Starting phenix.real_space_refine on Thu Mar 5 18:09:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i8u_52738/03_2026/9i8u_52738.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i8u_52738/03_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_52738/03_2026/9i8u_52738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i8u_52738/03_2026/9i8u_52738.map" model { file = "/net/cci-nas-00/data/ceres_data/9i8u_52738/03_2026/9i8u_52738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i8u_52738/03_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-5986/lib/python3.9/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, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.42, per 1000 atoms: 0.19 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: 2.21 Conformation dependent library (CDL) restraints added in 784.2 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: 0.50 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: 5.50 Time building geometry restraints manager: 3.16 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.410 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3882 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 covalent geometry : bond 0.00541 (12021) covalent geometry : angle 0.66096 (16385) hydrogen bonds : bond 0.12145 ( 943) hydrogen bonds : angle 6.26911 ( 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 : 0.535 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: 0.2476 time to fit residues: 56.0970 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 : 0.490 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4809 r_free = 0.4809 target = 0.286176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.261815 restraints weight = 37992.625| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 1.65 r_work: 0.4387 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12021 Z= 0.206 Angle : 0.680 9.590 16385 Z= 0.370 Chirality : 0.041 0.213 1906 Planarity : 0.005 0.042 2022 Dihedral : 4.377 18.597 1614 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.91 % Allowed : 6.15 % Favored : 92.94 % 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: 0.88 (0.21), residues: 1531 helix: 0.96 (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 0.006 0.001 ARG A 213 TYR 0.015 0.001 TYR A 553 PHE 0.042 0.002 PHE A 319 TRP 0.033 0.002 TRP A 194 HIS 0.010 0.002 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00449 (12021) covalent geometry : angle 0.68022 (16385) hydrogen bonds : bond 0.04794 ( 943) hydrogen bonds : angle 4.60580 ( 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 144 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.558 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: 0.7325 (ptpp) cc_final: 0.6888 (tptp) REVERT: A 144 MET cc_start: 0.6146 (mmm) cc_final: 0.5794 (mpp) REVERT: A 194 TRP cc_start: 0.7640 (m100) cc_final: 0.6963 (m100) REVERT: A 362 TRP cc_start: 0.7889 (t60) cc_final: 0.6402 (t-100) REVERT: A 529 PHE cc_start: 0.4645 (t80) cc_final: 0.4434 (t80) REVERT: C 194 TRP cc_start: 0.7541 (m100) cc_final: 0.6447 (m-90) REVERT: B 121 LYS cc_start: 0.6524 (mppt) cc_final: 0.5279 (mppt) REVERT: B 144 MET cc_start: 0.6091 (mmm) cc_final: 0.5477 (tpp) REVERT: B 239 ASP cc_start: 0.6259 (t0) cc_final: 0.6019 (t0) outliers start: 11 outliers final: 7 residues processed: 140 average time/residue: 0.2219 time to fit residues: 45.7607 Evaluate side-chains 119 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain B residue 537 MET 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: 0.6980 chunk 97 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4589 r_free = 0.4589 target = 0.257016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.240026 restraints weight = 36134.111| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 0.77 r_work: 0.4157 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12021 Z= 0.203 Angle : 0.654 8.758 16385 Z= 0.358 Chirality : 0.039 0.183 1906 Planarity : 0.005 0.065 2022 Dihedral : 4.116 22.124 1614 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.16 % Allowed : 8.39 % Favored : 90.45 % 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: 1.36 (0.21), residues: 1531 helix: 1.26 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : -0.44 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 387 TYR 0.024 0.002 TYR A 553 PHE 0.036 0.002 PHE A 319 TRP 0.030 0.002 TRP A 194 HIS 0.006 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00450 (12021) covalent geometry : angle 0.65382 (16385) hydrogen bonds : bond 0.05578 ( 943) hydrogen bonds : angle 4.74399 ( 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 153 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.578 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 157 TYR cc_start: 0.7458 (m-80) cc_final: 0.6901 (m-80) REVERT: A 383 MET cc_start: 0.8483 (ttp) cc_final: 0.8158 (ttm) REVERT: A 392 ARG cc_start: 0.8329 (mmm160) cc_final: 0.7829 (tpp-160) REVERT: C 157 TYR cc_start: 0.7764 (m-80) cc_final: 0.7399 (m-80) REVERT: C 197 TYR cc_start: 0.7288 (m-10) cc_final: 0.6536 (m-80) REVERT: B 121 LYS cc_start: 0.6689 (mppt) cc_final: 0.5386 (mppt) REVERT: B 479 MET cc_start: 0.7671 (mtt) cc_final: 0.7077 (mtt) outliers start: 14 outliers final: 7 residues processed: 147 average time/residue: 0.2250 time to fit residues: 49.2162 Evaluate side-chains 123 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP 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: 0.9980 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN C 343 ASN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.224359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.192851 restraints weight = 35560.541| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.46 r_work: 0.3782 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12021 Z= 0.199 Angle : 0.617 9.065 16385 Z= 0.340 Chirality : 0.039 0.138 1906 Planarity : 0.004 0.039 2022 Dihedral : 4.228 21.182 1614 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.16 % Allowed : 9.72 % Favored : 89.12 % 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: 1.25 (0.21), residues: 1531 helix: 1.24 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : -0.70 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 558 TYR 0.012 0.001 TYR A 553 PHE 0.018 0.002 PHE C 319 TRP 0.020 0.002 TRP C 101 HIS 0.010 0.002 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00441 (12021) covalent geometry : angle 0.61714 (16385) hydrogen bonds : bond 0.04928 ( 943) hydrogen bonds : angle 4.42590 ( 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 150 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.512 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: C 135 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.6066 (tt0) REVERT: C 157 TYR cc_start: 0.8637 (m-80) cc_final: 0.8317 (m-80) REVERT: B 479 MET cc_start: 0.7982 (mtt) cc_final: 0.7683 (mtt) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.2275 time to fit residues: 48.6495 Evaluate side-chains 124 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP 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: 2.9990 chunk 147 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.0010 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.200220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.160433 restraints weight = 35254.543| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.83 r_work: 0.3494 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.9328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12021 Z= 0.212 Angle : 0.678 8.768 16385 Z= 0.374 Chirality : 0.039 0.179 1906 Planarity : 0.004 0.053 2022 Dihedral : 4.195 21.712 1614 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.74 % Allowed : 10.30 % Favored : 87.96 % 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: 1.21 (0.21), residues: 1531 helix: 1.24 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : -0.92 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 213 TYR 0.022 0.002 TYR A 553 PHE 0.028 0.002 PHE C 384 TRP 0.026 0.002 TRP C 194 HIS 0.014 0.002 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00458 (12021) covalent geometry : angle 0.67783 (16385) hydrogen bonds : bond 0.05557 ( 943) hydrogen bonds : angle 4.79167 ( 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 150 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.498 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: A 157 TYR cc_start: 0.8579 (m-80) cc_final: 0.8374 (m-80) REVERT: A 318 ILE cc_start: 0.8269 (mm) cc_final: 0.8023 (mt) REVERT: A 479 MET cc_start: 0.7894 (mpp) cc_final: 0.7507 (mtt) REVERT: C 144 MET cc_start: 0.6298 (mmm) cc_final: 0.6038 (mmm) REVERT: C 546 ASN cc_start: 0.6291 (m-40) cc_final: 0.6005 (m110) REVERT: B 150 MET cc_start: 0.5933 (ptm) cc_final: 0.5694 (ptp) REVERT: B 239 ASP cc_start: 0.8076 (t0) cc_final: 0.7806 (m-30) REVERT: B 489 LYS cc_start: 0.6984 (mtmm) cc_final: 0.6766 (mtpt) outliers start: 21 outliers final: 14 residues processed: 143 average time/residue: 0.2327 time to fit residues: 48.8636 Evaluate side-chains 120 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 371 TRP 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 C residue 517 ASN Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain B residue 174 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 439 GLN B 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.182126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.145159 restraints weight = 35405.291| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.66 r_work: 0.3340 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 1.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12021 Z= 0.231 Angle : 0.635 15.755 16385 Z= 0.350 Chirality : 0.039 0.139 1906 Planarity : 0.004 0.048 2022 Dihedral : 4.254 20.169 1614 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.74 % Allowed : 11.88 % 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: 1.10 (0.21), residues: 1531 helix: 1.17 (0.14), residues: 1228 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.012 0.001 TYR A 553 PHE 0.022 0.002 PHE A 465 TRP 0.021 0.002 TRP A 371 HIS 0.008 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00504 (12021) covalent geometry : angle 0.63547 (16385) hydrogen bonds : bond 0.05087 ( 943) hydrogen bonds : angle 4.58428 ( 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 142 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.493 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: A 157 TYR cc_start: 0.8821 (m-80) cc_final: 0.8029 (m-80) REVERT: A 318 ILE cc_start: 0.8385 (mm) cc_final: 0.8138 (mt) REVERT: A 499 THR cc_start: 0.5507 (OUTLIER) cc_final: 0.4848 (m) REVERT: C 144 MET cc_start: 0.6269 (mmm) cc_final: 0.6056 (mpp) REVERT: B 239 ASP cc_start: 0.8308 (t0) cc_final: 0.7355 (m-30) REVERT: B 489 LYS cc_start: 0.7120 (mtmm) cc_final: 0.6905 (mtpt) outliers start: 21 outliers final: 17 residues processed: 138 average time/residue: 0.1953 time to fit residues: 41.6801 Evaluate side-chains 130 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 256 LEU 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 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 467 THR Chi-restraints excluded: chain C residue 517 ASN Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 377 TRP 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: 0.6980 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.0010 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.181193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.143539 restraints weight = 35202.984| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.70 r_work: 0.3323 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 1.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12021 Z= 0.140 Angle : 0.522 6.772 16385 Z= 0.285 Chirality : 0.035 0.151 1906 Planarity : 0.003 0.040 2022 Dihedral : 4.004 18.548 1614 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.74 % Allowed : 12.46 % Favored : 85.80 % 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: 1.54 (0.21), residues: 1531 helix: 1.51 (0.14), residues: 1228 sheet: None (None), residues: 0 loop : -0.88 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.016 0.001 TYR A 553 PHE 0.018 0.001 PHE C 384 TRP 0.018 0.001 TRP C 194 HIS 0.007 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00291 (12021) covalent geometry : angle 0.52238 (16385) hydrogen bonds : bond 0.04559 ( 943) hydrogen bonds : angle 4.46613 ( 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 138 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.505 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: 0.4295 (tmm) cc_final: 0.1645 (mtp) REVERT: A 157 TYR cc_start: 0.8813 (m-80) cc_final: 0.8210 (m-80) REVERT: A 239 ASP cc_start: 0.7742 (t70) cc_final: 0.7295 (t0) REVERT: A 318 ILE cc_start: 0.8467 (mm) cc_final: 0.8232 (mt) REVERT: A 485 LEU cc_start: 0.7729 (tt) cc_final: 0.7068 (mp) REVERT: A 499 THR cc_start: 0.5582 (OUTLIER) cc_final: 0.4950 (m) REVERT: C 428 GLU cc_start: 0.7983 (mp0) cc_final: 0.7741 (mm-30) REVERT: B 150 MET cc_start: 0.6286 (ptp) cc_final: 0.5577 (ptm) REVERT: B 239 ASP cc_start: 0.8158 (t0) cc_final: 0.7696 (m-30) REVERT: B 439 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: B 489 LYS cc_start: 0.7057 (mtmm) cc_final: 0.6650 (mmmt) outliers start: 21 outliers final: 15 residues processed: 135 average time/residue: 0.2032 time to fit residues: 42.3305 Evaluate side-chains 129 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 517 ASN Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain B residue 98 ASN 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 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: 3.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 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: 0.0980 chunk 78 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.154581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.119800 restraints weight = 36095.003| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.56 r_work: 0.3056 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 1.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 12021 Z= 0.244 Angle : 0.752 15.669 16385 Z= 0.407 Chirality : 0.048 0.844 1906 Planarity : 0.006 0.123 2022 Dihedral : 4.648 24.619 1614 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.57 % Allowed : 11.30 % 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: 0.37 (0.20), residues: 1531 helix: 0.73 (0.14), residues: 1229 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 554 TYR 0.016 0.002 TYR C 304 PHE 0.049 0.003 PHE C 465 TRP 0.023 0.002 TRP B 194 HIS 0.019 0.003 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00555 (12021) covalent geometry : angle 0.75192 (16385) hydrogen bonds : bond 0.05852 ( 943) hydrogen bonds : angle 4.94417 ( 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 152 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 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 89 SER cc_start: 0.7191 (m) cc_final: 0.6965 (t) REVERT: A 150 MET cc_start: 0.4253 (tmm) cc_final: 0.3054 (mtp) REVERT: A 453 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5909 (ttm) REVERT: A 542 LYS cc_start: 0.8255 (tttt) cc_final: 0.8004 (tttt) REVERT: C 428 GLU cc_start: 0.8029 (mp0) cc_final: 0.7787 (mm-30) REVERT: B 121 LYS cc_start: 0.7326 (mttp) cc_final: 0.7115 (mttm) REVERT: B 239 ASP cc_start: 0.8268 (t0) cc_final: 0.7345 (m-30) REVERT: B 439 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: B 489 LYS cc_start: 0.7422 (mtmm) cc_final: 0.7024 (mmmt) REVERT: B 554 ARG cc_start: 0.7477 (mmm-85) cc_final: 0.6943 (mmm160) outliers start: 31 outliers final: 18 residues processed: 142 average time/residue: 0.2256 time to fit residues: 47.2019 Evaluate side-chains 129 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain C residue 69 ILE 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 389 SER Chi-restraints excluded: chain C residue 517 ASN Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 358 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=1.50 ------------------------------------------------------------------------------- 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: 0.5980 chunk 79 optimal weight: 0.5980 chunk 68 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.156799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.117099 restraints weight = 36096.502| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.80 r_work: 0.3028 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 1.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12021 Z= 0.149 Angle : 0.537 6.915 16385 Z= 0.295 Chirality : 0.036 0.135 1906 Planarity : 0.004 0.042 2022 Dihedral : 4.173 20.558 1614 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.41 % Allowed : 12.79 % Favored : 85.80 % 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: 1.14 (0.21), residues: 1531 helix: 1.29 (0.14), residues: 1216 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 315 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 0.024 0.002 PHE C 465 TRP 0.018 0.001 TRP C 194 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00310 (12021) covalent geometry : angle 0.53695 (16385) hydrogen bonds : bond 0.04684 ( 943) hydrogen bonds : angle 4.56675 ( 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 135 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.7114 (m) cc_final: 0.6891 (t) REVERT: A 150 MET cc_start: 0.4124 (tmm) cc_final: 0.3322 (mtp) REVERT: B 239 ASP cc_start: 0.8162 (t0) cc_final: 0.7335 (m-30) REVERT: B 439 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: B 489 LYS cc_start: 0.7260 (mtmm) cc_final: 0.6847 (mmmt) REVERT: B 554 ARG cc_start: 0.7472 (mmm-85) cc_final: 0.6995 (mmm160) outliers start: 17 outliers final: 14 residues processed: 130 average time/residue: 0.2269 time to fit residues: 43.8160 Evaluate side-chains 126 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 371 TRP Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 517 ASN Chi-restraints excluded: chain C residue 543 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 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: 5.9990 chunk 94 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 147 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.155078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.115768 restraints weight = 36175.613| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.80 r_work: 0.3004 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 1.3510 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= 0.143 Angle : 0.528 7.067 16385 Z= 0.288 Chirality : 0.036 0.173 1906 Planarity : 0.004 0.056 2022 Dihedral : 3.967 19.973 1614 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.50 % Allowed : 12.79 % Favored : 85.71 % 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: 1.51 (0.21), residues: 1531 helix: 1.56 (0.14), residues: 1228 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 194 HIS 0.007 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00310 (12021) covalent geometry : angle 0.52768 (16385) hydrogen bonds : bond 0.04372 ( 943) hydrogen bonds : angle 4.41098 ( 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 133 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.7248 (m) cc_final: 0.7007 (t) REVERT: A 310 MET cc_start: 0.7467 (tpp) cc_final: 0.6359 (ttm) REVERT: B 439 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: B 489 LYS cc_start: 0.7229 (mtmm) cc_final: 0.6757 (mmmt) REVERT: B 554 ARG cc_start: 0.7436 (mmm-85) cc_final: 0.6918 (mmm160) outliers start: 18 outliers final: 15 residues processed: 128 average time/residue: 0.2414 time to fit residues: 45.1027 Evaluate side-chains 124 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 ASP 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 482 HIS Chi-restraints excluded: chain C residue 543 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 3 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.151549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.112787 restraints weight = 36289.868| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.78 r_work: 0.2970 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 1.3784 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= 0.159 Angle : 0.535 6.885 16385 Z= 0.292 Chirality : 0.036 0.151 1906 Planarity : 0.004 0.044 2022 Dihedral : 3.969 21.255 1614 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.25 % Allowed : 13.54 % Favored : 85.22 % 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: 1.52 (0.21), residues: 1531 helix: 1.55 (0.14), residues: 1223 sheet: None (None), residues: 0 loop : -1.14 (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 0.018 0.001 TRP C 194 HIS 0.008 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00350 (12021) covalent geometry : angle 0.53491 (16385) hydrogen bonds : bond 0.04420 ( 943) hydrogen bonds : angle 4.41996 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5153.83 seconds wall clock time: 87 minutes 55.26 seconds (5275.26 seconds total)