Starting phenix.real_space_refine on Wed Feb 12 10:00:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xur_33477/02_2025/7xur_33477.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xur_33477/02_2025/7xur_33477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xur_33477/02_2025/7xur_33477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xur_33477/02_2025/7xur_33477.map" model { file = "/net/cci-nas-00/data/ceres_data/7xur_33477/02_2025/7xur_33477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xur_33477/02_2025/7xur_33477.cif" } resolution = 3.49 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= 0.048 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 48 5.49 5 S 37 5.16 5 C 4789 2.51 5 N 1358 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2575 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 3 Chain: "B" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2970 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 346} Chain breaks: 3 Chain: "C" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1218 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "X" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 491 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "Y" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3989 SG CYS B 221 47.978 59.465 63.902 1.00 45.55 S ATOM 4755 SG CYS B 317 47.149 63.072 65.218 1.00 41.15 S ATOM 5077 SG CYS B 354 42.014 56.574 39.587 1.00 56.99 S ATOM 5101 SG CYS B 357 42.759 54.951 36.094 1.00 61.59 S ATOM 5292 SG CYS B 380 45.586 56.425 38.451 1.00 57.93 S ATOM 5313 SG CYS B 383 43.384 58.310 36.240 1.00 60.97 S Time building chain proxies: 5.30, per 1000 atoms: 0.68 Number of scatterers: 7749 At special positions: 0 Unit cell: (76.396, 109.752, 119.436, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 37 16.00 P 48 15.00 O 1515 8.00 N 1358 7.00 C 4789 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 938.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 313 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 319 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 317 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 221 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 383 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 380 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 357 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 354 " Number of angles added : 8 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1546 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 53.1% alpha, 6.0% beta 23 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.786A pdb=" N ARG A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.753A pdb=" N LEU A 179 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 180 " --> pdb=" O GLU A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.842A pdb=" N ASN A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.016A pdb=" N LEU A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 264 through 270 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.955A pdb=" N GLN A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.767A pdb=" N GLU A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.583A pdb=" N CYS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 364 removed outlier: 3.922A pdb=" N ASP A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.834A pdb=" N ILE A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 423 through 431 removed outlier: 4.289A pdb=" N GLU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 457 through 472 removed outlier: 3.518A pdb=" N GLU A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 487 through 502 removed outlier: 3.728A pdb=" N LEU A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 380 through 388 removed outlier: 3.976A pdb=" N ARG B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.764A pdb=" N PHE B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 removed outlier: 4.069A pdb=" N ASP C 10 " --> pdb=" O GLY C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 36 removed outlier: 3.530A pdb=" N THR C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 47 through 67 removed outlier: 3.514A pdb=" N LEU C 67 " --> pdb=" O TRP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.902A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 removed outlier: 3.793A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 3.799A pdb=" N ALA C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.608A pdb=" N SER B 183 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE B 326 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 181 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 289 through 292 removed outlier: 3.737A pdb=" N LEU B 310 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 317 " --> pdb=" O HIS B 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 379 Processing sheet with id=AA4, first strand: chain 'C' and resid 97 through 99 281 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.77 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: 1.21 - 1.33: 2109 1.33 - 1.45: 1741 1.45 - 1.57: 4032 1.57 - 1.69: 94 1.69 - 1.81: 54 Bond restraints: 8030 Sorted by residual: bond pdb=" C4' DG Y 56 " pdb=" O4' DG Y 56 " ideal model delta sigma weight residual 1.450 1.430 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C1' DG X -67 " pdb=" N9 DG X -67 " ideal model delta sigma weight residual 1.460 1.440 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA VAL B 356 " pdb=" CB VAL B 356 " ideal model delta sigma weight residual 1.545 1.536 0.009 9.10e-03 1.21e+04 9.44e-01 bond pdb=" C PRO C 68 " pdb=" N PRO C 69 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.94e-01 bond pdb=" CG LEU B 207 " pdb=" CD1 LEU B 207 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.14e-01 ... (remaining 8025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 10644 1.75 - 3.50: 330 3.50 - 5.25: 43 5.25 - 7.00: 9 7.00 - 8.75: 2 Bond angle restraints: 11028 Sorted by residual: angle pdb=" N PRO C 68 " pdb=" CA PRO C 68 " pdb=" C PRO C 68 " ideal model delta sigma weight residual 110.70 115.46 -4.76 1.22e+00 6.72e-01 1.52e+01 angle pdb=" C LYS B 199 " pdb=" N PRO B 200 " pdb=" CA PRO B 200 " ideal model delta sigma weight residual 119.84 123.76 -3.92 1.25e+00 6.40e-01 9.81e+00 angle pdb=" CA PRO C 93 " pdb=" C PRO C 93 " pdb=" O PRO C 93 " ideal model delta sigma weight residual 123.07 119.40 3.67 1.38e+00 5.25e-01 7.07e+00 angle pdb=" CA PRO C 68 " pdb=" C PRO C 68 " pdb=" N PRO C 69 " ideal model delta sigma weight residual 117.93 121.09 -3.16 1.20e+00 6.94e-01 6.93e+00 angle pdb=" CA LYS B 199 " pdb=" C LYS B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 118.83 116.55 2.28 8.70e-01 1.32e+00 6.87e+00 ... (remaining 11023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3825 17.61 - 35.21: 594 35.21 - 52.81: 206 52.81 - 70.42: 58 70.42 - 88.02: 14 Dihedral angle restraints: 4697 sinusoidal: 2314 harmonic: 2383 Sorted by residual: dihedral pdb=" CA TRP B 277 " pdb=" C TRP B 277 " pdb=" N SER B 278 " pdb=" CA SER B 278 " ideal model delta harmonic sigma weight residual 180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA SER A 287 " pdb=" C SER A 287 " pdb=" N GLU A 288 " pdb=" CA GLU A 288 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA HIS C 119 " pdb=" C HIS C 119 " pdb=" N PHE C 120 " pdb=" CA PHE C 120 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 995 0.061 - 0.122: 153 0.122 - 0.183: 6 0.183 - 0.244: 0 0.244 - 0.305: 1 Chirality restraints: 1155 Sorted by residual: chirality pdb=" CB VAL A 376 " pdb=" CA VAL A 376 " pdb=" CG1 VAL A 376 " pdb=" CG2 VAL A 376 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PRO B 35 " pdb=" N PRO B 35 " pdb=" C PRO B 35 " pdb=" CB PRO B 35 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CG LEU A 387 " pdb=" CB LEU A 387 " pdb=" CD1 LEU A 387 " pdb=" CD2 LEU A 387 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1152 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 117 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO B 118 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 307 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 308 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 67 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO C 68 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " -0.023 5.00e-02 4.00e+02 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 932 2.75 - 3.28: 7331 3.28 - 3.82: 12430 3.82 - 4.36: 14458 4.36 - 4.90: 24478 Nonbonded interactions: 59629 Sorted by model distance: nonbonded pdb=" OD1 ASN B 185 " pdb=" OG1 THR B 203 " model vdw 2.207 3.040 nonbonded pdb=" NE2 GLN A 490 " pdb=" OP2 DT X -65 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASN B 170 " pdb=" N SER B 171 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR B 125 " pdb=" OD1 ASP B 126 " model vdw 2.273 3.040 nonbonded pdb=" NE1 TRP A 456 " pdb=" OE1 GLN A 490 " model vdw 2.275 3.120 ... (remaining 59624 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: 1.770 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.720 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.005 0.035 8030 Z= 0.288 Angle : 0.722 8.747 11028 Z= 0.417 Chirality : 0.042 0.305 1155 Planarity : 0.004 0.068 1250 Dihedral : 19.356 88.023 3151 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.26 (0.28), residues: 796 helix: -0.31 (0.27), residues: 362 sheet: -1.45 (0.93), residues: 32 loop : -2.74 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 317 HIS 0.005 0.001 HIS B 331 PHE 0.011 0.002 PHE C 72 TYR 0.017 0.002 TYR A 389 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.836 Fit side-chains REVERT: A 299 ARG cc_start: 0.7718 (tpp-160) cc_final: 0.6992 (tpt170) REVERT: B 119 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6233 (pm20) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2540 time to fit residues: 22.8282 Evaluate side-chains 55 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS B 152 GLN B 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.112878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099952 restraints weight = 17601.831| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.16 r_work: 0.3484 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8030 Z= 0.220 Angle : 0.644 9.411 11028 Z= 0.355 Chirality : 0.042 0.223 1155 Planarity : 0.005 0.065 1250 Dihedral : 20.665 89.806 1434 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.28 % Allowed : 6.93 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.96 (0.28), residues: 796 helix: -0.04 (0.27), residues: 361 sheet: -1.49 (0.91), residues: 32 loop : -2.57 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 317 HIS 0.021 0.002 HIS A 340 PHE 0.014 0.001 PHE B 251 TYR 0.017 0.002 TYR A 389 ARG 0.005 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.757 Fit side-chains REVERT: A 299 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.6975 (tpt170) REVERT: B 119 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6002 (pm20) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.2357 time to fit residues: 20.6013 Evaluate side-chains 59 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 312 HIS B 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.113840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100668 restraints weight = 17942.971| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.19 r_work: 0.3491 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8030 Z= 0.209 Angle : 0.592 8.873 11028 Z= 0.327 Chirality : 0.040 0.190 1155 Planarity : 0.004 0.064 1250 Dihedral : 20.334 89.414 1434 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.55 % Allowed : 10.80 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.28), residues: 796 helix: 0.11 (0.27), residues: 367 sheet: -2.28 (0.72), residues: 46 loop : -2.42 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 317 HIS 0.003 0.001 HIS B 331 PHE 0.011 0.001 PHE B 251 TYR 0.016 0.002 TYR A 389 ARG 0.003 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.787 Fit side-chains REVERT: A 299 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.6795 (tpt170) REVERT: A 356 MET cc_start: 0.7815 (tpt) cc_final: 0.7157 (ttm) REVERT: A 501 LYS cc_start: 0.5076 (mttp) cc_final: 0.4829 (mttp) REVERT: B 119 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6060 (pm20) outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 0.2251 time to fit residues: 21.4436 Evaluate side-chains 62 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 0.0470 chunk 63 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 286 ASN B 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.114733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101391 restraints weight = 17423.361| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.23 r_work: 0.3503 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8030 Z= 0.184 Angle : 0.554 8.716 11028 Z= 0.306 Chirality : 0.038 0.168 1155 Planarity : 0.004 0.062 1250 Dihedral : 20.239 88.433 1434 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.97 % Allowed : 12.47 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.53 (0.28), residues: 796 helix: 0.30 (0.27), residues: 368 sheet: -1.18 (0.93), residues: 34 loop : -2.38 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 317 HIS 0.003 0.001 HIS B 331 PHE 0.014 0.001 PHE A 283 TYR 0.015 0.001 TYR A 389 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.859 Fit side-chains REVERT: A 299 ARG cc_start: 0.7818 (tpp-160) cc_final: 0.6855 (tpt170) REVERT: B 119 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6069 (pm20) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.2495 time to fit residues: 23.6423 Evaluate side-chains 66 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 0.0030 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.114090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100775 restraints weight = 17522.670| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.22 r_work: 0.3495 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8030 Z= 0.198 Angle : 0.561 8.655 11028 Z= 0.310 Chirality : 0.039 0.163 1155 Planarity : 0.005 0.071 1250 Dihedral : 20.187 86.464 1434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.83 % Allowed : 13.57 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.46 (0.28), residues: 796 helix: 0.33 (0.27), residues: 368 sheet: -1.15 (0.95), residues: 34 loop : -2.30 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 317 HIS 0.002 0.001 HIS A 289 PHE 0.014 0.001 PHE A 283 TYR 0.014 0.001 TYR A 389 ARG 0.007 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.860 Fit side-chains REVERT: A 299 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.6867 (tpt170) REVERT: B 119 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6086 (pm20) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.2404 time to fit residues: 21.3245 Evaluate side-chains 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 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 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098177 restraints weight = 17445.868| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.11 r_work: 0.3454 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8030 Z= 0.323 Angle : 0.640 8.810 11028 Z= 0.349 Chirality : 0.042 0.188 1155 Planarity : 0.005 0.065 1250 Dihedral : 20.434 82.782 1434 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.39 % Allowed : 14.82 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.28), residues: 796 helix: 0.05 (0.26), residues: 372 sheet: -1.33 (0.94), residues: 34 loop : -2.51 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 317 HIS 0.004 0.001 HIS B 43 PHE 0.015 0.002 PHE A 283 TYR 0.015 0.002 TYR A 389 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.855 Fit side-chains REVERT: A 299 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.6913 (tpt170) REVERT: B 119 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6141 (pm20) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.2364 time to fit residues: 22.3148 Evaluate side-chains 66 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 69 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.114702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101469 restraints weight = 17654.344| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.18 r_work: 0.3505 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8030 Z= 0.171 Angle : 0.551 8.607 11028 Z= 0.305 Chirality : 0.038 0.153 1155 Planarity : 0.004 0.061 1250 Dihedral : 20.136 77.785 1434 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.69 % Allowed : 16.62 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.43 (0.29), residues: 796 helix: 0.40 (0.27), residues: 367 sheet: -2.11 (0.76), residues: 46 loop : -2.22 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 PHE 0.017 0.001 PHE A 283 TYR 0.014 0.001 TYR A 389 ARG 0.003 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.806 Fit side-chains REVERT: A 299 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.6867 (tpt170) REVERT: B 119 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6092 (pm20) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.2401 time to fit residues: 21.2315 Evaluate side-chains 62 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 0.0070 chunk 45 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.114952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101659 restraints weight = 17597.572| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.18 r_work: 0.3507 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8030 Z= 0.174 Angle : 0.549 8.201 11028 Z= 0.301 Chirality : 0.038 0.148 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.053 70.551 1434 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.83 % Allowed : 16.76 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.26 (0.29), residues: 796 helix: 0.47 (0.27), residues: 368 sheet: -1.18 (0.95), residues: 34 loop : -2.16 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 PHE 0.010 0.001 PHE B 251 TYR 0.013 0.001 TYR A 389 ARG 0.007 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.822 Fit side-chains REVERT: A 299 ARG cc_start: 0.7748 (tpp-160) cc_final: 0.6861 (tpt170) REVERT: B 119 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6092 (pm20) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.2549 time to fit residues: 23.4287 Evaluate side-chains 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 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 = 0.3792 r_free = 0.3792 target = 0.114500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101224 restraints weight = 17721.876| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.18 r_work: 0.3499 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8030 Z= 0.193 Angle : 0.559 8.048 11028 Z= 0.308 Chirality : 0.038 0.154 1155 Planarity : 0.005 0.086 1250 Dihedral : 20.059 70.412 1434 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.83 % Allowed : 16.76 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.24 (0.29), residues: 796 helix: 0.51 (0.27), residues: 367 sheet: -1.24 (0.95), residues: 34 loop : -2.16 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 PHE 0.011 0.001 PHE B 251 TYR 0.013 0.001 TYR A 389 ARG 0.014 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.918 Fit side-chains REVERT: A 299 ARG cc_start: 0.7753 (tpp-160) cc_final: 0.6857 (tpt170) REVERT: B 119 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6085 (pm20) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.2470 time to fit residues: 22.9822 Evaluate side-chains 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 chunk 72 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.116631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103127 restraints weight = 17624.522| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.23 r_work: 0.3528 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8030 Z= 0.156 Angle : 0.544 8.182 11028 Z= 0.301 Chirality : 0.037 0.137 1155 Planarity : 0.005 0.085 1250 Dihedral : 19.904 66.899 1434 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 0.83 % Allowed : 16.34 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.17 (0.29), residues: 796 helix: 0.61 (0.27), residues: 368 sheet: -2.12 (0.75), residues: 46 loop : -2.06 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 PHE 0.011 0.001 PHE A 449 TYR 0.013 0.001 TYR A 389 ARG 0.005 0.000 ARG B 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.830 Fit side-chains REVERT: A 299 ARG cc_start: 0.7740 (tpp-160) cc_final: 0.6978 (tpt170) REVERT: A 387 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8315 (mp) REVERT: B 119 GLU cc_start: 0.7457 (mm-30) cc_final: 0.5990 (pm20) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2226 time to fit residues: 21.4077 Evaluate side-chains 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.115089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101688 restraints weight = 17502.109| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.20 r_work: 0.3506 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8030 Z= 0.199 Angle : 0.567 7.857 11028 Z= 0.312 Chirality : 0.039 0.148 1155 Planarity : 0.005 0.084 1250 Dihedral : 20.000 67.815 1434 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.40 % Favored : 94.47 % Rotamer: Outliers : 0.69 % Allowed : 17.31 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.13 (0.29), residues: 796 helix: 0.59 (0.27), residues: 369 sheet: -1.35 (0.92), residues: 34 loop : -2.08 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 PHE 0.010 0.001 PHE B 251 TYR 0.013 0.001 TYR A 443 ARG 0.004 0.000 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.96 seconds wall clock time: 54 minutes 27.12 seconds (3267.12 seconds total)