Starting phenix.real_space_refine on Wed Mar 4 10:12:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sd0_25044/03_2026/7sd0_25044.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sd0_25044/03_2026/7sd0_25044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sd0_25044/03_2026/7sd0_25044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sd0_25044/03_2026/7sd0_25044.map" model { file = "/net/cci-nas-00/data/ceres_data/7sd0_25044/03_2026/7sd0_25044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sd0_25044/03_2026/7sd0_25044.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6177 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 4911 2.51 5 N 1316 2.21 5 O 1456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7729 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3930 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 25, 'TRANS': 473} Chain breaks: 1 Chain: "B" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1407 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 165} Chain: "C" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2357 Classifications: {'peptide': 292} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 278} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.01, per 1000 atoms: 0.26 Number of scatterers: 7729 At special positions: 0 Unit cell: (89.666, 85.476, 104.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 2 24.99 S 40 16.00 P 3 15.00 Mg 1 11.99 O 1456 8.00 N 1316 7.00 C 4911 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=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 35.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.539A pdb=" N LEU A 191 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.709A pdb=" N GLY A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.547A pdb=" N ILE A 257 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 258 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.736A pdb=" N GLY A 281 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.972A pdb=" N SER A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.539A pdb=" N PHE A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 removed outlier: 4.368A pdb=" N GLY A 399 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.511A pdb=" N VAL A 421 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.553A pdb=" N GLY A 445 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 447 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.593A pdb=" N ILE A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 removed outlier: 3.834A pdb=" N ILE A 513 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 557 through 564 removed outlier: 3.737A pdb=" N GLY A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.754A pdb=" N THR B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 115 removed outlier: 3.958A pdb=" N PHE B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 137 through 148 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.693A pdb=" N PHE B 168 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.805A pdb=" N ILE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 80 removed outlier: 3.585A pdb=" N LEU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 74 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.549A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.501A pdb=" N CYS C 127 " --> pdb=" O ASN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.876A pdb=" N ILE C 133 " --> pdb=" O SER C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 144 removed outlier: 3.549A pdb=" N LYS C 141 " --> pdb=" O TYR C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.651A pdb=" N LYS C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 removed outlier: 4.261A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 207 removed outlier: 3.805A pdb=" N ASP C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 removed outlier: 3.806A pdb=" N VAL C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.757A pdb=" N ALA A 65 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N PHE C 293 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS C 60 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.788A pdb=" N LEU A 105 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 289 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN A 313 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 312 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 361 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.612A pdb=" N ASP A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 453 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 499 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 523 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 522 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.116A pdb=" N TYR B 14 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 66 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 16 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 88 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 124 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 90 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN B 126 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR B 92 " --> pdb=" O ASN B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 52 through 55 removed outlier: 6.001A pdb=" N LEU C 53 " --> pdb=" O ILE C 164 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1309 1.30 - 1.43: 1865 1.43 - 1.56: 4627 1.56 - 1.69: 7 1.69 - 1.82: 61 Bond restraints: 7869 Sorted by residual: bond pdb=" CA ASP C 92 " pdb=" C ASP C 92 " ideal model delta sigma weight residual 1.532 1.462 0.070 9.60e-03 1.09e+04 5.33e+01 bond pdb=" C ASP C 208 " pdb=" O ASP C 208 " ideal model delta sigma weight residual 1.240 1.170 0.070 1.24e-02 6.50e+03 3.21e+01 bond pdb=" CA HIS C 125 " pdb=" C HIS C 125 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.66e-02 3.63e+03 2.74e+01 bond pdb=" CA GLN C 262 " pdb=" C GLN C 262 " ideal model delta sigma weight residual 1.522 1.452 0.070 1.40e-02 5.10e+03 2.50e+01 bond pdb=" N GLN C 262 " pdb=" CA GLN C 262 " ideal model delta sigma weight residual 1.458 1.392 0.066 1.33e-02 5.65e+03 2.45e+01 ... (remaining 7864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 10262 2.29 - 4.58: 317 4.58 - 6.87: 49 6.87 - 9.16: 23 9.16 - 11.45: 6 Bond angle restraints: 10657 Sorted by residual: angle pdb=" N SER C 268 " pdb=" CA SER C 268 " pdb=" C SER C 268 " ideal model delta sigma weight residual 112.59 121.87 -9.28 1.22e+00 6.72e-01 5.79e+01 angle pdb=" N HIS C 173 " pdb=" CA HIS C 173 " pdb=" C HIS C 173 " ideal model delta sigma weight residual 111.07 118.65 -7.58 1.07e+00 8.73e-01 5.02e+01 angle pdb=" N TYR C 69 " pdb=" CA TYR C 69 " pdb=" C TYR C 69 " ideal model delta sigma weight residual 112.38 120.62 -8.24 1.22e+00 6.72e-01 4.56e+01 angle pdb=" C ALA C 269 " pdb=" N PRO C 270 " pdb=" CA PRO C 270 " ideal model delta sigma weight residual 120.21 114.20 6.01 9.60e-01 1.09e+00 3.93e+01 angle pdb=" N TYR C 272 " pdb=" CA TYR C 272 " pdb=" C TYR C 272 " ideal model delta sigma weight residual 110.30 119.49 -9.19 1.50e+00 4.44e-01 3.76e+01 ... (remaining 10652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 4345 16.69 - 33.37: 392 33.37 - 50.06: 91 50.06 - 66.74: 13 66.74 - 83.43: 7 Dihedral angle restraints: 4848 sinusoidal: 2029 harmonic: 2819 Sorted by residual: dihedral pdb=" N ASP C 64 " pdb=" C ASP C 64 " pdb=" CA ASP C 64 " pdb=" CB ASP C 64 " ideal model delta harmonic sigma weight residual 122.80 133.86 -11.06 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" C ARG C 246 " pdb=" N ARG C 246 " pdb=" CA ARG C 246 " pdb=" CB ARG C 246 " ideal model delta harmonic sigma weight residual -122.60 -133.30 10.70 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C ARG C 96 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " pdb=" CB ARG C 96 " ideal model delta harmonic sigma weight residual -122.60 -132.33 9.73 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1104 0.091 - 0.181: 89 0.181 - 0.272: 16 0.272 - 0.363: 11 0.363 - 0.454: 8 Chirality restraints: 1228 Sorted by residual: chirality pdb=" CA ASP C 64 " pdb=" N ASP C 64 " pdb=" C ASP C 64 " pdb=" CB ASP C 64 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA ARG C 246 " pdb=" N ARG C 246 " pdb=" C ARG C 246 " pdb=" CB ARG C 246 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA ARG C 261 " pdb=" N ARG C 261 " pdb=" C ARG C 261 " pdb=" CB ARG C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1225 not shown) Planarity restraints: 1366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ILE C 295 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU C 296 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 90 " 0.018 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C LEU C 90 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU C 90 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY C 91 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 89 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C PHE C 89 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE C 89 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 90 " 0.016 2.00e-02 2.50e+03 ... (remaining 1363 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 26 2.43 - 3.05: 4865 3.05 - 3.67: 11840 3.67 - 4.28: 17782 4.28 - 4.90: 29613 Nonbonded interactions: 64126 Sorted by model distance: nonbonded pdb=" OD1 ASN C 124 " pdb="MN MN C 400 " model vdw 1.813 2.320 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 501 " model vdw 1.848 2.170 nonbonded pdb=" O GLN A 474 " pdb=" OG1 THR A 497 " model vdw 2.229 3.040 nonbonded pdb=" O THR A 494 " pdb=" ND2 ASN A 518 " model vdw 2.232 3.120 nonbonded pdb=" O GLY C 80 " pdb=" OH TYR C 87 " model vdw 2.243 3.040 ... (remaining 64121 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.007 0.099 7869 Z= 0.469 Angle : 0.972 11.454 10657 Z= 0.579 Chirality : 0.069 0.454 1228 Planarity : 0.005 0.049 1366 Dihedral : 13.551 83.428 3018 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.91 % Allowed : 2.28 % Favored : 96.81 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.27), residues: 957 helix: -1.87 (0.27), residues: 289 sheet: -1.57 (0.48), residues: 138 loop : -0.86 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.012 0.002 TYR C 93 PHE 0.011 0.001 PHE C 257 TRP 0.015 0.001 TRP C 206 HIS 0.012 0.002 HIS C 248 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 7869) covalent geometry : angle 0.97188 (10657) hydrogen bonds : bond 0.29094 ( 220) hydrogen bonds : angle 8.61469 ( 510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 446 ASN cc_start: 0.7828 (m110) cc_final: 0.7468 (m110) REVERT: C 31 GLN cc_start: 0.7339 (mt0) cc_final: 0.6813 (tm-30) REVERT: C 32 GLU cc_start: 0.7889 (pm20) cc_final: 0.7668 (pm20) REVERT: C 219 ASN cc_start: 0.7288 (m110) cc_final: 0.6951 (m110) outliers start: 8 outliers final: 3 residues processed: 129 average time/residue: 0.5544 time to fit residues: 75.7358 Evaluate side-chains 80 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 chunk 74 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 498 HIS B 58 ASN B 71 GLN B 148 HIS C 125 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.115526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091435 restraints weight = 16632.280| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.73 r_work: 0.3540 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7869 Z= 0.128 Angle : 0.636 8.596 10657 Z= 0.326 Chirality : 0.043 0.156 1228 Planarity : 0.004 0.041 1366 Dihedral : 5.710 76.139 1072 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.48 % Allowed : 11.16 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.27), residues: 957 helix: -1.07 (0.29), residues: 300 sheet: -1.70 (0.39), residues: 171 loop : -0.71 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.022 0.001 TYR A 469 PHE 0.024 0.001 PHE A 571 TRP 0.007 0.001 TRP C 206 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7869) covalent geometry : angle 0.63616 (10657) hydrogen bonds : bond 0.04888 ( 220) hydrogen bonds : angle 5.58934 ( 510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 ASN cc_start: 0.7704 (m110) cc_final: 0.7303 (m110) REVERT: B 59 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7554 (mm-40) REVERT: C 31 GLN cc_start: 0.7253 (mt0) cc_final: 0.6616 (tm-30) REVERT: C 32 GLU cc_start: 0.8348 (pm20) cc_final: 0.7689 (pm20) REVERT: C 34 GLU cc_start: 0.8179 (mp0) cc_final: 0.7909 (mp0) REVERT: C 183 MET cc_start: 0.8011 (mpp) cc_final: 0.7765 (mpp) REVERT: C 283 MET cc_start: 0.8232 (ttm) cc_final: 0.7989 (ttm) outliers start: 13 outliers final: 3 residues processed: 99 average time/residue: 0.5468 time to fit residues: 57.6640 Evaluate side-chains 76 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 344 GLN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.110196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.085412 restraints weight = 17148.218| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.80 r_work: 0.3397 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7869 Z= 0.267 Angle : 0.721 8.565 10657 Z= 0.368 Chirality : 0.046 0.153 1228 Planarity : 0.004 0.048 1366 Dihedral : 5.737 74.158 1068 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.94 % Allowed : 13.78 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.26), residues: 957 helix: -1.17 (0.29), residues: 303 sheet: -2.15 (0.38), residues: 176 loop : -0.95 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 43 TYR 0.019 0.002 TYR C 70 PHE 0.019 0.002 PHE A 66 TRP 0.006 0.002 TRP B 60 HIS 0.009 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 7869) covalent geometry : angle 0.72064 (10657) hydrogen bonds : bond 0.05243 ( 220) hydrogen bonds : angle 5.75938 ( 510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.323 Fit side-chains REVERT: A 127 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: A 332 LYS cc_start: 0.8624 (tptp) cc_final: 0.8378 (tptp) REVERT: A 446 ASN cc_start: 0.7711 (m110) cc_final: 0.7304 (m110) REVERT: B 59 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7546 (mm-40) REVERT: B 96 ASP cc_start: 0.7856 (t70) cc_final: 0.7244 (p0) REVERT: C 32 GLU cc_start: 0.8504 (pm20) cc_final: 0.8221 (pm20) REVERT: C 33 ASN cc_start: 0.8648 (p0) cc_final: 0.8021 (p0) REVERT: C 34 GLU cc_start: 0.8332 (mp0) cc_final: 0.7580 (mp0) REVERT: C 183 MET cc_start: 0.8334 (mpp) cc_final: 0.8079 (mpp) outliers start: 17 outliers final: 7 residues processed: 89 average time/residue: 0.5472 time to fit residues: 51.9627 Evaluate side-chains 79 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 317 ASN B 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.113207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088056 restraints weight = 17276.613| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.92 r_work: 0.3452 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7869 Z= 0.135 Angle : 0.612 9.984 10657 Z= 0.312 Chirality : 0.042 0.149 1228 Planarity : 0.004 0.045 1366 Dihedral : 5.192 62.488 1068 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.16 % Allowed : 14.58 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.27), residues: 957 helix: -1.05 (0.29), residues: 316 sheet: -2.17 (0.37), residues: 175 loop : -0.85 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.012 0.001 TYR C 70 PHE 0.022 0.002 PHE A 571 TRP 0.004 0.001 TRP B 60 HIS 0.008 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7869) covalent geometry : angle 0.61181 (10657) hydrogen bonds : bond 0.04088 ( 220) hydrogen bonds : angle 5.26845 ( 510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: A 332 LYS cc_start: 0.8648 (tptp) cc_final: 0.8391 (tptp) REVERT: A 446 ASN cc_start: 0.7586 (m110) cc_final: 0.7164 (m110) REVERT: A 535 PHE cc_start: 0.9005 (m-80) cc_final: 0.8539 (t80) REVERT: B 59 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7529 (mm-40) REVERT: C 32 GLU cc_start: 0.8475 (pm20) cc_final: 0.8157 (pm20) REVERT: C 33 ASN cc_start: 0.8589 (p0) cc_final: 0.8303 (OUTLIER) REVERT: C 183 MET cc_start: 0.8214 (mpp) cc_final: 0.7998 (mpp) outliers start: 19 outliers final: 8 residues processed: 101 average time/residue: 0.5115 time to fit residues: 55.3988 Evaluate side-chains 83 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.112456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.087762 restraints weight = 16976.476| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.82 r_work: 0.3437 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7869 Z= 0.155 Angle : 0.632 13.164 10657 Z= 0.320 Chirality : 0.042 0.147 1228 Planarity : 0.004 0.045 1366 Dihedral : 5.186 62.046 1068 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.62 % Allowed : 15.83 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.27), residues: 957 helix: -1.00 (0.29), residues: 316 sheet: -2.21 (0.38), residues: 174 loop : -0.88 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.013 0.001 TYR C 70 PHE 0.015 0.001 PHE C 258 TRP 0.005 0.001 TRP A 401 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7869) covalent geometry : angle 0.63242 (10657) hydrogen bonds : bond 0.04036 ( 220) hydrogen bonds : angle 5.19402 ( 510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.321 Fit side-chains REVERT: A 127 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: A 332 LYS cc_start: 0.8642 (tptp) cc_final: 0.8373 (tptp) REVERT: A 446 ASN cc_start: 0.7581 (m110) cc_final: 0.7166 (m110) REVERT: A 535 PHE cc_start: 0.8984 (m-80) cc_final: 0.8630 (t80) REVERT: B 59 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7509 (mm-40) REVERT: B 96 ASP cc_start: 0.7836 (t70) cc_final: 0.7158 (p0) REVERT: C 32 GLU cc_start: 0.8523 (pm20) cc_final: 0.8208 (pm20) REVERT: C 33 ASN cc_start: 0.8553 (p0) cc_final: 0.8154 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: C 183 MET cc_start: 0.8242 (mpp) cc_final: 0.8023 (mpp) outliers start: 23 outliers final: 8 residues processed: 91 average time/residue: 0.5117 time to fit residues: 49.8604 Evaluate side-chains 81 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 79 optimal weight: 0.0870 chunk 82 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.114234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.089594 restraints weight = 16856.828| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.83 r_work: 0.3481 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7869 Z= 0.115 Angle : 0.609 13.904 10657 Z= 0.305 Chirality : 0.041 0.149 1228 Planarity : 0.004 0.044 1366 Dihedral : 4.983 59.096 1068 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.71 % Allowed : 16.63 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.27), residues: 957 helix: -0.87 (0.29), residues: 316 sheet: -2.03 (0.37), residues: 193 loop : -0.79 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 43 TYR 0.018 0.001 TYR A 469 PHE 0.018 0.001 PHE C 258 TRP 0.007 0.001 TRP A 401 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7869) covalent geometry : angle 0.60865 (10657) hydrogen bonds : bond 0.03583 ( 220) hydrogen bonds : angle 4.99640 ( 510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.332 Fit side-chains REVERT: A 103 MET cc_start: 0.7493 (mmm) cc_final: 0.6978 (mmp) REVERT: A 127 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: A 332 LYS cc_start: 0.8656 (tptp) cc_final: 0.8407 (tptp) REVERT: A 446 ASN cc_start: 0.7550 (m110) cc_final: 0.7139 (m110) REVERT: A 535 PHE cc_start: 0.9041 (m-80) cc_final: 0.8652 (t80) REVERT: B 96 ASP cc_start: 0.7730 (t70) cc_final: 0.7114 (p0) REVERT: C 32 GLU cc_start: 0.8455 (pm20) cc_final: 0.7790 (pm20) REVERT: C 33 ASN cc_start: 0.8589 (p0) cc_final: 0.8098 (m110) REVERT: C 34 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7966 (mp0) outliers start: 15 outliers final: 4 residues processed: 92 average time/residue: 0.5094 time to fit residues: 50.2648 Evaluate side-chains 79 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.0040 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.115327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.090462 restraints weight = 16900.183| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.83 r_work: 0.3514 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7869 Z= 0.109 Angle : 0.612 13.014 10657 Z= 0.308 Chirality : 0.041 0.158 1228 Planarity : 0.004 0.044 1366 Dihedral : 4.858 58.405 1068 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.71 % Allowed : 17.77 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.27), residues: 957 helix: -0.77 (0.30), residues: 311 sheet: -2.02 (0.37), residues: 183 loop : -0.83 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 43 TYR 0.014 0.001 TYR C 137 PHE 0.048 0.001 PHE C 258 TRP 0.003 0.001 TRP B 60 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7869) covalent geometry : angle 0.61188 (10657) hydrogen bonds : bond 0.03373 ( 220) hydrogen bonds : angle 4.83948 ( 510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.331 Fit side-chains REVERT: A 103 MET cc_start: 0.7432 (mmm) cc_final: 0.6883 (mmp) REVERT: A 127 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: A 332 LYS cc_start: 0.8623 (tptp) cc_final: 0.8376 (tptp) REVERT: A 446 ASN cc_start: 0.7493 (m110) cc_final: 0.7079 (m110) REVERT: A 535 PHE cc_start: 0.8961 (m-80) cc_final: 0.8543 (t80) REVERT: B 79 GLU cc_start: 0.7143 (mp0) cc_final: 0.6629 (mt-10) REVERT: C 32 GLU cc_start: 0.8465 (pm20) cc_final: 0.8054 (pm20) REVERT: C 33 ASN cc_start: 0.8657 (p0) cc_final: 0.8184 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7764 (mp0) outliers start: 15 outliers final: 6 residues processed: 92 average time/residue: 0.4654 time to fit residues: 46.1621 Evaluate side-chains 82 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.113800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.088609 restraints weight = 17233.275| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.95 r_work: 0.3444 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7869 Z= 0.125 Angle : 0.629 12.678 10657 Z= 0.317 Chirality : 0.042 0.164 1228 Planarity : 0.004 0.047 1366 Dihedral : 4.883 59.055 1067 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.37 % Allowed : 19.02 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.27), residues: 957 helix: -0.78 (0.30), residues: 311 sheet: -2.01 (0.37), residues: 183 loop : -0.79 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 43 TYR 0.016 0.001 TYR A 469 PHE 0.047 0.001 PHE C 258 TRP 0.003 0.001 TRP B 60 HIS 0.008 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7869) covalent geometry : angle 0.62871 (10657) hydrogen bonds : bond 0.03515 ( 220) hydrogen bonds : angle 4.93732 ( 510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.316 Fit side-chains REVERT: A 103 MET cc_start: 0.7422 (mmm) cc_final: 0.7150 (mmp) REVERT: A 267 ASP cc_start: 0.5075 (t70) cc_final: 0.4581 (t0) REVERT: A 332 LYS cc_start: 0.8676 (tptp) cc_final: 0.8409 (tptp) REVERT: A 446 ASN cc_start: 0.7498 (m110) cc_final: 0.7079 (m110) REVERT: A 535 PHE cc_start: 0.8978 (m-80) cc_final: 0.8556 (t80) REVERT: B 79 GLU cc_start: 0.7245 (mp0) cc_final: 0.6702 (mt-10) REVERT: B 96 ASP cc_start: 0.7739 (t70) cc_final: 0.7192 (p0) REVERT: C 32 GLU cc_start: 0.8492 (pm20) cc_final: 0.8074 (pm20) REVERT: C 33 ASN cc_start: 0.8653 (p0) cc_final: 0.8159 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7753 (mp0) outliers start: 12 outliers final: 7 residues processed: 85 average time/residue: 0.4852 time to fit residues: 44.1790 Evaluate side-chains 80 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 0.0270 chunk 16 optimal weight: 0.0170 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 317 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN B 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.114214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.089471 restraints weight = 17065.885| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.82 r_work: 0.3486 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7869 Z= 0.125 Angle : 0.639 12.262 10657 Z= 0.322 Chirality : 0.042 0.178 1228 Planarity : 0.004 0.048 1366 Dihedral : 4.962 59.111 1067 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.37 % Allowed : 19.13 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.27), residues: 957 helix: -0.80 (0.30), residues: 310 sheet: -2.07 (0.38), residues: 173 loop : -0.90 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 43 TYR 0.016 0.001 TYR C 137 PHE 0.049 0.002 PHE A 571 TRP 0.003 0.001 TRP B 60 HIS 0.010 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7869) covalent geometry : angle 0.63949 (10657) hydrogen bonds : bond 0.03581 ( 220) hydrogen bonds : angle 4.94944 ( 510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.330 Fit side-chains REVERT: A 103 MET cc_start: 0.7681 (mmm) cc_final: 0.7083 (mmp) REVERT: A 127 GLU cc_start: 0.7433 (pt0) cc_final: 0.7215 (pm20) REVERT: A 332 LYS cc_start: 0.8671 (tptp) cc_final: 0.8443 (tptp) REVERT: A 446 ASN cc_start: 0.7498 (m110) cc_final: 0.7088 (m110) REVERT: A 535 PHE cc_start: 0.9018 (m-80) cc_final: 0.8592 (t80) REVERT: B 79 GLU cc_start: 0.7243 (mp0) cc_final: 0.6711 (mt-10) REVERT: C 32 GLU cc_start: 0.8546 (pm20) cc_final: 0.8117 (pm20) REVERT: C 33 ASN cc_start: 0.8642 (p0) cc_final: 0.8145 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7787 (mp0) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 0.5089 time to fit residues: 47.4099 Evaluate side-chains 83 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 50 optimal weight: 0.3980 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.114988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.090447 restraints weight = 17007.243| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.82 r_work: 0.3527 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7869 Z= 0.116 Angle : 0.651 11.917 10657 Z= 0.332 Chirality : 0.042 0.172 1228 Planarity : 0.004 0.048 1366 Dihedral : 4.918 58.273 1067 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.14 % Allowed : 19.70 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.27), residues: 957 helix: -0.80 (0.30), residues: 310 sheet: -2.01 (0.38), residues: 171 loop : -0.88 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 43 TYR 0.016 0.001 TYR A 469 PHE 0.067 0.002 PHE A 571 TRP 0.005 0.001 TRP A 401 HIS 0.009 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7869) covalent geometry : angle 0.65110 (10657) hydrogen bonds : bond 0.03461 ( 220) hydrogen bonds : angle 4.89784 ( 510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.312 Fit side-chains REVERT: A 103 MET cc_start: 0.7717 (mmm) cc_final: 0.7073 (mmp) REVERT: A 127 GLU cc_start: 0.7604 (pt0) cc_final: 0.7194 (pm20) REVERT: A 332 LYS cc_start: 0.8680 (tptp) cc_final: 0.8453 (tptp) REVERT: A 446 ASN cc_start: 0.7472 (m110) cc_final: 0.7060 (m110) REVERT: A 535 PHE cc_start: 0.9017 (m-80) cc_final: 0.8597 (t80) REVERT: B 79 GLU cc_start: 0.7228 (mp0) cc_final: 0.6749 (mt-10) REVERT: B 96 ASP cc_start: 0.7663 (t70) cc_final: 0.7130 (p0) REVERT: C 32 GLU cc_start: 0.8471 (pm20) cc_final: 0.8063 (pm20) REVERT: C 33 ASN cc_start: 0.8638 (p0) cc_final: 0.8144 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7743 (mp0) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.5081 time to fit residues: 45.6860 Evaluate side-chains 80 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.0000 chunk 2 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.116501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.092335 restraints weight = 16765.949| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.81 r_work: 0.3530 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7869 Z= 0.114 Angle : 0.655 11.704 10657 Z= 0.334 Chirality : 0.041 0.184 1228 Planarity : 0.004 0.049 1366 Dihedral : 4.860 57.842 1067 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.25 % Allowed : 19.82 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.27), residues: 957 helix: -0.77 (0.30), residues: 311 sheet: -1.98 (0.37), residues: 184 loop : -0.79 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.021 0.001 TYR C 137 PHE 0.077 0.002 PHE A 571 TRP 0.004 0.001 TRP A 401 HIS 0.007 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7869) covalent geometry : angle 0.65523 (10657) hydrogen bonds : bond 0.03397 ( 220) hydrogen bonds : angle 4.83557 ( 510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2728.10 seconds wall clock time: 47 minutes 10.61 seconds (2830.61 seconds total)