp) REVERT: A 407 LYS cc_start: 0.8499 (mmtp) cc_final: 0.8149 (mttt) REVERT: A 413 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7736 (tmtt) REVERT: B 199 VAL cc_start: 0.8754 (t) cc_final: 0.8467 (p) REVERT: B 400 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (m) REVERT: D 30 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7661 (t80) outliers start: 36 outliers final: 26 residues processed: 155 average time/residue: 0.2398 time to fit residues: 51.5637 Evaluate side-chains 145 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 92 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN D 84 ASN D 144 ASN C 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122715 restraints weight = 12588.212| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.35 r_work: 0.3328 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8718 Z= 0.197 Angle : 0.611 8.706 11816 Z= 0.315 Chirality : 0.043 0.152 1339 Planarity : 0.005 0.051 1486 Dihedral : 6.212 55.925 1214 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.38 % Favored : 93.34 % Rotamer: Outliers : 4.57 % Allowed : 18.26 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.27), residues: 1081 helix: 1.51 (0.22), residues: 568 sheet: -1.85 (0.53), residues: 93 loop : -2.14 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 PHE 0.030 0.001 PHE A 183 TYR 0.013 0.001 TYR D 83 ARG 0.006 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7367 (t-170) REVERT: A 182 MET cc_start: 0.8145 (mmm) cc_final: 0.7907 (mmt) REVERT: A 335 GLN cc_start: 0.8443 (tt0) cc_final: 0.8173 (tt0) REVERT: A 388 LYS cc_start: 0.7983 (mttm) cc_final: 0.7178 (tttp) REVERT: A 407 LYS cc_start: 0.8426 (mmtp) cc_final: 0.8122 (mttt) REVERT: A 413 LYS cc_start: 0.8229 (mmtm) cc_final: 0.7730 (tmtt) REVERT: B 199 VAL cc_start: 0.8762 (t) cc_final: 0.8472 (p) REVERT: B 299 THR cc_start: 0.8490 (p) cc_final: 0.8162 (p) REVERT: B 466 LEU cc_start: 0.8215 (tt) cc_final: 0.7998 (tt) REVERT: D 30 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7602 (t80) REVERT: C 6 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8352 (mtm180) outliers start: 42 outliers final: 28 residues processed: 149 average time/residue: 0.2471 time to fit residues: 51.1961 Evaluate side-chains 144 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121265 restraints weight = 12507.665| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.33 r_work: 0.3310 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8718 Z= 0.240 Angle : 0.625 8.360 11816 Z= 0.321 Chirality : 0.043 0.154 1339 Planarity : 0.005 0.051 1486 Dihedral : 6.123 53.917 1212 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.75 % Favored : 92.97 % Rotamer: Outliers : 4.78 % Allowed : 18.26 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.27), residues: 1081 helix: 1.59 (0.22), residues: 560 sheet: -1.90 (0.51), residues: 105 loop : -2.10 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 PHE 0.031 0.002 PHE A 183 TYR 0.016 0.001 TYR C 9 ARG 0.006 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: A 125 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7438 (t-170) REVERT: A 335 GLN cc_start: 0.8483 (tt0) cc_final: 0.8233 (tt0) REVERT: A 388 LYS cc_start: 0.7990 (mttm) cc_final: 0.7172 (tttp) REVERT: A 407 LYS cc_start: 0.8416 (mmtp) cc_final: 0.8139 (mttt) REVERT: A 413 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7740 (tmtt) REVERT: B 199 VAL cc_start: 0.8771 (t) cc_final: 0.8485 (p) REVERT: B 299 THR cc_start: 0.8598 (p) cc_final: 0.8261 (p) REVERT: B 417 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8096 (mm-30) REVERT: D 30 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7713 (t80) REVERT: C 6 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8355 (mtm180) outliers start: 44 outliers final: 31 residues processed: 148 average time/residue: 0.2686 time to fit residues: 54.8379 Evaluate side-chains 144 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118924 restraints weight = 12468.575| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.45 r_work: 0.3274 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8718 Z= 0.192 Angle : 0.602 8.674 11816 Z= 0.310 Chirality : 0.042 0.154 1339 Planarity : 0.005 0.052 1486 Dihedral : 6.029 51.548 1212 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.20 % Favored : 93.62 % Rotamer: Outliers : 3.80 % Allowed : 19.13 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.27), residues: 1081 helix: 1.61 (0.22), residues: 563 sheet: -1.67 (0.54), residues: 93 loop : -1.97 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 PHE 0.028 0.001 PHE A 183 TYR 0.012 0.001 TYR D 83 ARG 0.008 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: A 125 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7445 (t-170) REVERT: A 182 MET cc_start: 0.8086 (mmp) cc_final: 0.7751 (mmt) REVERT: A 335 GLN cc_start: 0.8517 (tt0) cc_final: 0.8244 (tt0) REVERT: A 388 LYS cc_start: 0.7906 (mttm) cc_final: 0.7088 (tttp) REVERT: A 413 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7719 (tmtt) REVERT: B 29 PHE cc_start: 0.7433 (t80) cc_final: 0.7036 (m-80) REVERT: B 199 VAL cc_start: 0.8723 (t) cc_final: 0.8432 (p) REVERT: B 299 THR cc_start: 0.8569 (p) cc_final: 0.8238 (p) REVERT: B 417 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8101 (mm-30) REVERT: C 6 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8308 (mtm180) outliers start: 35 outliers final: 31 residues processed: 140 average time/residue: 0.2128 time to fit residues: 40.8122 Evaluate side-chains 143 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN B 24 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117651 restraints weight = 12562.267| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.38 r_work: 0.3273 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8718 Z= 0.214 Angle : 0.615 8.753 11816 Z= 0.316 Chirality : 0.043 0.151 1339 Planarity : 0.005 0.052 1486 Dihedral : 5.914 51.957 1210 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.88 % Rotamer: Outliers : 4.57 % Allowed : 18.91 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.27), residues: 1081 helix: 1.59 (0.22), residues: 566 sheet: -1.80 (0.52), residues: 105 loop : -1.97 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 PHE 0.029 0.001 PHE A 183 TYR 0.017 0.001 TYR C 9 ARG 0.007 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7259 (pm20) REVERT: A 125 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7467 (t-170) REVERT: A 335 GLN cc_start: 0.8508 (tt0) cc_final: 0.8227 (tt0) REVERT: A 388 LYS cc_start: 0.7923 (mttm) cc_final: 0.7123 (tttp) REVERT: A 413 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7732 (tmtt) REVERT: B 199 VAL cc_start: 0.8780 (t) cc_final: 0.8497 (p) REVERT: B 299 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8230 (p) REVERT: D 30 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7696 (t80) REVERT: C 6 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8270 (mtm180) outliers start: 42 outliers final: 32 residues processed: 144 average time/residue: 0.2087 time to fit residues: 41.4411 Evaluate side-chains 147 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 97 optimal weight: 0.9980 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119166 restraints weight = 12616.782| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.46 r_work: 0.3273 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8718 Z= 0.197 Angle : 0.614 11.023 11816 Z= 0.314 Chirality : 0.042 0.151 1339 Planarity : 0.005 0.052 1486 Dihedral : 5.850 52.391 1210 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.11 % Favored : 93.71 % Rotamer: Outliers : 3.91 % Allowed : 19.57 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.27), residues: 1081 helix: 1.64 (0.23), residues: 566 sheet: -1.86 (0.48), residues: 115 loop : -1.92 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 PHE 0.028 0.001 PHE A 183 TYR 0.011 0.001 TYR D 83 ARG 0.007 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: A 125 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7493 (t-170) REVERT: A 388 LYS cc_start: 0.7932 (mttm) cc_final: 0.7098 (tttp) REVERT: A 413 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7689 (tmtt) REVERT: B 199 VAL cc_start: 0.8741 (t) cc_final: 0.8450 (p) REVERT: B 299 THR cc_start: 0.8517 (p) cc_final: 0.8189 (p) REVERT: D 30 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7667 (t80) REVERT: C 6 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8254 (mtm180) outliers start: 36 outliers final: 31 residues processed: 139 average time/residue: 0.2161 time to fit residues: 41.2645 Evaluate side-chains 143 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 45 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.148087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122297 restraints weight = 12438.987| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.43 r_work: 0.3317 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8718 Z= 0.161 Angle : 0.586 10.175 11816 Z= 0.299 Chirality : 0.042 0.170 1339 Planarity : 0.005 0.053 1486 Dihedral : 5.519 57.081 1207 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.11 % Favored : 93.71 % Rotamer: Outliers : 3.59 % Allowed : 19.89 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.27), residues: 1081 helix: 1.75 (0.23), residues: 565 sheet: -1.73 (0.48), residues: 114 loop : -1.88 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 239 HIS 0.003 0.001 HIS B 214 PHE 0.033 0.001 PHE D 61 TYR 0.021 0.001 TYR C 9 ARG 0.006 0.000 ARG E 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: A 125 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7476 (t-170) REVERT: A 246 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7523 (ptt-90) REVERT: A 388 LYS cc_start: 0.7895 (mttm) cc_final: 0.7073 (tttp) REVERT: A 413 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7611 (tmtt) REVERT: B 117 ASP cc_start: 0.8394 (p0) cc_final: 0.8087 (p0) REVERT: B 118 GLU cc_start: 0.7866 (mp0) cc_final: 0.7601 (tp30) REVERT: B 199 VAL cc_start: 0.8600 (t) cc_final: 0.8311 (p) REVERT: B 299 THR cc_start: 0.8436 (p) cc_final: 0.8100 (p) REVERT: D 30 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7713 (t80) REVERT: D 97 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7524 (mt0) REVERT: C 6 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8239 (mtm180) outliers start: 33 outliers final: 24 residues processed: 147 average time/residue: 0.2078 time to fit residues: 42.3987 Evaluate side-chains 141 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120113 restraints weight = 12514.075| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.38 r_work: 0.3303 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8718 Z= 0.196 Angle : 0.616 11.676 11816 Z= 0.314 Chirality : 0.042 0.160 1339 Planarity : 0.005 0.054 1486 Dihedral : 5.424 58.571 1205 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.20 % Favored : 93.62 % Rotamer: Outliers : 3.59 % Allowed : 20.65 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.27), residues: 1081 helix: 1.68 (0.23), residues: 572 sheet: -1.69 (0.48), residues: 115 loop : -1.85 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 239 HIS 0.003 0.001 HIS B 214 PHE 0.030 0.001 PHE A 183 TYR 0.019 0.001 TYR D 83 ARG 0.007 0.000 ARG E 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3647.40 seconds wall clock time: 65 minutes 13.54 seconds (3913.54 seconds total)