Starting phenix.real_space_refine on Fri Jun 6 12:17:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xur_33477/06_2025/7xur_33477.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xur_33477/06_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_33477/06_2025/7xur_33477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xur_33477/06_2025/7xur_33477.map" model { file = "/net/cci-nas-00/data/ceres_data/7xur_33477/06_2025/7xur_33477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xur_33477/06_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-5710/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: 5.33, per 1000 atoms: 0.69 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 936.6 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: 2.40 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: 2.34 Time building geometry restraints manager: 2.27 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: 1.390 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.350 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- 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 8038 Z= 0.210 Angle : 0.749 14.600 11036 Z= 0.419 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 Details of bonding type rmsd hydrogen bonds : bond 0.17228 ( 334) hydrogen bonds : angle 6.97897 ( 904) metal coordination : bond 0.01213 ( 8) metal coordination : angle 7.37709 ( 8) covalent geometry : bond 0.00463 ( 8030) covalent geometry : angle 0.72231 (11028) *********************** 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 : 0.899 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: 0.2488 time to fit residues: 22.3676 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 : 0.853 ------------------------------------------------------------------------------- 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): 0.3573 rms_B_bonded: 2.16 r_work: 0.3484 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 8038 Z= 0.161 Angle : 0.670 12.666 11036 Z= 0.357 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 Details of bonding type rmsd hydrogen bonds : bond 0.05189 ( 334) hydrogen bonds : angle 5.15286 ( 904) metal coordination : bond 0.00786 ( 8) metal coordination : angle 6.88222 ( 8) covalent geometry : bond 0.00357 ( 8030) covalent geometry : angle 0.64435 (11028) *********************** 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 : 0.828 Fit side-chains REVERT: A 299 ARG cc_start: 0.8009 (tpp-160) cc_final: 0.6973 (tpt170) REVERT: B 119 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6004 (pm20) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.3953 time to fit residues: 33.9805 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 : 0.852 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.113704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100445 restraints weight = 17743.922| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.22 r_work: 0.3488 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8038 Z= 0.150 Angle : 0.615 12.390 11036 Z= 0.328 Chirality : 0.040 0.190 1155 Planarity : 0.004 0.064 1250 Dihedral : 20.334 89.401 1434 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.55 % Allowed : 10.66 % Favored : 88.78 % 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 : -2.41 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 317 HIS 0.004 0.001 HIS A 340 PHE 0.011 0.001 PHE B 251 TYR 0.016 0.002 TYR A 389 ARG 0.004 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 334) hydrogen bonds : angle 4.89567 ( 904) metal coordination : bond 0.00599 ( 8) metal coordination : angle 6.31668 ( 8) covalent geometry : bond 0.00337 ( 8030) covalent geometry : angle 0.59137 (11028) *********************** 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 70 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.557 Fit side-chains REVERT: A 299 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.6792 (tpt170) REVERT: A 356 MET cc_start: 0.7807 (tpt) cc_final: 0.7136 (ttm) REVERT: A 501 LYS cc_start: 0.5057 (mttp) cc_final: 0.4810 (mttp) REVERT: B 119 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6045 (pm20) outliers start: 4 outliers final: 1 residues processed: 70 average time/residue: 0.4323 time to fit residues: 42.2618 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 : 1.074 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.0770 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.114950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101781 restraints weight = 17623.665| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.17 r_work: 0.3511 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8038 Z= 0.129 Angle : 0.574 11.408 11036 Z= 0.307 Chirality : 0.038 0.173 1155 Planarity : 0.004 0.062 1250 Dihedral : 20.234 88.648 1434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.83 % Allowed : 12.47 % Favored : 86.70 % 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: -1.56 (0.28), residues: 796 helix: 0.31 (0.27), residues: 368 sheet: -2.06 (0.75), residues: 46 loop : -2.34 (0.28), residues: 382 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 0.014 0.001 PHE A 283 TYR 0.015 0.001 TYR A 389 ARG 0.003 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 334) hydrogen bonds : angle 4.72479 ( 904) metal coordination : bond 0.00602 ( 8) metal coordination : angle 5.90323 ( 8) covalent geometry : bond 0.00287 ( 8030) covalent geometry : angle 0.55201 (11028) *********************** 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: 6 poor density : 67 time to evaluate : 0.773 Fit side-chains REVERT: A 299 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.6887 (tpt170) REVERT: B 119 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6098 (pm20) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2251 time to fit residues: 21.2473 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 : 0.760 ------------------------------------------------------------------------------- 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: 0.5980 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.114662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101391 restraints weight = 17679.197| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.19 r_work: 0.3504 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8038 Z= 0.136 Angle : 0.573 11.247 11036 Z= 0.306 Chirality : 0.038 0.156 1155 Planarity : 0.005 0.070 1250 Dihedral : 20.125 85.889 1434 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.11 % Allowed : 13.30 % 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: 0.36 (0.27), residues: 368 sheet: -2.03 (0.76), residues: 46 loop : -2.23 (0.28), residues: 382 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 0.015 0.001 PHE A 283 TYR 0.014 0.001 TYR A 389 ARG 0.008 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 334) hydrogen bonds : angle 4.66422 ( 904) metal coordination : bond 0.00567 ( 8) metal coordination : angle 5.75302 ( 8) covalent geometry : bond 0.00302 ( 8030) covalent geometry : angle 0.55229 (11028) *********************** 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 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.800 Fit side-chains REVERT: A 299 ARG cc_start: 0.7774 (tpp-160) cc_final: 0.6869 (tpt170) REVERT: B 119 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6085 (pm20) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.2465 time to fit residues: 22.5811 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 : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 376 VAL 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: 0.8980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.114063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.100821 restraints weight = 17469.782| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.19 r_work: 0.3492 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8038 Z= 0.145 Angle : 0.581 11.001 11036 Z= 0.309 Chirality : 0.039 0.157 1155 Planarity : 0.004 0.062 1250 Dihedral : 20.135 81.605 1434 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.25 % Allowed : 14.68 % Favored : 84.07 % 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: -1.41 (0.29), residues: 796 helix: 0.42 (0.27), residues: 367 sheet: -2.06 (0.76), residues: 46 loop : -2.21 (0.28), residues: 383 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 0.018 0.001 PHE A 283 TYR 0.014 0.001 TYR A 389 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 334) hydrogen bonds : angle 4.65827 ( 904) metal coordination : bond 0.00615 ( 8) metal coordination : angle 5.90001 ( 8) covalent geometry : bond 0.00329 ( 8030) covalent geometry : angle 0.55916 (11028) *********************** 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 75 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.911 Fit side-chains REVERT: A 299 ARG cc_start: 0.7785 (tpp-160) cc_final: 0.6856 (tpt170) REVERT: B 119 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6077 (pm20) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.2439 time to fit residues: 23.8097 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 : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 376 VAL 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 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 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 = 0.3774 r_free = 0.3774 target = 0.113382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100185 restraints weight = 17737.080| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.17 r_work: 0.3482 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8038 Z= 0.159 Angle : 0.602 11.414 11036 Z= 0.319 Chirality : 0.039 0.161 1155 Planarity : 0.004 0.056 1250 Dihedral : 20.151 76.200 1434 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 1.11 % Allowed : 15.79 % Favored : 83.10 % 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: -1.34 (0.29), residues: 796 helix: 0.42 (0.27), residues: 367 sheet: -1.21 (0.95), residues: 34 loop : -2.22 (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 B 43 PHE 0.011 0.001 PHE B 251 TYR 0.014 0.001 TYR A 389 ARG 0.013 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 334) hydrogen bonds : angle 4.69085 ( 904) metal coordination : bond 0.00666 ( 8) metal coordination : angle 6.09046 ( 8) covalent geometry : bond 0.00361 ( 8030) covalent geometry : angle 0.57937 (11028) *********************** 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 69 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.830 Fit side-chains REVERT: A 299 ARG cc_start: 0.7777 (tpp-160) cc_final: 0.7016 (tpt170) REVERT: B 119 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6095 (pm20) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.2504 time to fit residues: 22.3872 Evaluate side-chains 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 376 VAL 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 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 0.0170 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.0070 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.116733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.103404 restraints weight = 17501.933| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.17 r_work: 0.3534 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8038 Z= 0.113 Angle : 0.546 9.996 11036 Z= 0.293 Chirality : 0.037 0.144 1155 Planarity : 0.005 0.081 1250 Dihedral : 19.892 68.552 1434 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 0.97 % Allowed : 16.34 % 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: -1.20 (0.29), residues: 796 helix: 0.59 (0.27), residues: 367 sheet: -2.04 (0.75), residues: 46 loop : -2.09 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 317 HIS 0.002 0.001 HIS B 331 PHE 0.012 0.001 PHE B 47 TYR 0.013 0.001 TYR A 389 ARG 0.006 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 334) hydrogen bonds : angle 4.49013 ( 904) metal coordination : bond 0.00386 ( 8) metal coordination : angle 5.48330 ( 8) covalent geometry : bond 0.00246 ( 8030) covalent geometry : angle 0.52620 (11028) *********************** 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 75 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.896 Fit side-chains REVERT: A 299 ARG cc_start: 0.7723 (tpp-160) cc_final: 0.6967 (tpt170) REVERT: A 341 ASN cc_start: 0.7937 (t0) cc_final: 0.7736 (t0) REVERT: B 119 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6007 (pm20) outliers start: 7 outliers final: 2 residues processed: 74 average time/residue: 0.2477 time to fit residues: 24.4951 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 : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 285 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 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 = 0.3798 r_free = 0.3798 target = 0.114810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101538 restraints weight = 17659.229| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.17 r_work: 0.3506 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8038 Z= 0.141 Angle : 0.573 10.814 11036 Z= 0.304 Chirality : 0.038 0.146 1155 Planarity : 0.005 0.083 1250 Dihedral : 19.962 69.107 1434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.15 % Favored : 94.72 % Rotamer: Outliers : 0.83 % Allowed : 16.48 % 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: -1.18 (0.29), residues: 796 helix: 0.59 (0.27), residues: 369 sheet: -2.15 (0.74), residues: 46 loop : -2.05 (0.29), residues: 381 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 389 ARG 0.008 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 334) hydrogen bonds : angle 4.53826 ( 904) metal coordination : bond 0.00602 ( 8) metal coordination : angle 5.71295 ( 8) covalent geometry : bond 0.00319 ( 8030) covalent geometry : angle 0.55247 (11028) *********************** 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 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.884 Fit side-chains REVERT: A 299 ARG cc_start: 0.7702 (tpp-160) cc_final: 0.6812 (tpt170) REVERT: A 341 ASN cc_start: 0.7964 (t0) cc_final: 0.7756 (t0) REVERT: A 499 MET cc_start: 0.7391 (ptt) cc_final: 0.6741 (mmp) REVERT: B 119 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6050 (pm20) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2229 time to fit residues: 21.5739 Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL 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: 4.9990 chunk 1 optimal weight: 0.0170 chunk 72 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 15 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.117182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103814 restraints weight = 17848.502| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.19 r_work: 0.3539 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8038 Z= 0.113 Angle : 0.543 9.835 11036 Z= 0.291 Chirality : 0.037 0.142 1155 Planarity : 0.004 0.082 1250 Dihedral : 19.800 65.774 1434 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.42 % Allowed : 17.17 % 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: -1.07 (0.29), residues: 796 helix: 0.68 (0.28), residues: 369 sheet: -2.12 (0.72), residues: 46 loop : -1.99 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.007 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 334) hydrogen bonds : angle 4.42098 ( 904) metal coordination : bond 0.00416 ( 8) metal coordination : angle 5.30155 ( 8) covalent geometry : bond 0.00246 ( 8030) covalent geometry : angle 0.52452 (11028) ********************** 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 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 299 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.6951 (tpt170) REVERT: A 387 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 499 MET cc_start: 0.7535 (ptt) cc_final: 0.6828 (mmp) REVERT: B 119 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6090 (pm20) outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.2229 time to fit residues: 21.5508 Evaluate side-chains 66 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU 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 26 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.116437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103013 restraints weight = 17431.924| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.16 r_work: 0.3528 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8038 Z= 0.123 Angle : 0.559 10.297 11036 Z= 0.297 Chirality : 0.037 0.140 1155 Planarity : 0.004 0.082 1250 Dihedral : 19.825 65.454 1434 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.55 % Allowed : 17.31 % Favored : 82.13 % 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: -1.05 (0.29), residues: 796 helix: 0.66 (0.27), residues: 371 sheet: -2.01 (0.73), residues: 46 loop : -1.97 (0.29), residues: 379 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 0.010 0.001 PHE B 251 TYR 0.012 0.001 TYR A 443 ARG 0.006 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 334) hydrogen bonds : angle 4.44325 ( 904) metal coordination : bond 0.00469 ( 8) metal coordination : angle 5.41646 ( 8) covalent geometry : bond 0.00274 ( 8030) covalent geometry : angle 0.54013 (11028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3409.30 seconds wall clock time: 60 minutes 20.46 seconds (3620.46 seconds total)