Starting phenix.real_space_refine on Wed Mar 12 13:30:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upi_26667/03_2025/7upi_26667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upi_26667/03_2025/7upi_26667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7upi_26667/03_2025/7upi_26667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upi_26667/03_2025/7upi_26667.map" model { file = "/net/cci-nas-00/data/ceres_data/7upi_26667/03_2025/7upi_26667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upi_26667/03_2025/7upi_26667.cif" } resolution = 2.89 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 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 Cl 1 4.86 5 C 4937 2.51 5 N 1324 2.21 5 O 1467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7775 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 165} Chain: "B" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2356 Classifications: {'peptide': 293} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 279} Chain: "C" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3977 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 27, 'TRANS': 477} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.27, per 1000 atoms: 0.68 Number of scatterers: 7775 At special positions: 0 Unit cell: (101.46, 92.916, 92.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mn 2 24.99 Cl 1 17.00 S 40 16.00 P 3 15.00 Mg 1 11.99 O 1467 8.00 N 1324 7.00 C 4937 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: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 35.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.560A pdb=" N THR A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.507A pdb=" N PHE A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.950A pdb=" N PHE A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.572A pdb=" N ILE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 145 through 157 removed outlier: 3.744A pdb=" N TRP B 149 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 removed outlier: 4.019A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.657A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.560A pdb=" N LYS C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 237 removed outlier: 3.534A pdb=" N GLY C 235 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.968A pdb=" N GLY C 281 " --> pdb=" O ASP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 306 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 395 through 401 removed outlier: 4.599A pdb=" N GLY C 399 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP C 401 " --> pdb=" O PHE C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 424 removed outlier: 3.584A pdb=" N SER C 422 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 464 through 470 Processing helix chain 'C' and resid 487 through 493 removed outlier: 3.833A pdb=" N GLY C 491 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 516 removed outlier: 3.585A pdb=" N GLY C 514 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 516 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 540 Processing helix chain 'C' and resid 557 through 564 removed outlier: 3.605A pdb=" N GLY C 564 " --> pdb=" O ILE C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 56 removed outlier: 6.572A pdb=" N TYR A 14 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A 66 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 16 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 88 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 124 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 90 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASN A 126 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR A 92 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 55 removed outlier: 6.414A pdb=" N LEU B 53 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE B 170 " --> pdb=" O CYS B 245 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 244 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU B 266 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG B 246 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.171A pdb=" N LYS B 60 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE B 293 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 6.775A pdb=" N ASP B 208 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.983A pdb=" N LEU C 151 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C 220 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C 243 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU C 289 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN C 313 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 312 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU C 336 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU C 360 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 476 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 499 " --> pdb=" O TYR C 523 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 597 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: 2.37 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1680 1.33 - 1.45: 1573 1.45 - 1.57: 4598 1.57 - 1.69: 5 1.69 - 1.81: 59 Bond restraints: 7915 Sorted by residual: bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.460 1.487 -0.027 7.30e-03 1.88e+04 1.37e+01 bond pdb=" N GLN B 249 " pdb=" CA GLN B 249 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N HIS B 248 " pdb=" CA HIS B 248 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.12e+00 bond pdb=" C LYS A 127 " pdb=" N VAL A 128 " ideal model delta sigma weight residual 1.336 1.365 -0.028 1.17e-02 7.31e+03 5.82e+00 bond pdb=" C2 GTP A 201 " pdb=" N3 GTP A 201 " ideal model delta sigma weight residual 1.380 1.332 0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 7910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 10634 2.42 - 4.84: 71 4.84 - 7.26: 9 7.26 - 9.69: 6 9.69 - 12.11: 4 Bond angle restraints: 10724 Sorted by residual: angle pdb=" PB GTP A 201 " pdb=" O3B GTP A 201 " pdb=" PG GTP A 201 " ideal model delta sigma weight residual 120.50 132.61 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" PA GTP A 201 " pdb=" O3A GTP A 201 " pdb=" PB GTP A 201 " ideal model delta sigma weight residual 120.50 131.86 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C1' GTP A 201 " pdb=" C2' GTP A 201 " pdb=" C3' GTP A 201 " ideal model delta sigma weight residual 111.00 99.71 11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CA GLN B 68 " pdb=" C GLN B 68 " pdb=" O GLN B 68 " ideal model delta sigma weight residual 122.41 118.10 4.31 1.21e+00 6.83e-01 1.27e+01 angle pdb=" C TYR B 70 " pdb=" CA TYR B 70 " pdb=" CB TYR B 70 " ideal model delta sigma weight residual 110.67 117.48 -6.81 1.92e+00 2.71e-01 1.26e+01 ... (remaining 10719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 4829 28.99 - 57.98: 25 57.98 - 86.97: 1 86.97 - 115.97: 2 115.97 - 144.96: 4 Dihedral angle restraints: 4861 sinusoidal: 2022 harmonic: 2839 Sorted by residual: dihedral pdb=" C8 GTP A 201 " pdb=" C1' GTP A 201 " pdb=" N9 GTP A 201 " pdb=" O4' GTP A 201 " ideal model delta sinusoidal sigma weight residual 104.59 -40.36 144.96 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O3B GTP A 201 " pdb=" O3A GTP A 201 " pdb=" PB GTP A 201 " pdb=" PA GTP A 201 " ideal model delta sinusoidal sigma weight residual -68.92 74.77 -143.69 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' GTP A 201 " pdb=" O5' GTP A 201 " pdb=" PA GTP A 201 " pdb=" O3A GTP A 201 " ideal model delta sinusoidal sigma weight residual 69.27 -60.23 129.50 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1110 0.059 - 0.118: 117 0.118 - 0.177: 8 0.177 - 0.236: 3 0.236 - 0.296: 1 Chirality restraints: 1239 Sorted by residual: chirality pdb=" C3' GTP A 201 " pdb=" C2' GTP A 201 " pdb=" C4' GTP A 201 " pdb=" O3' GTP A 201 " both_signs ideal model delta sigma weight residual False -2.47 -2.77 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL A 128 " pdb=" CA VAL A 128 " pdb=" CG1 VAL A 128 " pdb=" CG2 VAL A 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL A 128 " pdb=" N VAL A 128 " pdb=" C VAL A 128 " pdb=" CB VAL A 128 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 1236 not shown) Planarity restraints: 1376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 70 " -0.029 2.00e-02 2.50e+03 1.69e-02 5.71e+00 pdb=" CG TYR B 70 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 70 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 67 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C GLY B 67 " -0.019 2.00e-02 2.50e+03 pdb=" O GLY B 67 " 0.007 2.00e-02 2.50e+03 pdb=" N GLN B 68 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 70 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.21e+00 pdb=" C TYR B 70 " 0.019 2.00e-02 2.50e+03 pdb=" O TYR B 70 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP B 71 " -0.007 2.00e-02 2.50e+03 ... (remaining 1373 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 16 2.45 - 3.07: 5117 3.07 - 3.68: 11252 3.68 - 4.29: 18278 4.29 - 4.90: 30404 Nonbonded interactions: 65067 Sorted by model distance: nonbonded pdb=" OD1 ASN B 124 " pdb="MN MN B 401 " model vdw 1.843 2.320 nonbonded pdb=" OD2 ASP B 92 " pdb="MN MN B 401 " model vdw 1.934 2.320 nonbonded pdb=" OG SER A 27 " pdb="MG MG A 202 " model vdw 1.984 2.170 nonbonded pdb=" O2G GTP A 201 " pdb="MG MG A 202 " model vdw 1.984 2.170 nonbonded pdb=" NE2 HIS B 66 " pdb="MN MN B 402 " model vdw 2.052 2.400 ... (remaining 65062 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.120 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:22.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 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 : 0.002 0.071 7915 Z= 0.166 Angle : 0.547 12.107 10724 Z= 0.271 Chirality : 0.041 0.296 1239 Planarity : 0.003 0.027 1376 Dihedral : 9.087 144.958 3017 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 964 helix: -0.18 (0.30), residues: 326 sheet: -0.36 (0.39), residues: 196 loop : 0.38 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 149 HIS 0.003 0.000 HIS B 248 PHE 0.005 0.001 PHE B 118 TYR 0.036 0.001 TYR B 70 ARG 0.001 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7958 (mp0) cc_final: 0.7721 (mp0) REVERT: C 567 PHE cc_start: 0.8644 (m-80) cc_final: 0.8328 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.4502 time to fit residues: 103.0531 Evaluate side-chains 42 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.048276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.037373 restraints weight = 27158.734| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 3.31 r_work: 0.2425 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 7915 Z= 0.245 Angle : 0.505 7.562 10724 Z= 0.258 Chirality : 0.040 0.132 1239 Planarity : 0.004 0.066 1376 Dihedral : 9.786 148.702 1055 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.57 % Allowed : 4.86 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 964 helix: -0.26 (0.31), residues: 336 sheet: -0.49 (0.38), residues: 196 loop : 0.37 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 401 HIS 0.003 0.001 HIS B 239 PHE 0.015 0.001 PHE C 535 TYR 0.013 0.001 TYR B 70 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9073 (mp0) cc_final: 0.8699 (mp0) REVERT: B 290 MET cc_start: 0.9232 (tpp) cc_final: 0.8815 (tpt) REVERT: C 567 PHE cc_start: 0.9068 (m-80) cc_final: 0.8589 (m-80) outliers start: 5 outliers final: 1 residues processed: 45 average time/residue: 1.3587 time to fit residues: 65.6213 Evaluate side-chains 41 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 85 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.047648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.036585 restraints weight = 27356.454| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 3.34 r_work: 0.2405 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7915 Z= 0.221 Angle : 0.478 6.554 10724 Z= 0.245 Chirality : 0.040 0.129 1239 Planarity : 0.003 0.032 1376 Dihedral : 9.514 147.207 1055 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.45 % Allowed : 4.86 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.28), residues: 964 helix: -0.28 (0.31), residues: 336 sheet: -0.64 (0.38), residues: 196 loop : 0.35 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 401 HIS 0.002 0.001 HIS B 66 PHE 0.007 0.001 PHE B 118 TYR 0.017 0.001 TYR B 70 ARG 0.006 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9106 (mp0) cc_final: 0.8736 (mp0) REVERT: C 94 LEU cc_start: 0.9565 (mt) cc_final: 0.9296 (mp) REVERT: C 362 MET cc_start: 0.9134 (mtm) cc_final: 0.8286 (ptp) REVERT: C 567 PHE cc_start: 0.9071 (m-80) cc_final: 0.8608 (m-80) outliers start: 4 outliers final: 1 residues processed: 45 average time/residue: 1.3416 time to fit residues: 64.9506 Evaluate side-chains 39 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.036200 restraints weight = 27490.239| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 3.33 r_work: 0.2396 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7915 Z= 0.221 Angle : 0.469 6.539 10724 Z= 0.241 Chirality : 0.039 0.127 1239 Planarity : 0.003 0.034 1376 Dihedral : 9.182 147.709 1055 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.45 % Allowed : 5.09 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 964 helix: -0.20 (0.31), residues: 330 sheet: -0.65 (0.38), residues: 196 loop : 0.39 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 60 HIS 0.002 0.001 HIS B 239 PHE 0.006 0.001 PHE B 118 TYR 0.015 0.001 TYR B 70 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 55 GLU cc_start: 0.9147 (tt0) cc_final: 0.8881 (mt-10) REVERT: C 386 MET cc_start: 0.9637 (mmm) cc_final: 0.9398 (mmp) REVERT: C 567 PHE cc_start: 0.9103 (m-80) cc_final: 0.8622 (m-80) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 1.3082 time to fit residues: 58.8168 Evaluate side-chains 37 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.036588 restraints weight = 27339.035| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 3.31 r_work: 0.2404 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7915 Z= 0.175 Angle : 0.466 7.113 10724 Z= 0.239 Chirality : 0.039 0.144 1239 Planarity : 0.003 0.034 1376 Dihedral : 8.766 146.625 1055 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.23 % Allowed : 5.43 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 964 helix: -0.19 (0.31), residues: 330 sheet: -0.66 (0.38), residues: 196 loop : 0.38 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 401 HIS 0.003 0.001 HIS B 239 PHE 0.007 0.001 PHE C 398 TYR 0.014 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 55 GLU cc_start: 0.9208 (tt0) cc_final: 0.8959 (mt-10) REVERT: A 73 GLU cc_start: 0.9333 (mp0) cc_final: 0.8657 (mp0) REVERT: C 94 LEU cc_start: 0.9547 (mp) cc_final: 0.9330 (mp) REVERT: C 362 MET cc_start: 0.9063 (mtm) cc_final: 0.8309 (ptp) REVERT: C 567 PHE cc_start: 0.9133 (m-80) cc_final: 0.8661 (m-80) outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 1.3777 time to fit residues: 62.0325 Evaluate side-chains 39 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 95 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.036801 restraints weight = 27234.911| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 3.34 r_work: 0.2416 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7915 Z= 0.148 Angle : 0.470 8.376 10724 Z= 0.238 Chirality : 0.039 0.136 1239 Planarity : 0.003 0.033 1376 Dihedral : 8.401 144.332 1055 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.23 % Allowed : 5.66 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.28), residues: 964 helix: -0.19 (0.31), residues: 330 sheet: -0.68 (0.38), residues: 199 loop : 0.44 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 206 HIS 0.003 0.000 HIS B 239 PHE 0.005 0.001 PHE A 106 TYR 0.013 0.001 TYR B 70 ARG 0.002 0.000 ARG C 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.9196 (tt0) cc_final: 0.8946 (mt-10) REVERT: C 94 LEU cc_start: 0.9563 (mp) cc_final: 0.9334 (mp) REVERT: C 362 MET cc_start: 0.9020 (mtm) cc_final: 0.8311 (ptp) REVERT: C 567 PHE cc_start: 0.9145 (m-80) cc_final: 0.8691 (m-80) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 1.3948 time to fit residues: 61.1468 Evaluate side-chains 39 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.047005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.036313 restraints weight = 27278.389| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 3.37 r_work: 0.2402 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7915 Z= 0.193 Angle : 0.486 9.132 10724 Z= 0.245 Chirality : 0.039 0.144 1239 Planarity : 0.003 0.036 1376 Dihedral : 8.311 143.402 1055 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.34 % Allowed : 5.88 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.28), residues: 964 helix: -0.19 (0.31), residues: 330 sheet: -0.66 (0.38), residues: 196 loop : 0.41 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 206 HIS 0.004 0.001 HIS B 239 PHE 0.006 0.001 PHE A 106 TYR 0.013 0.001 TYR B 70 ARG 0.001 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.9207 (tt0) cc_final: 0.8941 (mt-10) REVERT: A 73 GLU cc_start: 0.9339 (mp0) cc_final: 0.8750 (mp0) REVERT: C 94 LEU cc_start: 0.9564 (mt) cc_final: 0.9320 (mp) REVERT: C 362 MET cc_start: 0.9113 (mtm) cc_final: 0.8274 (ptp) REVERT: C 567 PHE cc_start: 0.9169 (m-80) cc_final: 0.8718 (m-80) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 1.4013 time to fit residues: 60.1972 Evaluate side-chains 39 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 66 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.036821 restraints weight = 27315.468| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 3.37 r_work: 0.2416 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7915 Z= 0.138 Angle : 0.489 9.972 10724 Z= 0.245 Chirality : 0.039 0.128 1239 Planarity : 0.003 0.032 1376 Dihedral : 8.092 141.309 1055 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.11 % Allowed : 6.22 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.28), residues: 964 helix: -0.18 (0.31), residues: 330 sheet: -0.71 (0.37), residues: 199 loop : 0.45 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 206 HIS 0.003 0.000 HIS B 239 PHE 0.005 0.001 PHE A 106 TYR 0.012 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.9227 (tt0) cc_final: 0.8975 (mt-10) REVERT: C 94 LEU cc_start: 0.9571 (mt) cc_final: 0.9325 (mp) REVERT: C 362 MET cc_start: 0.9043 (mtm) cc_final: 0.8357 (ptp) REVERT: C 567 PHE cc_start: 0.9176 (m-80) cc_final: 0.8711 (m-80) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 1.4525 time to fit residues: 62.2773 Evaluate side-chains 38 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 57 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.047230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.036552 restraints weight = 27616.295| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 3.39 r_work: 0.2408 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7915 Z= 0.165 Angle : 0.491 10.631 10724 Z= 0.245 Chirality : 0.039 0.128 1239 Planarity : 0.003 0.031 1376 Dihedral : 8.023 140.453 1055 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.11 % Allowed : 6.45 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 964 helix: -0.16 (0.31), residues: 330 sheet: -0.66 (0.38), residues: 196 loop : 0.44 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 206 HIS 0.004 0.001 HIS B 239 PHE 0.010 0.001 PHE C 535 TYR 0.012 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.9240 (tt0) cc_final: 0.8982 (mt-10) REVERT: A 73 GLU cc_start: 0.9353 (mp0) cc_final: 0.8699 (mp0) REVERT: A 79 GLU cc_start: 0.8787 (mp0) cc_final: 0.8572 (pm20) REVERT: C 94 LEU cc_start: 0.9558 (mt) cc_final: 0.9296 (mp) REVERT: C 173 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.8755 (tmm) REVERT: C 362 MET cc_start: 0.9112 (mtm) cc_final: 0.8319 (ptp) REVERT: C 567 PHE cc_start: 0.9184 (m-80) cc_final: 0.8720 (m-80) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 1.4537 time to fit residues: 60.6702 Evaluate side-chains 40 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.047245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.036537 restraints weight = 27582.162| |-----------------------------------------------------------------------------| r_work (start): 0.2572 rms_B_bonded: 3.38 r_work: 0.2407 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7915 Z= 0.166 Angle : 0.494 11.176 10724 Z= 0.248 Chirality : 0.039 0.128 1239 Planarity : 0.003 0.031 1376 Dihedral : 7.985 139.988 1055 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.28), residues: 964 helix: -0.17 (0.31), residues: 330 sheet: -0.69 (0.38), residues: 196 loop : 0.46 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 206 HIS 0.004 0.001 HIS B 239 PHE 0.006 0.001 PHE A 106 TYR 0.012 0.001 TYR B 70 ARG 0.001 0.000 ARG B 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.9232 (tt0) cc_final: 0.8977 (mt-10) REVERT: C 94 LEU cc_start: 0.9564 (mt) cc_final: 0.9311 (mp) REVERT: C 362 MET cc_start: 0.9095 (mtm) cc_final: 0.8281 (ptp) REVERT: C 567 PHE cc_start: 0.9171 (m-80) cc_final: 0.8704 (m-80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 1.4629 time to fit residues: 62.6054 Evaluate side-chains 38 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.047016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.036326 restraints weight = 27305.364| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 3.37 r_work: 0.2401 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7915 Z= 0.183 Angle : 0.504 11.262 10724 Z= 0.254 Chirality : 0.039 0.128 1239 Planarity : 0.003 0.035 1376 Dihedral : 7.990 140.093 1055 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.11 % Allowed : 6.56 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 964 helix: -0.17 (0.31), residues: 330 sheet: -0.68 (0.38), residues: 196 loop : 0.46 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 206 HIS 0.004 0.001 HIS B 239 PHE 0.010 0.001 PHE C 398 TYR 0.012 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3984.43 seconds wall clock time: 69 minutes 6.71 seconds (4146.71 seconds total)