Starting phenix.real_space_refine on Fri Sep 11 04:45:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xur_33477/09_2026/7xur_33477.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xur_33477/09_2026/7xur_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_33477/09_2026/7xur_33477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xur_33477/09_2026/7xur_33477.map" model { file = "/net/cci-nas-00/data/ceres_data/7xur_33477/09_2026/7xur_33477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xur_33477/09_2026/7xur_33477.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xur_33477/09_2026/7xur_33477.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xur_33477/09_2026/7xur_33477.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 1.84, per 1000 atoms: 0.24 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: 0.70 Conformation dependent library (CDL) restraints added in 485.9 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: 0.86 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: 0.94 Time building geometry restraints manager: 0.94 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=" C3' DG Y 56 " pdb=" C2' DG Y 56 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.29e+00 bond pdb=" C3' DA Y 54 " pdb=" O3' DA Y 54 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.16e+00 bond pdb=" C1' DT X -44 " pdb=" N1 DT X -44 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.97e+00 bond pdb=" N1 DC X -62 " pdb=" C6 DC X -62 " ideal model delta sigma weight residual 1.367 1.353 0.014 6.00e-03 2.78e+04 5.42e+00 bond pdb=" C3' DT Y 58 " pdb=" C2' DT Y 58 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.31e+00 ... (remaining 8025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 10551 1.75 - 3.50: 423 3.50 - 5.25: 43 5.25 - 7.00: 9 7.00 - 8.75: 2 Bond angle restraints: 11028 Sorted by residual: angle pdb=" O4' DG X -49 " pdb=" C4' DG X -49 " pdb=" C3' DG X -49 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" N3 DT X -64 " pdb=" C4 DT X -64 " pdb=" O4 DT X -64 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT X -65 " pdb=" C4 DT X -65 " pdb=" O4 DT X -65 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT X -59 " pdb=" C4 DT X -59 " pdb=" O4 DT X -59 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" O4 DT X -64 " pdb=" C4 DT X -64 " pdb=" C5 DT X -64 " ideal model delta sigma weight residual 124.90 122.02 2.88 7.00e-01 2.04e+00 1.69e+01 ... (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: 969 0.061 - 0.122: 176 0.122 - 0.183: 9 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=" C3' DT X -65 " pdb=" C4' DT X -65 " pdb=" O3' DT X -65 " pdb=" C2' DT X -65 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.81e-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: 1.930 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: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 9.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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= 0.335 Angle : 0.790 14.600 11036 Z= 0.531 Chirality : 0.045 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (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 ARG 0.004 0.000 ARG B 64 TYR 0.017 0.002 TYR A 389 PHE 0.011 0.002 PHE C 72 TRP 0.020 0.001 TRP A 317 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.33 ( 8030) covalent geometry : angle 0.76522 / 0.53 (11028) hydrogen bonds : bond 0.17228 / 11.89 ( 334) hydrogen bonds : angle 6.97897 / 5.01 ( 904) metal coordination : bond 0.01213 / 0.70 ( 8) metal coordination : angle 7.37709 / 6.03 ( 8) *********************** 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 : 0.312 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: 0.1095 time to fit residues: 9.9574 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 : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3760 r_free = 0.3760 target = 0.112152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099285 restraints weight = 17668.536| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.14 r_work: 0.3470 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8038 Z= 0.174 Angle : 0.712 12.514 11036 Z= 0.378 Chirality : 0.045 0.230 1155 Planarity : 0.005 0.066 1250 Dihedral : 20.617 89.039 1434 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.28 % Allowed : 6.79 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.28), residues: 796 helix: -0.22 (0.26), residues: 368 sheet: -1.57 (0.89), residues: 32 loop : -2.63 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 455 TYR 0.017 0.002 TYR A 389 PHE 0.012 0.002 PHE B 252 TRP 0.019 0.001 TRP A 317 HIS 0.022 0.002 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 8030) covalent geometry : angle 0.68908 / 0.38 (11028) hydrogen bonds : bond 0.05737 / 3.77 ( 334) hydrogen bonds : angle 5.29495 / 3.66 ( 904) metal coordination : bond 0.00915 / 0.56 ( 8) metal coordination : angle 6.73090 / 5.56 ( 8) *********************** 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 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.222 Fit side-chains REVERT: A 299 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7011 (tpt170) REVERT: B 119 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6041 (pm20) outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 0.1066 time to fit residues: 9.0667 Evaluate side-chains 60 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 23 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.0030 chunk 54 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 312 HIS B 198 HIS C 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.114420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101390 restraints weight = 17763.955| |-----------------------------------------------------------------------------| r_work (start): 0.3594 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: 0.7812 moved from start: 0.1301 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= 0.129 Angle : 0.622 11.864 11036 Z= 0.336 Chirality : 0.042 0.195 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.649 88.519 1434 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.69 % Allowed : 9.56 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.28), residues: 796 helix: 0.18 (0.27), residues: 358 sheet: -1.09 (0.96), residues: 32 loop : -2.35 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 140 TYR 0.017 0.002 TYR A 389 PHE 0.012 0.001 PHE B 251 TRP 0.015 0.001 TRP A 317 HIS 0.004 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 8030) covalent geometry : angle 0.60002 / 0.33 (11028) hydrogen bonds : bond 0.04703 / 3.06 ( 334) hydrogen bonds : angle 4.93282 / 3.39 ( 904) metal coordination : bond 0.00714 / 0.45 ( 8) metal coordination : angle 6.12561 / 5.10 ( 8) *********************** 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 74 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.417 Fit side-chains REVERT: A 299 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.6905 (tpt170) REVERT: A 501 LYS cc_start: 0.4915 (mttp) cc_final: 0.4657 (mttp) REVERT: B 119 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6004 (pm20) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 0.1069 time to fit residues: 10.5051 Evaluate side-chains 60 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.0020 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.113513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100298 restraints weight = 17912.724| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.24 r_work: 0.3485 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8038 Z= 0.144 Angle : 0.619 11.843 11036 Z= 0.331 Chirality : 0.042 0.188 1155 Planarity : 0.005 0.065 1250 Dihedral : 20.457 89.559 1434 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.55 % Allowed : 12.33 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.28), residues: 796 helix: 0.14 (0.27), residues: 365 sheet: -2.08 (0.74), residues: 46 loop : -2.43 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 64 TYR 0.016 0.002 TYR A 471 PHE 0.017 0.001 PHE A 283 TRP 0.015 0.001 TRP A 317 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8030) covalent geometry : angle 0.59681 / 0.33 (11028) hydrogen bonds : bond 0.04646 / 3.03 ( 334) hydrogen bonds : angle 4.89978 / 3.36 ( 904) metal coordination : bond 0.00643 / 0.43 ( 8) metal coordination : angle 6.09677 / 5.08 ( 8) *********************** 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 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.246 Fit side-chains REVERT: A 299 ARG cc_start: 0.7885 (tpp-160) cc_final: 0.6834 (tpt170) REVERT: B 119 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6011 (pm20) outliers start: 4 outliers final: 1 residues processed: 65 average time/residue: 0.1047 time to fit residues: 9.1586 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 : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.113634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.100418 restraints weight = 17752.910| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.23 r_work: 0.3488 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1533 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= 0.137 Angle : 0.603 11.679 11036 Z= 0.323 Chirality : 0.041 0.177 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.442 87.409 1434 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.11 % Allowed : 13.57 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.28), residues: 796 helix: 0.19 (0.27), residues: 367 sheet: -2.05 (0.75), residues: 46 loop : -2.36 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 64 TYR 0.015 0.002 TYR A 389 PHE 0.014 0.001 PHE A 283 TRP 0.015 0.001 TRP A 317 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 8030) covalent geometry : angle 0.58168 / 0.32 (11028) hydrogen bonds : bond 0.04376 / 2.88 ( 334) hydrogen bonds : angle 4.80754 / 3.29 ( 904) metal coordination : bond 0.00621 / 0.41 ( 8) metal coordination : angle 5.96820 / 4.95 ( 8) *********************** 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 : 0.292 Fit side-chains REVERT: A 299 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.6811 (tpt170) REVERT: A 501 LYS cc_start: 0.5103 (mttp) cc_final: 0.4893 (mttp) REVERT: B 119 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6029 (pm20) outliers start: 8 outliers final: 3 residues processed: 70 average time/residue: 0.1004 time to fit residues: 9.4874 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain B residue 335 LEU 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 14 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.0770 chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100880 restraints weight = 17708.117| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.20 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: 0.7828 moved from start: 0.1644 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= 0.132 Angle : 0.596 11.553 11036 Z= 0.320 Chirality : 0.041 0.168 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.324 84.863 1434 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.83 % Allowed : 14.82 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.28), residues: 796 helix: 0.27 (0.27), residues: 367 sheet: -2.00 (0.76), residues: 46 loop : -2.28 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.015 0.001 TYR A 389 PHE 0.019 0.001 PHE A 283 TRP 0.014 0.001 TRP A 317 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 8030) covalent geometry : angle 0.57478 / 0.32 (11028) hydrogen bonds : bond 0.04221 / 2.79 ( 334) hydrogen bonds : angle 4.75546 / 3.24 ( 904) metal coordination : bond 0.00610 / 0.41 ( 8) metal coordination : angle 5.91112 / 4.92 ( 8) *********************** 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 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.288 Fit side-chains REVERT: A 299 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.6835 (tpt170) REVERT: B 119 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6050 (pm20) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 0.0947 time to fit residues: 8.5886 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 : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain B residue 335 LEU 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 63 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099796 restraints weight = 17574.231| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.23 r_work: 0.3479 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8038 Z= 0.159 Angle : 0.618 11.762 11036 Z= 0.330 Chirality : 0.042 0.171 1155 Planarity : 0.004 0.064 1250 Dihedral : 20.313 82.285 1434 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.83 % Allowed : 14.82 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.28), residues: 796 helix: 0.30 (0.27), residues: 366 sheet: -2.08 (0.77), residues: 46 loop : -2.28 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 64 TYR 0.015 0.002 TYR A 389 PHE 0.017 0.001 PHE A 283 TRP 0.015 0.001 TRP A 317 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 8030) covalent geometry : angle 0.59643 / 0.33 (11028) hydrogen bonds : bond 0.04476 / 2.95 ( 334) hydrogen bonds : angle 4.80618 / 3.28 ( 904) metal coordination : bond 0.00662 / 0.43 ( 8) metal coordination : angle 6.02838 / 5.00 ( 8) *********************** 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 66 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.286 Fit side-chains REVERT: A 269 ILE cc_start: 0.5126 (pt) cc_final: 0.4864 (mm) REVERT: A 299 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.6827 (tpt170) REVERT: B 119 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6065 (pm20) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 0.1040 time to fit residues: 9.1293 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 : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain B residue 335 LEU 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 49 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.114470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101251 restraints weight = 17685.724| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.18 r_work: 0.3502 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8038 Z= 0.124 Angle : 0.591 11.505 11036 Z= 0.317 Chirality : 0.040 0.159 1155 Planarity : 0.004 0.062 1250 Dihedral : 20.223 80.394 1434 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.11 % Allowed : 14.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.29), residues: 796 helix: 0.40 (0.27), residues: 366 sheet: -2.02 (0.77), residues: 46 loop : -2.21 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 140 TYR 0.014 0.001 TYR A 389 PHE 0.015 0.001 PHE A 283 TRP 0.015 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8030) covalent geometry : angle 0.56924 / 0.32 (11028) hydrogen bonds : bond 0.04066 / 2.69 ( 334) hydrogen bonds : angle 4.69754 / 3.21 ( 904) metal coordination : bond 0.00568 / 0.38 ( 8) metal coordination : angle 5.88574 / 4.87 ( 8) *********************** 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 70 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.291 Fit side-chains REVERT: A 299 ARG cc_start: 0.7806 (tpp-160) cc_final: 0.6889 (tpt170) REVERT: A 499 MET cc_start: 0.7325 (ptt) cc_final: 0.6725 (mmp) REVERT: B 119 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6085 (pm20) outliers start: 8 outliers final: 4 residues processed: 69 average time/residue: 0.0978 time to fit residues: 9.0809 Evaluate side-chains 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.113355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100088 restraints weight = 17679.838| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.20 r_work: 0.3483 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1800 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= 0.158 Angle : 0.614 11.418 11036 Z= 0.328 Chirality : 0.042 0.164 1155 Planarity : 0.005 0.095 1250 Dihedral : 20.236 78.251 1434 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.83 % Allowed : 15.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.29), residues: 796 helix: 0.38 (0.27), residues: 366 sheet: -2.10 (0.77), residues: 46 loop : -2.21 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 75 TYR 0.015 0.002 TYR A 389 PHE 0.020 0.001 PHE A 283 TRP 0.015 0.001 TRP A 317 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8030) covalent geometry : angle 0.59192 / 0.33 (11028) hydrogen bonds : bond 0.04395 / 2.91 ( 334) hydrogen bonds : angle 4.74430 / 3.25 ( 904) metal coordination : bond 0.00652 / 0.42 ( 8) metal coordination : angle 6.06763 / 5.04 ( 8) *********************** 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 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.291 Fit side-chains REVERT: A 299 ARG cc_start: 0.7798 (tpp-160) cc_final: 0.6859 (tpt170) REVERT: B 119 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6053 (pm20) REVERT: B 335 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7346 (mp) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1085 time to fit residues: 9.1636 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 : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS 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 335 LEU 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 21 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101317 restraints weight = 17543.602| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.25 r_work: 0.3503 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8038 Z= 0.122 Angle : 0.584 10.815 11036 Z= 0.315 Chirality : 0.040 0.154 1155 Planarity : 0.005 0.089 1250 Dihedral : 20.146 76.115 1434 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.83 % Allowed : 15.79 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.29), residues: 796 helix: 0.43 (0.27), residues: 366 sheet: -2.12 (0.75), residues: 46 loop : -2.17 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 140 TYR 0.014 0.001 TYR A 389 PHE 0.020 0.001 PHE A 283 TRP 0.015 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8030) covalent geometry : angle 0.56250 / 0.31 (11028) hydrogen bonds : bond 0.03985 / 2.65 ( 334) hydrogen bonds : angle 4.66540 / 3.19 ( 904) metal coordination : bond 0.00516 / 0.37 ( 8) metal coordination : angle 5.80995 / 4.83 ( 8) ********************** 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 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.296 Fit side-chains REVERT: A 299 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.6890 (tpt170) REVERT: A 499 MET cc_start: 0.7078 (ptt) cc_final: 0.6591 (mmp) REVERT: B 119 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6085 (pm20) REVERT: B 335 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7264 (mp) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.1093 time to fit residues: 9.2278 Evaluate side-chains 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS 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 335 LEU 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 51 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098921 restraints weight = 17681.411| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.13 r_work: 0.3465 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8038 Z= 0.201 Angle : 0.659 11.900 11036 Z= 0.349 Chirality : 0.043 0.182 1155 Planarity : 0.005 0.085 1250 Dihedral : 20.263 75.174 1434 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.39 % Allowed : 15.65 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.28), residues: 796 helix: 0.34 (0.27), residues: 366 sheet: -1.39 (0.92), residues: 34 loop : -2.32 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.016 0.002 TYR A 389 PHE 0.018 0.002 PHE A 283 TRP 0.015 0.001 TRP A 317 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 ( 8030) covalent geometry : angle 0.63665 / 0.35 (11028) hydrogen bonds : bond 0.04856 / 3.22 ( 334) hydrogen bonds : angle 4.84459 / 3.31 ( 904) metal coordination : bond 0.00756 / 0.48 ( 8) metal coordination : angle 6.28579 / 5.21 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.54 seconds wall clock time: 26 minutes 25.67 seconds (1585.67 seconds total)