Starting phenix.real_space_refine on Wed Jul 30 22:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sd0_25044/07_2025/7sd0_25044.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sd0_25044/07_2025/7sd0_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_25044/07_2025/7sd0_25044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sd0_25044/07_2025/7sd0_25044.map" model { file = "/net/cci-nas-00/data/ceres_data/7sd0_25044/07_2025/7sd0_25044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sd0_25044/07_2025/7sd0_25044.cif" } resolution = 2.95 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= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.27, per 1000 atoms: 1.07 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: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.18 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: 3.81 Time building geometry restraints manager: 3.76 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 33.930 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:21.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.610 ------------------------------------------------------------------------------- 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 (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: -2.03 (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 TRP 0.015 0.001 TRP C 206 HIS 0.012 0.002 HIS C 248 PHE 0.011 0.001 PHE C 257 TYR 0.012 0.002 TYR C 93 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.29094 ( 220) hydrogen bonds : angle 8.61469 ( 510) covalent geometry : bond 0.00698 ( 7869) covalent geometry : angle 0.97188 (10657) *********************** 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 : 0.942 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: 1.2023 time to fit residues: 164.9333 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 : 0.932 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.0670 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 148 HIS C 125 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.116212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092144 restraints weight = 16568.986| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.73 r_work: 0.3552 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1786 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= 0.125 Angle : 0.631 8.620 10657 Z= 0.324 Chirality : 0.043 0.154 1228 Planarity : 0.004 0.041 1366 Dihedral : 5.666 75.994 1072 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.48 % Allowed : 11.05 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.60 (0.27), residues: 957 helix: -1.05 (0.29), residues: 300 sheet: -1.48 (0.39), residues: 180 loop : -0.74 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 206 HIS 0.008 0.001 HIS C 173 PHE 0.026 0.001 PHE A 571 TYR 0.022 0.001 TYR A 469 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 220) hydrogen bonds : angle 5.54255 ( 510) covalent geometry : bond 0.00281 ( 7869) covalent geometry : angle 0.63124 (10657) *********************** 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 108 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.7532 (t0) cc_final: 0.7299 (m-30) REVERT: A 446 ASN cc_start: 0.7692 (m110) cc_final: 0.7290 (m110) REVERT: B 59 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7551 (mm-40) REVERT: B 96 ASP cc_start: 0.7460 (t70) cc_final: 0.7221 (p0) REVERT: C 32 GLU cc_start: 0.8339 (pm20) cc_final: 0.8084 (pm20) REVERT: C 183 MET cc_start: 0.7971 (mpp) cc_final: 0.7692 (mpp) REVERT: C 283 MET cc_start: 0.8221 (ttm) cc_final: 0.7999 (ttm) outliers start: 13 outliers final: 3 residues processed: 104 average time/residue: 1.1005 time to fit residues: 122.3817 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 : 0.965 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 50.0000 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 0.0040 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.116362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.091878 restraints weight = 16886.466| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.83 r_work: 0.3557 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7869 Z= 0.117 Angle : 0.592 7.818 10657 Z= 0.303 Chirality : 0.041 0.138 1228 Planarity : 0.004 0.042 1366 Dihedral : 5.022 65.403 1068 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.48 % Allowed : 13.33 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.56 (0.27), residues: 957 helix: -0.94 (0.29), residues: 308 sheet: -1.52 (0.38), residues: 189 loop : -0.71 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 60 HIS 0.008 0.001 HIS A 247 PHE 0.018 0.001 PHE A 66 TYR 0.018 0.001 TYR A 469 ARG 0.003 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 220) hydrogen bonds : angle 5.14123 ( 510) covalent geometry : bond 0.00266 ( 7869) covalent geometry : angle 0.59217 (10657) *********************** 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 98 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 446 ASN cc_start: 0.7589 (m110) cc_final: 0.7178 (m110) REVERT: B 59 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7519 (mm-40) REVERT: C 32 GLU cc_start: 0.8301 (pm20) cc_final: 0.7996 (pm20) REVERT: C 33 ASN cc_start: 0.8696 (p0) cc_final: 0.8423 (p0) REVERT: C 137 TYR cc_start: 0.7530 (t80) cc_final: 0.7231 (t80) REVERT: C 183 MET cc_start: 0.8158 (mpp) cc_final: 0.7886 (mpp) outliers start: 13 outliers final: 5 residues processed: 94 average time/residue: 1.0805 time to fit residues: 108.9463 Evaluate side-chains 78 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 295 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.115964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.091445 restraints weight = 16916.649| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.81 r_work: 0.3537 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7869 Z= 0.117 Angle : 0.583 12.142 10657 Z= 0.296 Chirality : 0.041 0.133 1228 Planarity : 0.004 0.040 1366 Dihedral : 4.904 62.526 1068 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.51 % Allowed : 13.90 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.59 (0.27), residues: 957 helix: -0.89 (0.29), residues: 316 sheet: -1.61 (0.37), residues: 183 loop : -0.76 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 60 HIS 0.008 0.001 HIS A 247 PHE 0.022 0.001 PHE A 571 TYR 0.007 0.001 TYR C 134 ARG 0.003 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 220) hydrogen bonds : angle 4.99378 ( 510) covalent geometry : bond 0.00273 ( 7869) covalent geometry : angle 0.58303 (10657) *********************** 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: 22 poor density : 85 time to evaluate : 0.955 Fit side-chains REVERT: A 127 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: A 163 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7132 (m-30) REVERT: A 446 ASN cc_start: 0.7567 (m110) cc_final: 0.7171 (m110) REVERT: B 96 ASP cc_start: 0.7587 (t70) cc_final: 0.7135 (p0) REVERT: C 32 GLU cc_start: 0.8300 (pm20) cc_final: 0.7965 (pm20) REVERT: C 33 ASN cc_start: 0.8695 (p0) cc_final: 0.8362 (p0) REVERT: C 34 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: C 137 TYR cc_start: 0.7584 (t80) cc_final: 0.7339 (t80) REVERT: C 183 MET cc_start: 0.8254 (mpp) cc_final: 0.8023 (mpp) outliers start: 22 outliers final: 9 residues processed: 100 average time/residue: 0.9465 time to fit residues: 102.5045 Evaluate side-chains 88 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 A residue 163 ASP 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 61 ILE Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 ILE 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 86 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 344 GLN A 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.111304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.086499 restraints weight = 17142.574| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.83 r_work: 0.3437 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7869 Z= 0.216 Angle : 0.680 12.462 10657 Z= 0.344 Chirality : 0.044 0.138 1228 Planarity : 0.004 0.040 1366 Dihedral : 5.414 65.150 1068 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.08 % Allowed : 14.81 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.93 (0.26), residues: 957 helix: -1.01 (0.29), residues: 313 sheet: -2.04 (0.38), residues: 173 loop : -1.01 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.005 0.001 HIS A 247 PHE 0.023 0.002 PHE A 571 TYR 0.017 0.002 TYR A 469 ARG 0.004 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 220) hydrogen bonds : angle 5.35954 ( 510) covalent geometry : bond 0.00512 ( 7869) covalent geometry : angle 0.68013 (10657) *********************** 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 108 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: A 332 LYS cc_start: 0.8548 (tptp) cc_final: 0.8343 (tptp) REVERT: A 446 ASN cc_start: 0.7606 (m110) cc_final: 0.7193 (m110) REVERT: B 59 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7370 (mt0) REVERT: C 32 GLU cc_start: 0.8509 (pm20) cc_final: 0.8206 (pm20) REVERT: C 33 ASN cc_start: 0.8590 (p0) cc_final: 0.8212 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8113 (mp0) outliers start: 27 outliers final: 12 residues processed: 101 average time/residue: 1.1184 time to fit residues: 121.9006 Evaluate side-chains 86 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 367 ILE 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 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 24 optimal weight: 0.0670 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.113473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088937 restraints weight = 16839.875| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.79 r_work: 0.3503 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2702 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 : 0.618 12.917 10657 Z= 0.313 Chirality : 0.042 0.151 1228 Planarity : 0.004 0.042 1366 Dihedral : 5.057 59.616 1068 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.39 % Allowed : 16.17 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.84 (0.27), residues: 957 helix: -0.93 (0.29), residues: 316 sheet: -2.01 (0.37), residues: 173 loop : -0.95 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.007 0.001 HIS A 247 PHE 0.046 0.002 PHE A 571 TYR 0.008 0.001 TYR A 346 ARG 0.002 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 220) hydrogen bonds : angle 5.04305 ( 510) covalent geometry : bond 0.00289 ( 7869) covalent geometry : angle 0.61815 (10657) *********************** 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 103 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: A 332 LYS cc_start: 0.8593 (tptp) cc_final: 0.8373 (tptp) REVERT: A 446 ASN cc_start: 0.7533 (m110) cc_final: 0.7128 (m110) REVERT: B 79 GLU cc_start: 0.7245 (mp0) cc_final: 0.6680 (mt-10) REVERT: B 96 ASP cc_start: 0.7692 (t70) cc_final: 0.7191 (p0) REVERT: C 32 GLU cc_start: 0.8452 (pm20) cc_final: 0.8089 (pm20) REVERT: C 33 ASN cc_start: 0.8590 (p0) cc_final: 0.8187 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7997 (mp0) outliers start: 21 outliers final: 6 residues processed: 97 average time/residue: 1.1166 time to fit residues: 116.2076 Evaluate side-chains 83 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 226 THR 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 2 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.0030 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.111386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.086276 restraints weight = 17111.712| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.86 r_work: 0.3400 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7869 Z= 0.168 Angle : 0.651 12.703 10657 Z= 0.328 Chirality : 0.043 0.155 1228 Planarity : 0.004 0.044 1366 Dihedral : 5.228 60.785 1068 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.28 % Allowed : 17.08 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.90 (0.26), residues: 957 helix: -0.96 (0.29), residues: 311 sheet: -2.07 (0.37), residues: 173 loop : -1.00 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.007 0.001 HIS C 239 PHE 0.045 0.002 PHE C 258 TYR 0.016 0.001 TYR A 469 ARG 0.003 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 220) hydrogen bonds : angle 5.11950 ( 510) covalent geometry : bond 0.00399 ( 7869) covalent geometry : angle 0.65095 (10657) *********************** 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 96 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7494 (mmm) cc_final: 0.6953 (mmp) REVERT: A 127 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: A 332 LYS cc_start: 0.8592 (tptp) cc_final: 0.8327 (tptp) REVERT: A 446 ASN cc_start: 0.7546 (m110) cc_final: 0.7133 (m110) REVERT: C 32 GLU cc_start: 0.8547 (pm20) cc_final: 0.8154 (pm20) REVERT: C 33 ASN cc_start: 0.8574 (p0) cc_final: 0.8152 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7995 (mp0) outliers start: 20 outliers final: 8 residues processed: 91 average time/residue: 1.2503 time to fit residues: 124.1447 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 : 0.883 ------------------------------------------------------------------------------- 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 163 ASP 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 213 VAL Chi-restraints excluded: chain C residue 251 VAL 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 87 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.0470 chunk 43 optimal weight: 0.0040 overall best weight: 0.3890 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.115132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.090862 restraints weight = 16820.736| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.80 r_work: 0.3532 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2975 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= 0.113 Angle : 0.634 12.423 10657 Z= 0.320 Chirality : 0.042 0.177 1228 Planarity : 0.004 0.046 1366 Dihedral : 4.950 57.408 1068 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.59 % Allowed : 18.56 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.78 (0.27), residues: 957 helix: -0.94 (0.30), residues: 307 sheet: -2.01 (0.37), residues: 173 loop : -0.86 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.007 0.001 HIS C 239 PHE 0.055 0.002 PHE A 571 TYR 0.008 0.001 TYR C 114 ARG 0.002 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 220) hydrogen bonds : angle 4.87794 ( 510) covalent geometry : bond 0.00257 ( 7869) covalent geometry : angle 0.63429 (10657) *********************** 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 98 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7497 (mmm) cc_final: 0.6947 (mmp) REVERT: A 127 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: A 267 ASP cc_start: 0.4800 (t70) cc_final: 0.4543 (t70) REVERT: A 446 ASN cc_start: 0.7509 (m110) cc_final: 0.7087 (m110) REVERT: B 79 GLU cc_start: 0.7159 (mp0) cc_final: 0.6644 (mt-10) REVERT: B 96 ASP cc_start: 0.7622 (t70) cc_final: 0.7369 (p0) REVERT: C 32 GLU cc_start: 0.8430 (pm20) cc_final: 0.8020 (pm20) REVERT: C 33 ASN cc_start: 0.8595 (p0) cc_final: 0.8205 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8033 (mp0) outliers start: 14 outliers final: 7 residues processed: 92 average time/residue: 1.0152 time to fit residues: 100.4443 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 : 0.885 ------------------------------------------------------------------------------- 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 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 226 THR 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 11 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 70 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.115368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.090931 restraints weight = 17157.969| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.90 r_work: 0.3504 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7869 Z= 0.115 Angle : 0.640 11.817 10657 Z= 0.325 Chirality : 0.042 0.190 1228 Planarity : 0.004 0.048 1366 Dihedral : 4.927 58.755 1067 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.48 % Allowed : 18.68 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.77 (0.27), residues: 957 helix: -0.90 (0.30), residues: 310 sheet: -2.01 (0.37), residues: 171 loop : -0.89 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.008 0.001 HIS C 239 PHE 0.065 0.002 PHE A 571 TYR 0.016 0.001 TYR A 469 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 220) hydrogen bonds : angle 4.84565 ( 510) covalent geometry : bond 0.00269 ( 7869) covalent geometry : angle 0.64047 (10657) *********************** 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: 13 poor density : 79 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7590 (mmm) cc_final: 0.6951 (mmp) REVERT: A 127 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: A 267 ASP cc_start: 0.4935 (t70) cc_final: 0.4637 (t0) REVERT: A 446 ASN cc_start: 0.7449 (m110) cc_final: 0.7026 (m110) REVERT: B 79 GLU cc_start: 0.7221 (mp0) cc_final: 0.6723 (mt-10) REVERT: C 32 GLU cc_start: 0.8418 (pm20) cc_final: 0.8025 (pm20) REVERT: C 33 ASN cc_start: 0.8591 (p0) cc_final: 0.8184 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8057 (mp0) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 0.9963 time to fit residues: 91.2897 Evaluate side-chains 82 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 145 LEU 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 295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 0.0030 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.114025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.089869 restraints weight = 17059.029| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.82 r_work: 0.3512 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3160 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= 0.134 Angle : 0.661 11.438 10657 Z= 0.337 Chirality : 0.042 0.170 1228 Planarity : 0.004 0.047 1366 Dihedral : 5.044 59.216 1067 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.25 % Allowed : 19.13 % 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 (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: -1.77 (0.27), residues: 957 helix: -0.95 (0.30), residues: 310 sheet: -1.91 (0.38), residues: 179 loop : -0.87 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 60 HIS 0.008 0.001 HIS C 239 PHE 0.073 0.002 PHE A 571 TYR 0.010 0.001 TYR C 134 ARG 0.007 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 220) hydrogen bonds : angle 4.94941 ( 510) covalent geometry : bond 0.00319 ( 7869) covalent geometry : angle 0.66136 (10657) ********************** 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: 11 poor density : 77 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7716 (mmm) cc_final: 0.7460 (mmp) REVERT: A 446 ASN cc_start: 0.7509 (m110) cc_final: 0.7077 (m110) REVERT: B 79 GLU cc_start: 0.7244 (mp0) cc_final: 0.6768 (mt-10) REVERT: B 96 ASP cc_start: 0.7630 (t70) cc_final: 0.7299 (p0) REVERT: C 32 GLU cc_start: 0.8457 (pm20) cc_final: 0.8045 (pm20) REVERT: C 33 ASN cc_start: 0.8597 (p0) cc_final: 0.8187 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8029 (mp0) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.9935 time to fit residues: 89.0276 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 : 0.973 ------------------------------------------------------------------------------- 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 295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.0370 chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.114800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.090534 restraints weight = 17131.915| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.86 r_work: 0.3523 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3250 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= 0.119 Angle : 0.654 11.919 10657 Z= 0.331 Chirality : 0.042 0.166 1228 Planarity : 0.004 0.048 1366 Dihedral : 4.953 58.276 1067 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.14 % Allowed : 19.59 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.76 (0.27), residues: 957 helix: -0.91 (0.30), residues: 310 sheet: -1.90 (0.39), residues: 168 loop : -0.93 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 60 HIS 0.008 0.001 HIS C 239 PHE 0.064 0.002 PHE A 571 TYR 0.015 0.001 TYR A 469 ARG 0.007 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 220) hydrogen bonds : angle 4.89432 ( 510) covalent geometry : bond 0.00280 ( 7869) covalent geometry : angle 0.65447 (10657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5743.93 seconds wall clock time: 100 minutes 6.41 seconds (6006.41 seconds total)