Starting phenix.real_space_refine on Fri Jul 3 07:16:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sd0_25044/07_2026/7sd0_25044.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sd0_25044/07_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_25044/07_2026/7sd0_25044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sd0_25044/07_2026/7sd0_25044.map" model { file = "/net/cci-nas-00/data/ceres_data/7sd0_25044/07_2026/7sd0_25044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sd0_25044/07_2026/7sd0_25044.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sd0_25044/07_2026/7sd0_25044.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sd0_25044/07_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-6108/lib/python3.11/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: 1.53, per 1000 atoms: 0.20 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: 0.53 Conformation dependent library (CDL) restraints added in 386.8 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: 0.25 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: 1.41 Time building geometry restraints manager: 0.70 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: 4337 16.69 - 33.37: 381 33.37 - 50.06: 83 50.06 - 66.74: 13 66.74 - 83.43: 6 Dihedral angle restraints: 4820 sinusoidal: 2001 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 4817 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.190 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:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 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 : 13.255 83.428 2990 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/Z covalent geometry : bond 0.00698 / 0.47 ( 7869) covalent geometry : angle 0.97188 / 0.58 (10657) hydrogen bonds : bond 0.29094 / 19.22 ( 220) hydrogen bonds : angle 8.61469 / 6.11 ( 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 : 0.227 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: 0.5388 time to fit residues: 73.8935 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 : 0.321 ------------------------------------------------------------------------------- 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... A 265 ASN ** A 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 71 GLN 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 = 0.4081 r_free = 0.4081 target = 0.115609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091451 restraints weight = 16653.689| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.73 r_work: 0.3538 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1741 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= 0.129 Angle : 0.636 8.618 10657 Z= 0.326 Chirality : 0.043 0.154 1228 Planarity : 0.004 0.042 1366 Dihedral : 4.474 29.972 1044 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.59 % Allowed : 11.05 % 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: -1.69 (0.40), residues: 171 loop : -0.71 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.021 0.001 TYR A 469 PHE 0.025 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/Z covalent geometry : bond 0.00292 / 0.13 ( 7869) covalent geometry : angle 0.63565 / 0.33 (10657) hydrogen bonds : bond 0.05097 / 3.26 ( 220) hydrogen bonds : angle 5.60802 / 4.20 ( 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 105 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 ASN cc_start: 0.7695 (m110) cc_final: 0.7295 (m110) REVERT: B 55 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: B 59 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7549 (mm-40) REVERT: C 32 GLU cc_start: 0.8350 (pm20) cc_final: 0.8113 (pm20) REVERT: C 183 MET cc_start: 0.8004 (mpp) cc_final: 0.7675 (mpp) REVERT: C 283 MET cc_start: 0.8231 (ttm) cc_final: 0.7998 (ttm) outliers start: 14 outliers final: 3 residues processed: 101 average time/residue: 0.5253 time to fit residues: 56.5538 Evaluate side-chains 76 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 55 GLU 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: 3.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 81 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4020 r_free = 0.4020 target = 0.111701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.086945 restraints weight = 16985.803| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.80 r_work: 0.3425 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7869 Z= 0.215 Angle : 0.676 8.432 10657 Z= 0.345 Chirality : 0.044 0.137 1228 Planarity : 0.004 0.046 1366 Dihedral : 4.782 24.913 1040 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.16 % Allowed : 13.10 % Favored : 84.74 % 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: -1.90 (0.26), residues: 957 helix: -1.14 (0.29), residues: 309 sheet: -2.05 (0.38), residues: 173 loop : -0.87 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.018 0.002 TYR A 469 PHE 0.019 0.002 PHE A 66 TRP 0.006 0.001 TRP B 60 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 ( 7869) covalent geometry : angle 0.67603 / 0.34 (10657) hydrogen bonds : bond 0.04893 / 3.12 ( 220) hydrogen bonds : angle 5.56975 / 4.19 ( 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 94 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.317 Fit side-chains REVERT: A 332 LYS cc_start: 0.8614 (tptp) cc_final: 0.8399 (tptp) REVERT: A 446 ASN cc_start: 0.7683 (m110) cc_final: 0.7266 (m110) REVERT: A 457 GLU cc_start: 0.8498 (mp0) cc_final: 0.8231 (mp0) REVERT: B 55 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: B 59 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7577 (mm-40) REVERT: B 96 ASP cc_start: 0.7834 (t70) cc_final: 0.7250 (p0) REVERT: C 32 GLU cc_start: 0.8414 (pm20) cc_final: 0.8146 (pm20) REVERT: C 33 ASN cc_start: 0.8745 (p0) cc_final: 0.8371 (p0) REVERT: C 34 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: C 183 MET cc_start: 0.8294 (mpp) cc_final: 0.8054 (mpp) outliers start: 19 outliers final: 7 residues processed: 86 average time/residue: 0.5294 time to fit residues: 48.6676 Evaluate side-chains 79 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain B residue 55 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 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: 4.9990 chunk 35 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4063 r_free = 0.4063 target = 0.114285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.089704 restraints weight = 17095.228| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.85 r_work: 0.3475 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2363 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= 0.114 Angle : 0.598 12.690 10657 Z= 0.303 Chirality : 0.041 0.145 1228 Planarity : 0.004 0.044 1366 Dihedral : 4.359 19.422 1040 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.39 % Allowed : 14.12 % Favored : 83.49 % 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: -1.74 (0.27), residues: 957 helix: -0.98 (0.29), residues: 316 sheet: -1.85 (0.37), residues: 185 loop : -0.79 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.011 0.001 TYR C 70 PHE 0.016 0.001 PHE A 66 TRP 0.003 0.001 TRP C 206 HIS 0.009 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 7869) covalent geometry : angle 0.59803 / 0.30 (10657) hydrogen bonds : bond 0.03876 / 2.46 ( 220) hydrogen bonds : angle 5.10145 / 3.88 ( 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 112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7461 (pt0) cc_final: 0.7197 (pm20) REVERT: A 332 LYS cc_start: 0.8628 (tptp) cc_final: 0.8381 (tptp) REVERT: A 446 ASN cc_start: 0.7563 (m110) cc_final: 0.7147 (m110) REVERT: B 59 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7563 (mm-40) REVERT: C 32 GLU cc_start: 0.8395 (pm20) cc_final: 0.8057 (pm20) REVERT: C 33 ASN cc_start: 0.8679 (p0) cc_final: 0.8338 (p0) REVERT: C 34 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: C 137 TYR cc_start: 0.7615 (t80) cc_final: 0.7386 (t80) outliers start: 21 outliers final: 7 residues processed: 103 average time/residue: 0.4681 time to fit residues: 51.8017 Evaluate side-chains 85 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 146 VAL 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 295 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.110003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.085541 restraints weight = 17227.526| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.77 r_work: 0.3398 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7869 Z= 0.253 Angle : 0.707 13.842 10657 Z= 0.357 Chirality : 0.045 0.153 1228 Planarity : 0.004 0.047 1366 Dihedral : 4.930 27.201 1040 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.73 % Allowed : 15.83 % 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 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: -1.93 (0.27), residues: 957 helix: -0.98 (0.29), residues: 304 sheet: -2.27 (0.37), residues: 184 loop : -0.89 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.017 0.002 TYR C 70 PHE 0.022 0.002 PHE A 571 TRP 0.005 0.001 TRP A 401 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 ( 7869) covalent geometry : angle 0.70742 / 0.36 (10657) hydrogen bonds : bond 0.04688 / 2.98 ( 220) hydrogen bonds : angle 5.46928 / 4.11 ( 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 101 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.325 Fit side-chains REVERT: A 127 GLU cc_start: 0.7540 (pt0) cc_final: 0.7156 (pm20) REVERT: A 332 LYS cc_start: 0.8660 (tptp) cc_final: 0.8380 (tptp) REVERT: A 446 ASN cc_start: 0.7651 (m110) cc_final: 0.7241 (m110) REVERT: B 96 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7569 (p0) REVERT: C 32 GLU cc_start: 0.8614 (pm20) cc_final: 0.8341 (pm20) REVERT: C 33 ASN cc_start: 0.8580 (p0) cc_final: 0.8208 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8167 (mp0) outliers start: 24 outliers final: 9 residues processed: 91 average time/residue: 0.4963 time to fit residues: 48.5385 Evaluate side-chains 81 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR 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 79 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4053 r_free = 0.4053 target = 0.113514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.088547 restraints weight = 17062.187| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.86 r_work: 0.3465 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2703 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= 0.124 Angle : 0.619 12.811 10657 Z= 0.313 Chirality : 0.042 0.148 1228 Planarity : 0.004 0.047 1366 Dihedral : 4.444 20.134 1040 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.16 % Allowed : 16.63 % Favored : 81.21 % 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: -1.91 (0.27), residues: 957 helix: -0.92 (0.29), residues: 316 sheet: -2.23 (0.38), residues: 158 loop : -1.03 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 43 TYR 0.017 0.001 TYR A 469 PHE 0.019 0.001 PHE C 258 TRP 0.005 0.001 TRP B 60 HIS 0.007 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 7869) covalent geometry : angle 0.61945 / 0.31 (10657) hydrogen bonds : bond 0.03652 / 2.30 ( 220) hydrogen bonds : angle 5.00496 / 3.81 ( 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 99 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7522 (mmm) cc_final: 0.6997 (mmp) REVERT: A 127 GLU cc_start: 0.7505 (pt0) cc_final: 0.7188 (pm20) REVERT: A 332 LYS cc_start: 0.8653 (tptp) cc_final: 0.8385 (tptp) REVERT: A 446 ASN cc_start: 0.7560 (m110) cc_final: 0.7147 (m110) REVERT: A 456 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7265 (tt0) REVERT: B 59 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7397 (mm-40) REVERT: B 79 GLU cc_start: 0.7264 (mp0) cc_final: 0.6675 (mt-10) REVERT: C 32 GLU cc_start: 0.8554 (pm20) cc_final: 0.8168 (pm20) REVERT: C 33 ASN cc_start: 0.8585 (p0) cc_final: 0.8215 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8121 (mp0) outliers start: 19 outliers final: 7 residues processed: 94 average time/residue: 0.4895 time to fit residues: 49.4113 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 : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 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 213 VAL Chi-restraints excluded: chain C residue 251 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: 0.9980 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4054 r_free = 0.4054 target = 0.113436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088908 restraints weight = 16945.864| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.79 r_work: 0.3480 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7869 Z= 0.132 Angle : 0.627 12.818 10657 Z= 0.315 Chirality : 0.042 0.173 1228 Planarity : 0.004 0.048 1366 Dihedral : 4.443 20.593 1040 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.71 % Allowed : 18.22 % Favored : 80.07 % 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: -1.84 (0.27), residues: 957 helix: -0.89 (0.29), residues: 316 sheet: -2.25 (0.38), residues: 158 loop : -0.95 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 43 TYR 0.017 0.001 TYR C 137 PHE 0.045 0.002 PHE C 258 TRP 0.007 0.001 TRP A 401 HIS 0.007 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7869) covalent geometry : angle 0.62673 / 0.31 (10657) hydrogen bonds : bond 0.03669 / 2.30 ( 220) hydrogen bonds : angle 4.99007 / 3.80 ( 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 94 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7472 (mmm) cc_final: 0.6968 (mmp) REVERT: A 127 GLU cc_start: 0.7587 (pt0) cc_final: 0.7179 (pm20) REVERT: A 332 LYS cc_start: 0.8647 (tptp) cc_final: 0.8407 (tptp) REVERT: A 446 ASN cc_start: 0.7536 (m110) cc_final: 0.7133 (m110) REVERT: B 96 ASP cc_start: 0.7873 (t70) cc_final: 0.7302 (p0) REVERT: C 32 GLU cc_start: 0.8550 (pm20) cc_final: 0.8149 (pm20) REVERT: C 33 ASN cc_start: 0.8557 (p0) cc_final: 0.8195 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8141 (mp0) outliers start: 15 outliers final: 8 residues processed: 89 average time/residue: 0.4613 time to fit residues: 44.2562 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 : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 499 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 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 86 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 45 optimal weight: 0.0010 chunk 3 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN B 58 ASN ** C 125 HIS ** 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 = 0.3969 r_free = 0.3969 target = 0.110027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.084935 restraints weight = 17358.289| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.87 r_work: 0.3378 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7869 Z= 0.209 Angle : 0.689 12.536 10657 Z= 0.346 Chirality : 0.044 0.154 1228 Planarity : 0.004 0.047 1366 Dihedral : 4.795 22.523 1040 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.59 % Allowed : 18.79 % 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: -1.96 (0.27), residues: 957 helix: -0.96 (0.30), residues: 310 sheet: -2.34 (0.38), residues: 158 loop : -1.04 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.015 0.002 TYR C 70 PHE 0.047 0.002 PHE C 258 TRP 0.009 0.001 TRP A 401 HIS 0.009 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 7869) covalent geometry : angle 0.68918 / 0.35 (10657) hydrogen bonds : bond 0.04314 / 2.72 ( 220) hydrogen bonds : angle 5.29249 / 4.00 ( 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 90 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.331 Fit side-chains REVERT: A 100 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8392 (pp20) REVERT: A 332 LYS cc_start: 0.8648 (tptp) cc_final: 0.8364 (tptp) REVERT: A 446 ASN cc_start: 0.7540 (m110) cc_final: 0.7132 (m110) REVERT: B 35 GLN cc_start: 0.7988 (tt0) cc_final: 0.7602 (tt0) REVERT: B 79 GLU cc_start: 0.7379 (mp0) cc_final: 0.6771 (mt-10) REVERT: B 144 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6851 (ttp) REVERT: C 32 GLU cc_start: 0.8661 (pm20) cc_final: 0.8305 (pm20) REVERT: C 33 ASN cc_start: 0.8569 (p0) cc_final: 0.8170 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8083 (mp0) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.4939 time to fit residues: 45.5988 Evaluate side-chains 82 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 MET 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 226 THR Chi-restraints excluded: chain C residue 251 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: 4.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN A 317 ASN ** C 125 HIS ** 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 = 0.4010 r_free = 0.4010 target = 0.110984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.086663 restraints weight = 17060.804| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.77 r_work: 0.3439 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7869 Z= 0.176 Angle : 0.675 13.083 10657 Z= 0.339 Chirality : 0.043 0.158 1228 Planarity : 0.004 0.048 1366 Dihedral : 4.699 21.615 1040 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.94 % Allowed : 18.91 % 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: -1.95 (0.27), residues: 957 helix: -0.99 (0.30), residues: 309 sheet: -2.09 (0.38), residues: 167 loop : -1.06 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.018 0.002 TYR C 137 PHE 0.041 0.002 PHE C 258 TRP 0.010 0.001 TRP A 401 HIS 0.008 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 7869) covalent geometry : angle 0.67490 / 0.34 (10657) hydrogen bonds : bond 0.04104 / 2.59 ( 220) hydrogen bonds : angle 5.31453 / 4.02 ( 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: 17 poor density : 75 time to evaluate : 0.341 Fit side-chains REVERT: A 100 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8326 (pp20) REVERT: A 127 GLU cc_start: 0.7534 (pt0) cc_final: 0.7093 (pm20) REVERT: A 332 LYS cc_start: 0.8634 (tptp) cc_final: 0.8373 (tptp) REVERT: A 446 ASN cc_start: 0.7508 (m110) cc_final: 0.7091 (m110) REVERT: B 35 GLN cc_start: 0.7968 (tt0) cc_final: 0.7592 (tt0) REVERT: B 79 GLU cc_start: 0.7352 (mp0) cc_final: 0.6745 (mt-10) REVERT: C 32 GLU cc_start: 0.8676 (pm20) cc_final: 0.8296 (pm20) REVERT: C 33 ASN cc_start: 0.8559 (p0) cc_final: 0.8180 (OUTLIER) REVERT: C 34 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8100 (mp0) outliers start: 17 outliers final: 9 residues processed: 88 average time/residue: 0.4145 time to fit residues: 39.4833 Evaluate side-chains 82 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 499 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN A 317 ASN B 58 ASN ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.111302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.086693 restraints weight = 17211.856| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.83 r_work: 0.3409 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7869 Z= 0.153 Angle : 0.670 12.971 10657 Z= 0.338 Chirality : 0.043 0.156 1228 Planarity : 0.004 0.047 1366 Dihedral : 4.569 20.691 1040 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.14 % Allowed : 19.82 % Favored : 79.04 % 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: -1.88 (0.27), residues: 957 helix: -0.97 (0.30), residues: 309 sheet: -2.01 (0.39), residues: 167 loop : -1.02 (0.29), residues: 481 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 0.046 0.002 PHE A 571 TRP 0.007 0.001 TRP A 401 HIS 0.009 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 7869) covalent geometry : angle 0.66977 / 0.34 (10657) hydrogen bonds : bond 0.03886 / 2.45 ( 220) hydrogen bonds : angle 5.29360 / 4.01 ( 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 86 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.324 Fit side-chains REVERT: A 100 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8196 (pp20) REVERT: A 127 GLU cc_start: 0.7522 (pt0) cc_final: 0.7074 (pm20) REVERT: A 332 LYS cc_start: 0.8646 (tptp) cc_final: 0.8386 (tptp) REVERT: A 446 ASN cc_start: 0.7435 (m110) cc_final: 0.7009 (m110) REVERT: B 35 GLN cc_start: 0.7965 (tt0) cc_final: 0.7604 (tt0) REVERT: B 79 GLU cc_start: 0.7280 (mp0) cc_final: 0.6684 (mt-10) REVERT: B 96 ASP cc_start: 0.7783 (t70) cc_final: 0.7304 (p0) REVERT: C 32 GLU cc_start: 0.8643 (pm20) cc_final: 0.8238 (pm20) REVERT: C 33 ASN cc_start: 0.8561 (p0) cc_final: 0.8240 (OUTLIER) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.4681 time to fit residues: 42.8221 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN ** C 125 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.113214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.088779 restraints weight = 17070.816| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.81 r_work: 0.3493 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3177 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= 0.124 Angle : 0.644 12.221 10657 Z= 0.325 Chirality : 0.042 0.159 1228 Planarity : 0.004 0.047 1366 Dihedral : 4.340 19.922 1040 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.91 % Allowed : 20.05 % Favored : 79.04 % 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: -0.87 (0.30), residues: 305 sheet: -1.96 (0.38), residues: 180 loop : -0.87 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 340 TYR 0.024 0.001 TYR C 137 PHE 0.047 0.002 PHE C 258 TRP 0.004 0.001 TRP C 206 HIS 0.008 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 7869) covalent geometry : angle 0.64385 / 0.33 (10657) hydrogen bonds : bond 0.03513 / 2.19 ( 220) hydrogen bonds : angle 5.09178 / 3.86 ( 510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2635.50 seconds wall clock time: 45 minutes 50.17 seconds (2750.17 seconds total)