Starting phenix.real_space_refine on Mon Dec 30 09:45:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sd0_25044/12_2024/7sd0_25044.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sd0_25044/12_2024/7sd0_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_25044/12_2024/7sd0_25044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sd0_25044/12_2024/7sd0_25044.map" model { file = "/net/cci-nas-00/data/ceres_data/7sd0_25044/12_2024/7sd0_25044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sd0_25044/12_2024/7sd0_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.89, per 1000 atoms: 0.63 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: 1.95 Conformation dependent library (CDL) restraints added in 904.6 milliseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 35.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 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: 2.13 Time building geometry restraints manager: 2.26 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.510 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- 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= 0.455 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 *********************** 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 : 0.927 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: 1.1663 time to fit residues: 160.3104 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 : 0.920 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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= 0.184 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 *********************** 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 : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.7240 (t0) cc_final: 0.7030 (m-30) REVERT: A 446 ASN cc_start: 0.7598 (m110) cc_final: 0.7212 (m110) REVERT: C 183 MET cc_start: 0.7788 (mpp) cc_final: 0.7495 (mpp) REVERT: C 283 MET cc_start: 0.7818 (ttm) cc_final: 0.7555 (ttm) outliers start: 13 outliers final: 3 residues processed: 104 average time/residue: 1.1632 time to fit residues: 129.4907 Evaluate side-chains 77 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 47 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7869 Z= 0.227 Angle : 0.620 7.857 10657 Z= 0.318 Chirality : 0.042 0.138 1228 Planarity : 0.004 0.043 1366 Dihedral : 5.211 68.156 1068 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.82 % Allowed : 13.21 % Favored : 84.97 % 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: -1.65 (0.27), residues: 957 helix: -0.99 (0.29), residues: 308 sheet: -1.64 (0.37), residues: 192 loop : -0.74 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 60 HIS 0.007 0.001 HIS A 247 PHE 0.019 0.001 PHE A 66 TYR 0.019 0.001 TYR A 469 ARG 0.003 0.000 ARG C 43 *********************** 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 101 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 446 ASN cc_start: 0.7532 (m110) cc_final: 0.7126 (m110) REVERT: C 32 GLU cc_start: 0.7268 (pm20) cc_final: 0.7063 (pm20) REVERT: C 33 ASN cc_start: 0.8411 (p0) cc_final: 0.8192 (p0) REVERT: C 34 GLU cc_start: 0.8136 (mp0) cc_final: 0.7887 (mp0) REVERT: C 137 TYR cc_start: 0.7439 (t80) cc_final: 0.7169 (t80) REVERT: C 183 MET cc_start: 0.8027 (mpp) cc_final: 0.7806 (mpp) outliers start: 16 outliers final: 6 residues processed: 96 average time/residue: 1.0234 time to fit residues: 105.6122 Evaluate side-chains 77 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 244 ILE 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 85 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 91 optimal weight: 0.0370 chunk 45 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 2.1664 ------------------------------------------------------------------------------- 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 ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7869 Z= 0.301 Angle : 0.659 12.475 10657 Z= 0.334 Chirality : 0.043 0.135 1228 Planarity : 0.004 0.043 1366 Dihedral : 5.349 65.783 1068 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.85 % Allowed : 14.01 % Favored : 83.14 % 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: -1.87 (0.27), residues: 957 helix: -1.11 (0.29), residues: 316 sheet: -1.92 (0.37), residues: 183 loop : -0.86 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 60 HIS 0.008 0.001 HIS A 247 PHE 0.021 0.002 PHE A 571 TYR 0.009 0.001 TYR C 134 ARG 0.004 0.000 ARG C 43 *********************** 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: 25 poor density : 82 time to evaluate : 0.915 Fit side-chains REVERT: A 127 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: A 446 ASN cc_start: 0.7545 (m110) cc_final: 0.7140 (m110) REVERT: B 101 GLU cc_start: 0.8102 (pm20) cc_final: 0.7897 (pm20) REVERT: C 33 ASN cc_start: 0.8284 (p0) cc_final: 0.8061 (p0) REVERT: C 34 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: C 137 TYR cc_start: 0.7579 (t80) cc_final: 0.7360 (t80) outliers start: 25 outliers final: 11 residues processed: 98 average time/residue: 1.0501 time to fit residues: 110.6384 Evaluate side-chains 87 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 367 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 78 optimal weight: 0.0170 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7869 Z= 0.175 Angle : 0.611 12.732 10657 Z= 0.308 Chirality : 0.041 0.136 1228 Planarity : 0.003 0.044 1366 Dihedral : 4.979 59.048 1068 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.39 % Allowed : 15.83 % Favored : 81.78 % 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: -1.79 (0.27), residues: 957 helix: -0.95 (0.29), residues: 316 sheet: -1.81 (0.38), residues: 169 loop : -0.97 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 401 HIS 0.007 0.001 HIS A 247 PHE 0.015 0.001 PHE C 258 TYR 0.008 0.001 TYR C 114 ARG 0.002 0.000 ARG B 138 *********************** 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 106 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.713 Fit side-chains REVERT: A 127 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: A 446 ASN cc_start: 0.7468 (m110) cc_final: 0.7078 (m110) REVERT: C 34 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: C 137 TYR cc_start: 0.7555 (t80) cc_final: 0.7326 (t80) outliers start: 21 outliers final: 6 residues processed: 98 average time/residue: 1.0771 time to fit residues: 113.5675 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 : 0.968 ------------------------------------------------------------------------------- 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 A residue 303 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 7 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7869 Z= 0.245 Angle : 0.641 12.639 10657 Z= 0.323 Chirality : 0.042 0.148 1228 Planarity : 0.004 0.048 1366 Dihedral : 5.159 61.271 1068 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.62 % Allowed : 17.20 % Favored : 80.18 % 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: -1.85 (0.27), residues: 957 helix: -0.96 (0.29), residues: 315 sheet: -1.95 (0.38), residues: 176 loop : -0.97 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 60 HIS 0.006 0.001 HIS C 239 PHE 0.039 0.002 PHE C 258 TYR 0.016 0.001 TYR A 469 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.963 Fit side-chains REVERT: A 103 MET cc_start: 0.7471 (mmm) cc_final: 0.6891 (mmp) REVERT: A 127 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: A 446 ASN cc_start: 0.7489 (m110) cc_final: 0.7083 (m110) REVERT: C 34 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7874 (mp0) outliers start: 23 outliers final: 10 residues processed: 92 average time/residue: 0.9259 time to fit residues: 92.7755 Evaluate side-chains 79 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 367 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 33 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 317 ASN B 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2853 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= 0.195 Angle : 0.633 12.627 10657 Z= 0.317 Chirality : 0.042 0.166 1228 Planarity : 0.004 0.047 1366 Dihedral : 5.004 58.861 1068 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.16 % Allowed : 17.65 % Favored : 80.18 % 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: -0.87 (0.30), residues: 310 sheet: -1.89 (0.39), residues: 166 loop : -0.99 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.007 0.001 HIS C 239 PHE 0.030 0.001 PHE C 258 TYR 0.007 0.001 TYR C 70 ARG 0.002 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.060 Fit side-chains REVERT: A 127 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: A 446 ASN cc_start: 0.7453 (m110) cc_final: 0.7058 (m110) REVERT: B 79 GLU cc_start: 0.7093 (mp0) cc_final: 0.6546 (mt-10) REVERT: C 32 GLU cc_start: 0.7315 (pm20) cc_final: 0.6917 (pm20) REVERT: C 33 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7614 (m110) REVERT: C 34 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8000 (mp0) outliers start: 19 outliers final: 6 residues processed: 94 average time/residue: 1.0820 time to fit residues: 109.5290 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 : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 33 ASN 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 54 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 50.0000 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 80 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 480 ASN B 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3000 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= 0.184 Angle : 0.641 12.065 10657 Z= 0.322 Chirality : 0.042 0.156 1228 Planarity : 0.004 0.046 1366 Dihedral : 4.939 58.509 1068 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.71 % Allowed : 18.56 % Favored : 79.73 % 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: -1.72 (0.27), residues: 957 helix: -0.83 (0.30), residues: 310 sheet: -1.89 (0.39), residues: 166 loop : -0.94 (0.29), residues: 481 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 0.049 0.001 PHE C 258 TYR 0.016 0.001 TYR C 137 ARG 0.002 0.000 ARG C 43 *********************** 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 99 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.877 Fit side-chains REVERT: A 267 ASP cc_start: 0.4719 (t70) cc_final: 0.4208 (t0) REVERT: A 446 ASN cc_start: 0.7442 (m110) cc_final: 0.7033 (m110) REVERT: A 535 PHE cc_start: 0.8231 (t80) cc_final: 0.8023 (t80) REVERT: B 35 GLN cc_start: 0.7754 (tt0) cc_final: 0.7382 (tt0) REVERT: B 79 GLU cc_start: 0.7174 (mp0) cc_final: 0.6647 (mt-10) REVERT: C 32 GLU cc_start: 0.7316 (pm20) cc_final: 0.6960 (pm20) REVERT: C 33 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7684 (m-40) REVERT: C 34 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7844 (mp0) outliers start: 15 outliers final: 6 residues processed: 92 average time/residue: 1.0151 time to fit residues: 100.5929 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 : 0.998 ------------------------------------------------------------------------------- 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 33 ASN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 317 ASN B 58 ASN B 59 GLN B 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3109 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= 0.188 Angle : 0.648 11.834 10657 Z= 0.326 Chirality : 0.042 0.180 1228 Planarity : 0.004 0.046 1366 Dihedral : 4.968 58.603 1068 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.48 % Allowed : 19.13 % Favored : 79.38 % 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: -1.67 (0.27), residues: 957 helix: -0.84 (0.30), residues: 309 sheet: -1.91 (0.37), residues: 181 loop : -0.79 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 206 HIS 0.008 0.001 HIS C 239 PHE 0.049 0.002 PHE A 571 TYR 0.007 0.001 TYR C 70 ARG 0.002 0.000 ARG A 98 *********************** 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 93 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.936 Fit side-chains REVERT: A 103 MET cc_start: 0.7394 (mmp) cc_final: 0.6714 (mmp) REVERT: A 127 GLU cc_start: 0.7380 (pt0) cc_final: 0.6986 (pm20) REVERT: A 267 ASP cc_start: 0.4760 (t70) cc_final: 0.4255 (t0) REVERT: A 446 ASN cc_start: 0.7429 (m110) cc_final: 0.7019 (m110) REVERT: A 535 PHE cc_start: 0.8388 (t80) cc_final: 0.8177 (t80) REVERT: B 79 GLU cc_start: 0.7190 (mp0) cc_final: 0.6675 (mt-10) REVERT: C 32 GLU cc_start: 0.7323 (pm20) cc_final: 0.6961 (pm20) REVERT: C 33 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7680 (m-40) REVERT: C 34 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7840 (mp0) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 1.0107 time to fit residues: 97.0947 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 : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 ASN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3157 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= 0.269 Angle : 0.691 11.576 10657 Z= 0.354 Chirality : 0.043 0.169 1228 Planarity : 0.004 0.048 1366 Dihedral : 5.231 60.228 1068 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.37 % Allowed : 19.48 % 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 (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: -1.79 (0.27), residues: 957 helix: -0.89 (0.30), residues: 304 sheet: -2.07 (0.37), residues: 171 loop : -0.91 (0.29), residues: 482 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 0.065 0.002 PHE A 571 TYR 0.024 0.002 TYR C 137 ARG 0.009 0.000 ARG C 132 ********************** 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: 12 poor density : 74 time to evaluate : 0.848 Fit side-chains REVERT: A 127 GLU cc_start: 0.7315 (pt0) cc_final: 0.6894 (pm20) REVERT: A 446 ASN cc_start: 0.7434 (m110) cc_final: 0.7022 (m110) REVERT: A 535 PHE cc_start: 0.8446 (t80) cc_final: 0.8227 (t80) REVERT: C 32 GLU cc_start: 0.7458 (pm20) cc_final: 0.7093 (pm20) REVERT: C 33 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7558 (m-40) REVERT: C 34 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7833 (mp0) outliers start: 12 outliers final: 5 residues processed: 82 average time/residue: 0.9587 time to fit residues: 84.9951 Evaluate side-chains 78 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 33 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.0000 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 317 ASN B 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.114477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.090202 restraints weight = 16773.246| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.77 r_work: 0.3499 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7869 Z= 0.188 Angle : 0.669 11.031 10657 Z= 0.342 Chirality : 0.042 0.170 1228 Planarity : 0.004 0.047 1366 Dihedral : 5.040 57.362 1068 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.14 % Allowed : 20.27 % Favored : 78.59 % 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: 309 sheet: -1.95 (0.38), residues: 168 loop : -0.92 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 206 HIS 0.007 0.001 HIS C 239 PHE 0.075 0.002 PHE A 571 TYR 0.010 0.001 TYR C 137 ARG 0.008 0.000 ARG C 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.60 seconds wall clock time: 48 minutes 53.77 seconds (2933.77 seconds total)