Starting phenix.real_space_refine on Sun Jul 5 00:13:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i8u_52738/07_2026/9i8u_52738.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i8u_52738/07_2026/9i8u_52738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i8u_52738/07_2026/9i8u_52738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i8u_52738/07_2026/9i8u_52738.map" model { file = "/net/cci-nas-00/data/ceres_data/9i8u_52738/07_2026/9i8u_52738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i8u_52738/07_2026/9i8u_52738.cif" } resolution = 3.33 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= 0.012 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 K 1 8.98 5 S 48 5.16 5 C 7714 2.51 5 N 1906 2.21 5 O 2052 1.98 5 H 11812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 23533 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 7796 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 13, 'TRANS': 496} Chain breaks: 1 Chain: "C" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 7837 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 13, 'TRANS': 499} Chain breaks: 1 Chain: "B" Number of atoms: 7899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 7899 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 13, 'TRANS': 504} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 4.11, per 1000 atoms: 0.17 Number of scatterers: 23533 At special positions: 0 Unit cell: (115.998, 110.474, 89.1683, 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) K 1 19.00 S 48 16.00 O 2052 8.00 N 1906 7.00 C 7714 6.00 H 11812 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 623.2 milliseconds 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 62 through 80 removed outlier: 3.788A pdb=" N THR A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 120 removed outlier: 5.740A pdb=" N TRP A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.876A pdb=" N THR A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.654A pdb=" N LEU A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.714A pdb=" N HIS A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.529A pdb=" N PHE A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 removed outlier: 7.639A pdb=" N GLU A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 269 Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.622A pdb=" N ALA A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 324 Processing helix chain 'A' and resid 325 through 343 removed outlier: 3.865A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 359 through 389 removed outlier: 4.848A pdb=" N ILE A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 370 " --> pdb=" O TRP A 366 " (cutoff:3.500A) Proline residue: A 379 - end of helix removed outlier: 4.240A pdb=" N ARG A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 427 Proline residue: A 405 - end of helix removed outlier: 3.907A pdb=" N THR A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 453 through 481 removed outlier: 3.613A pdb=" N ALA A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 Processing helix chain 'A' and resid 513 through 546 removed outlier: 3.752A pdb=" N THR A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Proline residue: A 528 - end of helix removed outlier: 4.539A pdb=" N PHE A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 569 Processing helix chain 'C' and resid 59 through 120 Proline residue: C 65 - end of helix removed outlier: 7.483A pdb=" N ASP C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER C 83 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TRP C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.657A pdb=" N THR C 124 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.554A pdb=" N MET C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 168 removed outlier: 3.637A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 removed outlier: 3.531A pdb=" N HIS C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 209 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 232 removed outlier: 7.324A pdb=" N GLU C 227 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 268 removed outlier: 3.679A pdb=" N LYS C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 296 removed outlier: 3.583A pdb=" N ILE C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 323 Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.684A pdb=" N LEU C 330 " --> pdb=" O THR C 326 " (cutoff:3.500A) Proline residue: C 334 - end of helix removed outlier: 5.531A pdb=" N PHE C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLN C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 366 through 389 Proline residue: C 379 - end of helix Processing helix chain 'C' and resid 393 through 426 Proline residue: C 405 - end of helix removed outlier: 4.078A pdb=" N THR C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 447 Processing helix chain 'C' and resid 450 through 481 Processing helix chain 'C' and resid 488 through 511 removed outlier: 4.081A pdb=" N LEU C 506 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 527 removed outlier: 3.782A pdb=" N ASN C 517 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 518 " --> pdb=" O ALA C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 546 removed outlier: 4.398A pdb=" N VAL C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 571 Processing helix chain 'B' and resid 59 through 80 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 80 through 119 removed outlier: 5.507A pdb=" N TRP B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.680A pdb=" N THR B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.652A pdb=" N MET B 150 " --> pdb=" O PHE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 removed outlier: 5.022A pdb=" N THR B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 177 through 190 Processing helix chain 'B' and resid 191 through 209 Processing helix chain 'B' and resid 221 through 232 removed outlier: 7.777A pdb=" N GLU B 227 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 268 Processing helix chain 'B' and resid 275 through 295 Processing helix chain 'B' and resid 301 through 323 Processing helix chain 'B' and resid 325 through 343 removed outlier: 3.517A pdb=" N ILE B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) Proline residue: B 334 - end of helix removed outlier: 3.743A pdb=" N ASN B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 366 through 389 Proline residue: B 379 - end of helix removed outlier: 3.610A pdb=" N MET B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 427 Proline residue: B 405 - end of helix removed outlier: 3.832A pdb=" N THR B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.115A pdb=" N MET B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY B 462 " --> pdb=" O MET B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 511 Processing helix chain 'B' and resid 513 through 527 Processing helix chain 'B' and resid 528 through 546 removed outlier: 4.053A pdb=" N VAL B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 541 " --> pdb=" O MET B 537 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 569 removed outlier: 3.719A pdb=" N VAL B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' 943 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.37 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11809 1.03 - 1.22: 6 1.22 - 1.42: 5157 1.42 - 1.62: 6768 1.62 - 1.81: 93 Bond restraints: 23833 Sorted by residual: bond pdb=" CA VAL B 222 " pdb=" CB VAL B 222 " ideal model delta sigma weight residual 1.534 1.554 -0.020 6.80e-03 2.16e+04 8.60e+00 bond pdb=" CD1 PHE A 290 " pdb=" CE1 PHE A 290 " ideal model delta sigma weight residual 1.382 1.327 0.055 3.00e-02 1.11e+03 3.33e+00 bond pdb=" N ALA B 56 " pdb=" CA ALA B 56 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ALA C 56 " pdb=" CA ALA C 56 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 23828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 41646 1.62 - 3.25: 1227 3.25 - 4.87: 100 4.87 - 6.50: 25 6.50 - 8.12: 5 Bond angle restraints: 43003 Sorted by residual: angle pdb=" CA TYR A 553 " pdb=" CB TYR A 553 " pdb=" CG TYR A 553 " ideal model delta sigma weight residual 113.90 120.58 -6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" CA TRP C 194 " pdb=" CB TRP C 194 " pdb=" CG TRP C 194 " ideal model delta sigma weight residual 113.60 107.78 5.82 1.90e+00 2.77e-01 9.37e+00 angle pdb=" C ILE A 318 " pdb=" N PHE A 319 " pdb=" CA PHE A 319 " ideal model delta sigma weight residual 121.14 116.22 4.92 1.75e+00 3.27e-01 7.91e+00 angle pdb=" CA LYS C 81 " pdb=" CB LYS C 81 " pdb=" CG LYS C 81 " ideal model delta sigma weight residual 114.10 119.68 -5.58 2.00e+00 2.50e-01 7.79e+00 angle pdb=" CA VAL B 404 " pdb=" CB VAL B 404 " pdb=" CG2 VAL B 404 " ideal model delta sigma weight residual 110.40 115.07 -4.67 1.70e+00 3.46e-01 7.54e+00 ... (remaining 42998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 9693 16.33 - 32.67: 1062 32.67 - 49.00: 212 49.00 - 65.33: 204 65.33 - 81.66: 4 Dihedral angle restraints: 11175 sinusoidal: 5808 harmonic: 5367 Sorted by residual: dihedral pdb=" CA ILE C 125 " pdb=" C ILE C 125 " pdb=" N ARG C 126 " pdb=" CA ARG C 126 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TRP B 189 " pdb=" C TRP B 189 " pdb=" N THR B 190 " pdb=" CA THR B 190 " ideal model delta harmonic sigma weight residual 180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA SER A 480 " pdb=" C SER A 480 " pdb=" N GLN A 481 " pdb=" CA GLN A 481 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 11172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1194 0.033 - 0.066: 517 0.066 - 0.099: 155 0.099 - 0.132: 33 0.132 - 0.165: 7 Chirality restraints: 1906 Sorted by residual: chirality pdb=" CA TYR A 553 " pdb=" N TYR A 553 " pdb=" C TYR A 553 " pdb=" CB TYR A 553 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB THR C 522 " pdb=" CA THR C 522 " pdb=" OG1 THR C 522 " pdb=" CG2 THR C 522 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA PHE A 319 " pdb=" N PHE A 319 " pdb=" C PHE A 319 " pdb=" CB PHE A 319 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 1903 not shown) Planarity restraints: 3519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 222 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO B 223 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 414 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C SER B 414 " 0.038 2.00e-02 2.50e+03 pdb=" O SER B 414 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 415 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 414 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C SER C 414 " -0.036 2.00e-02 2.50e+03 pdb=" O SER C 414 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE C 415 " 0.012 2.00e-02 2.50e+03 ... (remaining 3516 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.33: 6285 2.33 - 3.03: 66875 3.03 - 3.74: 90500 3.74 - 4.44: 136814 4.44 - 5.14: 214305 Nonbonded interactions: 514779 Sorted by model distance: nonbonded pdb=" O LEU C 332 " pdb=" H SER C 336 " model vdw 1.631 2.450 nonbonded pdb=" HE2 HIS B 188 " pdb=" OG1 THR B 367 " model vdw 1.697 2.450 nonbonded pdb=" O GLY A 128 " pdb=" HE ARG A 210 " model vdw 1.708 2.450 nonbonded pdb=" O LEU B 385 " pdb=" HG SER B 389 " model vdw 1.719 2.450 nonbonded pdb=" O ALA B 435 " pdb="HE21 GLN B 439 " model vdw 1.740 2.450 ... (remaining 514774 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 57 through 296 or resid 300 through 569)) selection = (chain 'C' and resid 57 through 569) } 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: 4.380 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: 0.170 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3920 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 0.055 12021 Z= 0.236 Angle : 0.661 8.121 16385 Z= 0.365 Chirality : 0.040 0.165 1906 Planarity : 0.005 0.058 2022 Dihedral : 12.961 81.665 3998 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.21), residues: 1531 helix: 0.74 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.81 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 395 TYR 0.030 0.002 TYR A 553 PHE 0.032 0.002 PHE A 146 TRP 0.021 0.002 TRP C 194 HIS 0.005 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (12021) covalent geometry : angle 0.66096 / 0.36 (16385) hydrogen bonds : bond 0.12145 / 8.12 ( 943) hydrogen bonds : angle 6.26911 / 4.69 ( 2811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.6737 (ptpp) cc_final: 0.6082 (tptp) REVERT: A 401 VAL cc_start: 0.7118 (t) cc_final: 0.6828 (t) REVERT: C 458 MET cc_start: -0.0951 (ptp) cc_final: -0.2032 (tpp) REVERT: B 121 LYS cc_start: 0.5842 (mppt) cc_final: 0.5276 (mppt) REVERT: B 157 TYR cc_start: 0.7667 (m-80) cc_final: 0.6254 (m-80) REVERT: B 174 ASP cc_start: 0.6502 (p0) cc_final: 0.5840 (m-30) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2447 time to fit residues: 56.1377 Evaluate side-chains 112 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 GLN C 339 ASN C 451 GLN B 517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.277823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.254217 restraints weight = 37716.698| |-----------------------------------------------------------------------------| r_work (start): 0.4552 rms_B_bonded: 1.37 r_work: 0.4402 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12021 Z= 0.216 Angle : 0.671 9.126 16385 Z= 0.365 Chirality : 0.041 0.228 1906 Planarity : 0.005 0.041 2022 Dihedral : 4.356 18.715 1614 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.91 % Allowed : 5.90 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.21), residues: 1531 helix: 0.97 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 213 TYR 0.014 0.001 TYR A 553 PHE 0.040 0.002 PHE A 319 TRP 0.032 0.002 TRP A 194 HIS 0.010 0.002 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (12021) covalent geometry : angle 0.67119 / 0.36 (16385) hydrogen bonds : bond 0.04974 / 3.26 ( 943) hydrogen bonds : angle 4.66580 / 3.44 ( 2811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7330 (ptpp) cc_final: 0.6924 (tptp) REVERT: A 144 MET cc_start: 0.6065 (mmm) cc_final: 0.5778 (mpp) REVERT: A 194 TRP cc_start: 0.7592 (m100) cc_final: 0.7211 (m100) REVERT: C 194 TRP cc_start: 0.7464 (m100) cc_final: 0.6450 (m-90) REVERT: B 121 LYS cc_start: 0.6519 (mppt) cc_final: 0.5292 (mppt) REVERT: B 144 MET cc_start: 0.6113 (mmm) cc_final: 0.5568 (tpp) outliers start: 11 outliers final: 5 residues processed: 138 average time/residue: 0.2362 time to fit residues: 48.4845 Evaluate side-chains 116 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 549 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.251507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.218660 restraints weight = 36448.299| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.70 r_work: 0.4072 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 12021 Z= 0.197 Angle : 0.593 7.013 16385 Z= 0.326 Chirality : 0.038 0.145 1906 Planarity : 0.004 0.040 2022 Dihedral : 4.086 20.487 1614 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.08 % Allowed : 8.14 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.21), residues: 1531 helix: 1.33 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -0.47 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 387 TYR 0.022 0.002 TYR A 553 PHE 0.032 0.002 PHE A 319 TRP 0.024 0.002 TRP A 194 HIS 0.005 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (12021) covalent geometry : angle 0.59326 / 0.33 (16385) hydrogen bonds : bond 0.05222 / 3.43 ( 943) hydrogen bonds : angle 4.65034 / 3.44 ( 2811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7562 (ptpp) cc_final: 0.7027 (tptp) REVERT: A 157 TYR cc_start: 0.7321 (m-80) cc_final: 0.6796 (m-80) REVERT: C 157 TYR cc_start: 0.7663 (m-80) cc_final: 0.7289 (m-80) REVERT: C 197 TYR cc_start: 0.7010 (m-10) cc_final: 0.6261 (m-80) REVERT: B 476 MET cc_start: 0.7478 (mtt) cc_final: 0.7114 (mtt) REVERT: B 479 MET cc_start: 0.7654 (mtt) cc_final: 0.7081 (mtt) outliers start: 13 outliers final: 8 residues processed: 148 average time/residue: 0.2313 time to fit residues: 51.4369 Evaluate side-chains 125 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 549 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 147 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.212438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.178038 restraints weight = 35403.023| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.45 r_work: 0.3666 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.8234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 12021 Z= 0.265 Angle : 0.718 10.384 16385 Z= 0.397 Chirality : 0.042 0.231 1906 Planarity : 0.005 0.048 2022 Dihedral : 4.526 23.831 1614 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.16 % Allowed : 9.97 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.21), residues: 1531 helix: 0.88 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.82 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 568 TYR 0.012 0.001 TYR A 553 PHE 0.022 0.002 PHE C 465 TRP 0.042 0.002 TRP C 101 HIS 0.012 0.002 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 (12021) covalent geometry : angle 0.71751 / 0.40 (16385) hydrogen bonds : bond 0.05664 / 3.72 ( 943) hydrogen bonds : angle 4.74439 / 3.52 ( 2811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7364 (mmt) cc_final: 0.6890 (mmt) REVERT: C 546 ASN cc_start: 0.6370 (m-40) cc_final: 0.6042 (m110) outliers start: 14 outliers final: 10 residues processed: 150 average time/residue: 0.2379 time to fit residues: 52.3272 Evaluate side-chains 121 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 0.0060 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.207980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.167693 restraints weight = 35304.265| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.09 r_work: 0.3557 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.8926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12021 Z= 0.152 Angle : 0.529 6.614 16385 Z= 0.291 Chirality : 0.036 0.125 1906 Planarity : 0.003 0.040 2022 Dihedral : 4.050 19.074 1614 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.41 % Allowed : 10.71 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.21), residues: 1531 helix: 1.45 (0.14), residues: 1238 sheet: None (None), residues: 0 loop : -0.81 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.018 0.001 TYR A 553 PHE 0.020 0.002 PHE A 465 TRP 0.021 0.001 TRP C 194 HIS 0.007 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (12021) covalent geometry : angle 0.52915 / 0.29 (16385) hydrogen bonds : bond 0.04696 / 3.12 ( 943) hydrogen bonds : angle 4.46352 / 3.31 ( 2811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8542 (m-80) cc_final: 0.8205 (m-80) REVERT: C 144 MET cc_start: 0.6342 (mmm) cc_final: 0.6141 (mmm) REVERT: C 476 MET cc_start: 0.0994 (tpp) cc_final: 0.0110 (ptp) REVERT: C 546 ASN cc_start: 0.6251 (m-40) cc_final: 0.5947 (m110) REVERT: B 343 ASN cc_start: 0.8546 (m-40) cc_final: 0.8318 (m-40) outliers start: 17 outliers final: 11 residues processed: 124 average time/residue: 0.2024 time to fit residues: 39.0718 Evaluate side-chains 119 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 517 ASN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 98 ASN B 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.178174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.141345 restraints weight = 35479.279| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.65 r_work: 0.3304 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 1.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 12021 Z= 0.241 Angle : 0.685 17.392 16385 Z= 0.379 Chirality : 0.041 0.197 1906 Planarity : 0.005 0.051 2022 Dihedral : 4.379 20.362 1614 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.99 % Allowed : 11.21 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.21), residues: 1531 helix: 1.10 (0.14), residues: 1227 sheet: None (None), residues: 0 loop : -0.95 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 350 TYR 0.016 0.001 TYR A 553 PHE 0.047 0.003 PHE C 441 TRP 0.030 0.002 TRP C 371 HIS 0.015 0.002 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (12021) covalent geometry : angle 0.68540 / 0.38 (16385) hydrogen bonds : bond 0.05477 / 3.61 ( 943) hydrogen bonds : angle 4.76819 / 3.57 ( 2811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8884 (m-80) cc_final: 0.8195 (m-80) REVERT: A 310 MET cc_start: 0.6961 (tpp) cc_final: 0.6163 (ttm) REVERT: A 485 LEU cc_start: 0.7754 (tt) cc_final: 0.7074 (mp) REVERT: A 499 THR cc_start: 0.5718 (OUTLIER) cc_final: 0.5098 (m) REVERT: C 458 MET cc_start: 0.6891 (ptp) cc_final: 0.6471 (mtt) REVERT: B 208 THR cc_start: 0.8656 (t) cc_final: 0.8297 (m) outliers start: 24 outliers final: 18 residues processed: 141 average time/residue: 0.1865 time to fit residues: 40.7762 Evaluate side-chains 128 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 380 PHE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 517 ASN Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 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 = 0.3886 r_free = 0.3886 target = 0.178595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.140602 restraints weight = 35157.141| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.72 r_work: 0.3289 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 1.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12021 Z= 0.136 Angle : 0.512 7.267 16385 Z= 0.281 Chirality : 0.035 0.123 1906 Planarity : 0.004 0.052 2022 Dihedral : 4.065 19.338 1614 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.91 % Allowed : 11.71 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.21), residues: 1531 helix: 1.51 (0.14), residues: 1231 sheet: None (None), residues: 0 loop : -0.93 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 554 TYR 0.016 0.001 TYR A 553 PHE 0.020 0.001 PHE A 465 TRP 0.021 0.001 TRP C 371 HIS 0.007 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (12021) covalent geometry : angle 0.51192 / 0.28 (16385) hydrogen bonds : bond 0.04557 / 3.03 ( 943) hydrogen bonds : angle 4.46040 / 3.33 ( 2811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8862 (m-80) cc_final: 0.8213 (m-80) REVERT: A 485 LEU cc_start: 0.7717 (tt) cc_final: 0.7114 (mp) REVERT: A 489 LYS cc_start: 0.7156 (mmtt) cc_final: 0.6877 (mtpt) REVERT: B 71 LEU cc_start: 0.6657 (mm) cc_final: 0.6430 (mt) REVERT: B 208 THR cc_start: 0.8597 (t) cc_final: 0.8234 (m) REVERT: B 239 ASP cc_start: 0.7638 (m-30) cc_final: 0.7269 (m-30) REVERT: B 439 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: B 554 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7038 (mmm160) outliers start: 23 outliers final: 17 residues processed: 129 average time/residue: 0.2032 time to fit residues: 40.5556 Evaluate side-chains 128 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 380 PHE Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 517 ASN Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.160389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124856 restraints weight = 35756.689| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.58 r_work: 0.3108 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 1.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 12021 Z= 0.215 Angle : 0.641 10.639 16385 Z= 0.356 Chirality : 0.044 0.702 1906 Planarity : 0.004 0.051 2022 Dihedral : 4.313 20.030 1614 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.99 % Allowed : 11.46 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.20), residues: 1531 helix: 1.06 (0.14), residues: 1238 sheet: None (None), residues: 0 loop : -1.22 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 554 TYR 0.015 0.002 TYR A 553 PHE 0.045 0.002 PHE A 87 TRP 0.024 0.002 TRP A 76 HIS 0.014 0.002 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (12021) covalent geometry : angle 0.64091 / 0.36 (16385) hydrogen bonds : bond 0.05285 / 3.49 ( 943) hydrogen bonds : angle 4.66427 / 3.48 ( 2811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 SER cc_start: 0.8461 (m) cc_final: 0.8218 (p) REVERT: A 485 LEU cc_start: 0.7942 (tt) cc_final: 0.7682 (mp) REVERT: A 489 LYS cc_start: 0.7513 (mmtt) cc_final: 0.7139 (mtpt) REVERT: C 479 MET cc_start: 0.8138 (mpp) cc_final: 0.7899 (mtt) REVERT: B 208 THR cc_start: 0.8716 (t) cc_final: 0.8398 (m) REVERT: B 439 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: B 489 LYS cc_start: 0.7336 (mtpt) cc_final: 0.6688 (mmmt) outliers start: 24 outliers final: 17 residues processed: 135 average time/residue: 0.2201 time to fit residues: 45.4940 Evaluate side-chains 126 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 517 ASN Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.160312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.120653 restraints weight = 35820.070| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.79 r_work: 0.3067 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 1.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12021 Z= 0.152 Angle : 0.528 8.116 16385 Z= 0.287 Chirality : 0.036 0.154 1906 Planarity : 0.004 0.042 2022 Dihedral : 4.045 19.812 1614 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.33 % Allowed : 12.54 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.21), residues: 1531 helix: 1.47 (0.14), residues: 1224 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 554 TYR 0.015 0.001 TYR A 553 PHE 0.015 0.001 PHE C 465 TRP 0.019 0.001 TRP A 76 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (12021) covalent geometry : angle 0.52849 / 0.29 (16385) hydrogen bonds : bond 0.04494 / 2.99 ( 943) hydrogen bonds : angle 4.45672 / 3.32 ( 2811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.4755 (tmm) cc_final: 0.2443 (ttm) REVERT: A 473 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 485 LEU cc_start: 0.7895 (tt) cc_final: 0.7673 (mp) REVERT: B 208 THR cc_start: 0.8658 (t) cc_final: 0.8300 (m) REVERT: B 439 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: B 489 LYS cc_start: 0.7244 (mtpt) cc_final: 0.6565 (mmmt) REVERT: B 554 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.6945 (mmm160) outliers start: 16 outliers final: 11 residues processed: 123 average time/residue: 0.2193 time to fit residues: 41.3969 Evaluate side-chains 118 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 517 ASN Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 42 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.153792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.115339 restraints weight = 36156.337| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.74 r_work: 0.2999 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 1.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12021 Z= 0.183 Angle : 0.570 9.148 16385 Z= 0.311 Chirality : 0.037 0.206 1906 Planarity : 0.004 0.048 2022 Dihedral : 4.027 19.678 1614 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.33 % Allowed : 12.62 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.21), residues: 1531 helix: 1.48 (0.14), residues: 1223 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 554 TYR 0.015 0.001 TYR A 553 PHE 0.019 0.002 PHE C 441 TRP 0.020 0.002 TRP B 194 HIS 0.010 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (12021) covalent geometry : angle 0.56950 / 0.31 (16385) hydrogen bonds : bond 0.04672 / 3.10 ( 943) hydrogen bonds : angle 4.49100 / 3.35 ( 2811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.4599 (tmm) cc_final: 0.2799 (ttm) REVERT: A 473 SER cc_start: 0.8465 (m) cc_final: 0.8136 (p) REVERT: A 489 LYS cc_start: 0.7554 (mmtt) cc_final: 0.7244 (mtpt) REVERT: C 315 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7863 (mp) REVERT: B 208 THR cc_start: 0.8688 (t) cc_final: 0.8361 (m) REVERT: B 239 ASP cc_start: 0.7785 (m-30) cc_final: 0.7378 (m-30) REVERT: B 439 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: B 489 LYS cc_start: 0.7315 (mtpt) cc_final: 0.6586 (mmmt) outliers start: 16 outliers final: 11 residues processed: 124 average time/residue: 0.2421 time to fit residues: 44.7076 Evaluate side-chains 121 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 3 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.152154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.114346 restraints weight = 35968.687| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.71 r_work: 0.2991 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 1.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12021 Z= 0.152 Angle : 0.523 7.434 16385 Z= 0.284 Chirality : 0.036 0.134 1906 Planarity : 0.003 0.042 2022 Dihedral : 3.935 19.281 1614 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.25 % Allowed : 12.71 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.60 (0.21), residues: 1531 helix: 1.62 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -1.16 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 554 TYR 0.016 0.001 TYR A 553 PHE 0.017 0.001 PHE C 441 TRP 0.018 0.001 TRP C 371 HIS 0.007 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (12021) covalent geometry : angle 0.52332 / 0.28 (16385) hydrogen bonds : bond 0.04404 / 2.94 ( 943) hydrogen bonds : angle 4.39740 / 3.28 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5237.32 seconds wall clock time: 89 minutes 38.18 seconds (5378.18 seconds total)