Starting phenix.real_space_refine on Thu Jul 2 07:58:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xur_33477/07_2026/7xur_33477.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xur_33477/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xur_33477/07_2026/7xur_33477.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xur_33477/07_2026/7xur_33477.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xur_33477/07_2026/7xur_33477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xur_33477/07_2026/7xur_33477.map" model { file = "/net/cci-nas-00/data/ceres_data/7xur_33477/07_2026/7xur_33477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xur_33477/07_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-dev-6108/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: 1.95, per 1000 atoms: 0.25 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: 0.47 Conformation dependent library (CDL) restraints added in 375.1 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: 0.83 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: 0.89 Time building geometry restraints manager: 0.73 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: 10552 1.75 - 3.50: 422 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: 2.390 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.970 Find NCS groups from input model: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- 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 : 0.789 14.600 11036 Z= 0.530 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 0.76370 / 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 : 0.356 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: 0.0885 time to fit residues: 7.9187 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 : 0.190 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.112250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099368 restraints weight = 17699.556| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.14 r_work: 0.3473 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8038 Z= 0.174 Angle : 0.709 12.466 11036 Z= 0.377 Chirality : 0.045 0.237 1155 Planarity : 0.005 0.066 1250 Dihedral : 20.676 89.773 1434 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.28 % Allowed : 7.06 % Favored : 92.66 % 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: -2.05 (0.28), residues: 796 helix: -0.14 (0.27), residues: 362 sheet: -1.55 (0.89), residues: 32 loop : -2.60 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 140 TYR 0.017 0.002 TYR A 389 PHE 0.014 0.002 PHE B 251 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 0.68550 / 0.38 (11028) hydrogen bonds : bond 0.05593 / 3.69 ( 334) hydrogen bonds : angle 5.27068 / 3.65 ( 904) metal coordination : bond 0.00931 / 0.58 ( 8) metal coordination : angle 6.75082 / 5.59 ( 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 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.170 Fit side-chains REVERT: A 299 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7011 (tpt170) REVERT: B 119 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6015 (pm20) outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 0.0782 time to fit residues: 6.7603 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 : 0.161 ------------------------------------------------------------------------------- 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: 0.8980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.113968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101002 restraints weight = 17723.148| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.17 r_work: 0.3499 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1254 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= 0.131 Angle : 0.624 12.045 11036 Z= 0.337 Chirality : 0.042 0.198 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.683 88.387 1434 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.83 % Allowed : 9.83 % Favored : 89.34 % 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: -1.80 (0.28), residues: 796 helix: 0.11 (0.27), residues: 362 sheet: -2.07 (0.76), residues: 44 loop : -2.44 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 140 TYR 0.016 0.002 TYR A 389 PHE 0.012 0.001 PHE B 47 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 0.00267 / 0.13 ( 8030) covalent geometry : angle 0.60091 / 0.34 (11028) hydrogen bonds : bond 0.04788 / 3.11 ( 334) hydrogen bonds : angle 4.96945 / 3.42 ( 904) metal coordination : bond 0.00689 / 0.45 ( 8) metal coordination : angle 6.26641 / 5.22 ( 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 72 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.161 Fit side-chains REVERT: A 299 ARG cc_start: 0.7940 (tpp-160) cc_final: 0.6908 (tpt170) REVERT: A 501 LYS cc_start: 0.4950 (mttp) cc_final: 0.4699 (mttp) REVERT: B 119 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6021 (pm20) outliers start: 6 outliers final: 2 residues processed: 71 average time/residue: 0.0739 time to fit residues: 7.0390 Evaluate side-chains 61 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 MET 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: 1.9990 chunk 51 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN B 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.112561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099413 restraints weight = 17903.442| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.23 r_work: 0.3471 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8038 Z= 0.164 Angle : 0.641 12.222 11036 Z= 0.342 Chirality : 0.043 0.190 1155 Planarity : 0.005 0.065 1250 Dihedral : 20.521 89.239 1434 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.97 % Allowed : 11.91 % 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: -1.80 (0.28), residues: 796 helix: 0.13 (0.27), residues: 363 sheet: -2.17 (0.73), residues: 46 loop : -2.46 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 64 TYR 0.017 0.002 TYR A 471 PHE 0.012 0.001 PHE B 251 TRP 0.016 0.001 TRP A 317 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 8030) covalent geometry : angle 0.61823 / 0.34 (11028) hydrogen bonds : bond 0.04874 / 3.18 ( 334) hydrogen bonds : angle 4.96759 / 3.41 ( 904) metal coordination : bond 0.00701 / 0.47 ( 8) metal coordination : angle 6.33183 / 5.25 ( 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 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.204 Fit side-chains REVERT: A 299 ARG cc_start: 0.7859 (tpp-160) cc_final: 0.6772 (tpt170) REVERT: B 119 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6022 (pm20) outliers start: 7 outliers final: 2 residues processed: 67 average time/residue: 0.0833 time to fit residues: 7.5129 Evaluate side-chains 62 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 0.0020 overall best weight: 1.0192 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.112982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099943 restraints weight = 17753.289| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.17 r_work: 0.3481 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8038 Z= 0.147 Angle : 0.617 11.984 11036 Z= 0.330 Chirality : 0.042 0.180 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.513 87.103 1434 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.69 % Allowed : 13.85 % Favored : 85.46 % 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: -1.72 (0.28), residues: 796 helix: 0.18 (0.27), residues: 364 sheet: -2.13 (0.76), residues: 46 loop : -2.40 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.015 0.002 TYR A 471 PHE 0.019 0.001 PHE A 283 TRP 0.016 0.001 TRP A 317 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 8030) covalent geometry : angle 0.59492 / 0.33 (11028) hydrogen bonds : bond 0.04544 / 2.99 ( 334) hydrogen bonds : angle 4.87530 / 3.33 ( 904) metal coordination : bond 0.00674 / 0.45 ( 8) metal coordination : angle 6.16020 / 5.12 ( 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 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.198 Fit side-chains REVERT: A 299 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.6762 (tpt170) REVERT: A 501 LYS cc_start: 0.5117 (mttp) cc_final: 0.4913 (mttp) REVERT: B 119 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6056 (pm20) outliers start: 5 outliers final: 2 residues processed: 66 average time/residue: 0.0799 time to fit residues: 7.2095 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS 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: 2.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.112063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099056 restraints weight = 17815.336| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.15 r_work: 0.3464 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8038 Z= 0.178 Angle : 0.647 12.252 11036 Z= 0.344 Chirality : 0.043 0.184 1155 Planarity : 0.005 0.065 1250 Dihedral : 20.474 84.358 1434 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.39 % Allowed : 14.40 % Favored : 84.21 % 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: -1.69 (0.28), residues: 796 helix: 0.15 (0.27), residues: 365 sheet: -1.34 (0.93), residues: 34 loop : -2.41 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.016 0.002 TYR A 389 PHE 0.015 0.002 PHE A 283 TRP 0.016 0.001 TRP A 317 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 8030) covalent geometry : angle 0.62450 / 0.34 (11028) hydrogen bonds : bond 0.04815 / 3.17 ( 334) hydrogen bonds : angle 4.93787 / 3.37 ( 904) metal coordination : bond 0.00747 / 0.49 ( 8) metal coordination : angle 6.29265 / 5.23 ( 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 72 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.220 Fit side-chains REVERT: A 299 ARG cc_start: 0.7864 (tpp-160) cc_final: 0.6929 (tpt170) REVERT: A 501 LYS cc_start: 0.5181 (mttp) cc_final: 0.4946 (mttp) REVERT: B 119 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6078 (pm20) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.0779 time to fit residues: 7.3188 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 : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 51 TRP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 ILE 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: 0.9990 chunk 82 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.112711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099635 restraints weight = 17677.908| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.17 r_work: 0.3474 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1625 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= 0.153 Angle : 0.626 12.266 11036 Z= 0.334 Chirality : 0.042 0.172 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.416 82.517 1434 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.97 % Allowed : 15.51 % Favored : 83.52 % 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: -1.62 (0.28), residues: 796 helix: 0.23 (0.27), residues: 364 sheet: -1.32 (0.94), residues: 34 loop : -2.40 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.015 0.002 TYR A 389 PHE 0.017 0.001 PHE A 283 TRP 0.017 0.001 TRP A 317 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 8030) covalent geometry : angle 0.60288 / 0.33 (11028) hydrogen bonds : bond 0.04543 / 2.99 ( 334) hydrogen bonds : angle 4.85901 / 3.32 ( 904) metal coordination : bond 0.00658 / 0.44 ( 8) metal coordination : angle 6.27907 / 5.21 ( 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 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.258 Fit side-chains REVERT: A 269 ILE cc_start: 0.4979 (pt) cc_final: 0.4762 (mm) REVERT: A 299 ARG cc_start: 0.7797 (tpp-160) cc_final: 0.6743 (tpt170) REVERT: B 119 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6092 (pm20) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 0.0726 time to fit residues: 6.8806 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 : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.113932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.100705 restraints weight = 17659.296| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.20 r_work: 0.3493 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1751 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 : 0.598 11.503 11036 Z= 0.320 Chirality : 0.040 0.155 1155 Planarity : 0.004 0.063 1250 Dihedral : 20.279 79.969 1434 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.97 % Allowed : 15.93 % 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 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: -1.49 (0.29), residues: 796 helix: 0.31 (0.27), residues: 366 sheet: -1.28 (0.96), residues: 34 loop : -2.30 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 140 TYR 0.015 0.001 TYR A 389 PHE 0.017 0.001 PHE A 283 TRP 0.016 0.001 TRP A 317 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 8030) covalent geometry : angle 0.57590 / 0.32 (11028) hydrogen bonds : bond 0.04171 / 2.74 ( 334) hydrogen bonds : angle 4.75789 / 3.26 ( 904) metal coordination : bond 0.00560 / 0.38 ( 8) metal coordination : angle 5.94352 / 4.93 ( 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 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.167 Fit side-chains REVERT: A 299 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.6845 (tpt170) REVERT: A 499 MET cc_start: 0.7276 (ptt) cc_final: 0.6750 (mmp) REVERT: B 119 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6083 (pm20) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.0718 time to fit residues: 6.4275 Evaluate side-chains 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.114096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100726 restraints weight = 17667.118| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.23 r_work: 0.3492 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1826 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 : 0.591 11.103 11036 Z= 0.318 Chirality : 0.040 0.175 1155 Planarity : 0.005 0.092 1250 Dihedral : 20.230 78.171 1434 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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 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: 0.36 (0.27), residues: 366 sheet: -1.25 (0.95), residues: 34 loop : -2.27 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 75 TYR 0.015 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 0.00281 / 0.13 ( 8030) covalent geometry : angle 0.57044 / 0.32 (11028) hydrogen bonds : bond 0.04159 / 2.74 ( 334) hydrogen bonds : angle 4.72080 / 3.23 ( 904) metal coordination : bond 0.00520 / 0.36 ( 8) metal coordination : angle 5.83391 / 4.85 ( 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 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.222 Fit side-chains REVERT: A 299 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.6851 (tpt170) REVERT: B 119 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6072 (pm20) outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.0788 time to fit residues: 6.9088 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 : 0.251 ------------------------------------------------------------------------------- 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 B residue 326 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 34 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.115104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101728 restraints weight = 17600.828| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.23 r_work: 0.3508 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1940 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= 0.119 Angle : 0.576 10.548 11036 Z= 0.312 Chirality : 0.040 0.187 1155 Planarity : 0.005 0.089 1250 Dihedral : 20.138 75.668 1434 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.69 % Allowed : 16.48 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.39 (0.28), residues: 796 helix: 0.39 (0.27), residues: 366 sheet: -1.21 (0.95), residues: 34 loop : -2.25 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 64 TYR 0.015 0.001 TYR A 389 PHE 0.021 0.001 PHE A 283 TRP 0.015 0.001 TRP A 317 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 8030) covalent geometry : angle 0.55649 / 0.31 (11028) hydrogen bonds : bond 0.03919 / 2.60 ( 334) hydrogen bonds : angle 4.67053 / 3.19 ( 904) metal coordination : bond 0.00470 / 0.34 ( 8) metal coordination : angle 5.61138 / 4.67 ( 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 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.160 Fit side-chains REVERT: A 299 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.6863 (tpt170) REVERT: A 499 MET cc_start: 0.7038 (ptt) cc_final: 0.6549 (mmp) REVERT: B 119 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6067 (pm20) outliers start: 5 outliers final: 4 residues processed: 67 average time/residue: 0.0826 time to fit residues: 7.4173 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 0.0000 chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.113559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100223 restraints weight = 17623.599| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.23 r_work: 0.3484 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1927 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= 0.153 Angle : 0.605 11.208 11036 Z= 0.324 Chirality : 0.041 0.184 1155 Planarity : 0.005 0.083 1250 Dihedral : 20.174 73.724 1434 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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 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: -1.39 (0.29), residues: 796 helix: 0.40 (0.27), residues: 366 sheet: -1.29 (0.95), residues: 34 loop : -2.27 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.015 0.002 TYR A 389 PHE 0.019 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 0.00334 / 0.15 ( 8030) covalent geometry : angle 0.58427 / 0.32 (11028) hydrogen bonds : bond 0.04341 / 2.87 ( 334) hydrogen bonds : angle 4.72601 / 3.23 ( 904) metal coordination : bond 0.00584 / 0.39 ( 8) metal coordination : angle 5.88175 / 4.88 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1227.66 seconds wall clock time: 21 minutes 47.71 seconds (1307.71 seconds total)