Starting phenix.real_space_refine on Thu Jul 2 21:03:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2p_47460/07_2026/9e2p_47460.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2p_47460/07_2026/9e2p_47460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e2p_47460/07_2026/9e2p_47460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2p_47460/07_2026/9e2p_47460.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e2p_47460/07_2026/9e2p_47460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2p_47460/07_2026/9e2p_47460.map" } resolution = 3.57 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= 0.009 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 12 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 6512 2.51 5 N 1730 2.21 5 O 1966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 10282 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4730 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 32, 'TRANS': 554} Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 344 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 5, 'TRANS': 38} Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'GTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Restraints were copied for chains: C, D Time building chain proxies: 3.75, per 1000 atoms: 0.36 Number of scatterers: 10282 At special positions: 0 Unit cell: (97.18, 105.78, 124.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 56 16.00 P 12 15.00 Mg 2 11.99 O 1966 8.00 N 1730 7.00 C 6512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 298.9 milliseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 42.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.946A pdb=" N ILE A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.546A pdb=" N ASP A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.686A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 4.151A pdb=" N ILE A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.687A pdb=" N ALA A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.949A pdb=" N ARG A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.570A pdb=" N ASN A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.808A pdb=" N ASP A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 262 removed outlier: 3.677A pdb=" N GLY A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 274 removed outlier: 3.703A pdb=" N VAL A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 removed outlier: 4.420A pdb=" N GLN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.681A pdb=" N TRP A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 370 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.703A pdb=" N CYS A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 394 through 397 removed outlier: 4.065A pdb=" N SER A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 502 through 514 removed outlier: 3.894A pdb=" N TYR A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 549 removed outlier: 3.851A pdb=" N HIS A 549 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'B' and resid 584 through 594 removed outlier: 3.509A pdb=" N GLN B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.945A pdb=" N ILE C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 Processing helix chain 'C' and resid 87 through 96 removed outlier: 3.545A pdb=" N ASP C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 removed outlier: 4.686A pdb=" N ARG C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 138 removed outlier: 4.152A pdb=" N ILE C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 removed outlier: 3.686A pdb=" N ALA C 165 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.949A pdb=" N ARG C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.570A pdb=" N ASN C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 removed outlier: 3.809A pdb=" N ASP C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 262 removed outlier: 3.678A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 274 removed outlier: 3.704A pdb=" N VAL C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 removed outlier: 4.420A pdb=" N GLN C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'C' and resid 344 through 349 Processing helix chain 'C' and resid 359 through 373 removed outlier: 3.681A pdb=" N TRP C 366 " --> pdb=" O PHE C 362 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 370 " --> pdb=" O TRP C 366 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.703A pdb=" N CYS C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C 384 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 394 through 397 removed outlier: 4.066A pdb=" N SER C 397 " --> pdb=" O SER C 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 394 through 397' Processing helix chain 'C' and resid 404 through 412 Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 502 through 514 removed outlier: 3.893A pdb=" N TYR C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 508 " --> pdb=" O PHE C 504 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS C 514 " --> pdb=" O ILE C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 549 removed outlier: 3.849A pdb=" N HIS C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 579 Processing helix chain 'D' and resid 584 through 594 removed outlier: 3.510A pdb=" N GLN D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.892A pdb=" N LEU A 113 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR A 143 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 78 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 116 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 80 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN A 118 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR A 82 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG A 6 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N CYS A 79 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 8 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 81 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 10 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ALA A 83 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 5 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL A 56 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 5 " --> pdb=" O HIS C 54 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL C 56 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG C 6 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N CYS C 79 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 8 " --> pdb=" O CYS C 79 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL C 81 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C 10 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N ALA C 83 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 78 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 116 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 80 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN C 118 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR C 82 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 113 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR C 143 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 removed outlier: 4.039A pdb=" N GLU A 180 " --> pdb=" O CYS A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.742A pdb=" N ILE A 357 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 457 through 464 removed outlier: 9.380A pdb=" N VAL A 491 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG A 420 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N CYS A 493 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN A 422 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL A 495 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 424 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N ASP A 497 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 527 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N GLN A 555 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE A 524 " --> pdb=" O GLN A 555 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 174 through 175 removed outlier: 4.039A pdb=" N GLU C 180 " --> pdb=" O CYS C 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 299 through 301 Processing sheet with id=AA8, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.742A pdb=" N ILE C 357 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 457 through 464 removed outlier: 9.380A pdb=" N VAL C 491 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG C 420 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N CYS C 493 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN C 422 " --> pdb=" O CYS C 493 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL C 495 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 424 " --> pdb=" O VAL C 495 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N ASP C 497 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 527 " --> pdb=" O TYR C 496 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N GLN C 555 " --> pdb=" O CYS C 522 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE C 524 " --> pdb=" O GLN C 555 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 1008 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: 1.60 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.23: 83 1.23 - 1.55: 10292 1.55 - 1.87: 139 1.87 - 2.19: 0 2.19 - 2.51: 2 Bond restraints: 10516 Sorted by residual: bond pdb=" CB PRO B 571 " pdb=" CG PRO B 571 " ideal model delta sigma weight residual 1.492 2.509 -1.017 5.00e-02 4.00e+02 4.14e+02 bond pdb=" CB PRO D 571 " pdb=" CG PRO D 571 " ideal model delta sigma weight residual 1.492 2.509 -1.017 5.00e-02 4.00e+02 4.14e+02 bond pdb=" CG PRO D 571 " pdb=" CD PRO D 571 " ideal model delta sigma weight residual 1.503 0.911 0.592 3.40e-02 8.65e+02 3.03e+02 bond pdb=" CG PRO B 571 " pdb=" CD PRO B 571 " ideal model delta sigma weight residual 1.503 0.911 0.592 3.40e-02 8.65e+02 3.03e+02 bond pdb=" N PRO B 571 " pdb=" CD PRO B 571 " ideal model delta sigma weight residual 1.473 1.596 -0.123 1.40e-02 5.10e+03 7.77e+01 ... (remaining 10511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 18.25: 14304 18.25 - 36.49: 6 36.49 - 54.74: 0 54.74 - 72.98: 0 72.98 - 91.23: 2 Bond angle restraints: 14312 Sorted by residual: angle pdb=" CB PRO D 571 " pdb=" CG PRO D 571 " pdb=" CD PRO D 571 " ideal model delta sigma weight residual 106.10 14.87 91.23 3.20e+00 9.77e-02 8.13e+02 angle pdb=" CB PRO B 571 " pdb=" CG PRO B 571 " pdb=" CD PRO B 571 " ideal model delta sigma weight residual 106.10 14.93 91.17 3.20e+00 9.77e-02 8.12e+02 angle pdb=" N PRO D 571 " pdb=" CA PRO D 571 " pdb=" CB PRO D 571 " ideal model delta sigma weight residual 103.25 86.59 16.66 1.05e+00 9.07e-01 2.52e+02 angle pdb=" N PRO B 571 " pdb=" CA PRO B 571 " pdb=" CB PRO B 571 " ideal model delta sigma weight residual 103.25 86.59 16.66 1.05e+00 9.07e-01 2.52e+02 angle pdb=" CA PRO D 571 " pdb=" N PRO D 571 " pdb=" CD PRO D 571 " ideal model delta sigma weight residual 112.00 93.43 18.57 1.40e+00 5.10e-01 1.76e+02 ... (remaining 14307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.77: 6213 32.77 - 65.54: 135 65.54 - 98.30: 20 98.30 - 131.07: 10 131.07 - 163.84: 8 Dihedral angle restraints: 6386 sinusoidal: 2654 harmonic: 3732 Sorted by residual: dihedral pdb=" C8 GTP C 601 " pdb=" C1' GTP C 601 " pdb=" N9 GTP C 601 " pdb=" O4' GTP C 601 " ideal model delta sinusoidal sigma weight residual 104.59 -59.25 163.84 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -59.22 163.81 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C8 GTP C 603 " pdb=" C1' GTP C 603 " pdb=" N9 GTP C 603 " pdb=" O4' GTP C 603 " ideal model delta sinusoidal sigma weight residual 104.59 -58.84 163.43 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 6383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1323 0.077 - 0.154: 262 0.154 - 0.231: 17 0.231 - 0.308: 8 0.308 - 0.385: 2 Chirality restraints: 1612 Sorted by residual: chirality pdb=" CA PRO D 571 " pdb=" N PRO D 571 " pdb=" C PRO D 571 " pdb=" CB PRO D 571 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA PRO B 571 " pdb=" N PRO B 571 " pdb=" C PRO B 571 " pdb=" CB PRO B 571 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL C 233 " pdb=" CA VAL C 233 " pdb=" CG1 VAL C 233 " pdb=" CG2 VAL C 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1609 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 132 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO C 133 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 132 " -0.052 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO A 133 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 604 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO B 605 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 605 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 605 " -0.041 5.00e-02 4.00e+02 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 174 2.68 - 3.24: 8726 3.24 - 3.79: 14844 3.79 - 4.35: 19770 4.35 - 4.90: 32195 Nonbonded interactions: 75709 Sorted by model distance: nonbonded pdb=" O1G GTP A 601 " pdb="MG MG A 602 " model vdw 2.131 2.170 nonbonded pdb=" O1G GTP C 601 " pdb="MG MG C 602 " model vdw 2.132 2.170 nonbonded pdb=" O2B GTP A 601 " pdb="MG MG A 602 " model vdw 2.147 2.170 nonbonded pdb=" O2B GTP C 601 " pdb="MG MG C 602 " model vdw 2.148 2.170 nonbonded pdb=" OG1 THR C 18 " pdb="MG MG C 602 " model vdw 2.334 2.170 ... (remaining 75704 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.520 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.017 1.017 10516 Z= 0.480 Angle : 1.602 91.225 14312 Z= 0.725 Chirality : 0.062 0.385 1612 Planarity : 0.009 0.078 1818 Dihedral : 17.625 163.839 3962 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.17 % 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: -3.13 (0.20), residues: 1254 helix: -3.39 (0.13), residues: 514 sheet: 1.03 (0.43), residues: 166 loop : -1.62 (0.22), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 416 TYR 0.024 0.002 TYR A 496 PHE 0.029 0.002 PHE A 211 TRP 0.027 0.002 TRP B 589 HIS 0.005 0.001 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.01717 / 0.48 (10516) covalent geometry : angle 1.60186 / 0.73 (14312) hydrogen bonds : bond 0.24294 / 16.19 ( 344) hydrogen bonds : angle 8.63153 / 6.09 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.317 Fit side-chains REVERT: A 22 MET cc_start: 0.8530 (mmt) cc_final: 0.8113 (mmt) REVERT: C 22 MET cc_start: 0.8617 (mmt) cc_final: 0.8213 (mmt) REVERT: C 488 ILE cc_start: 0.8757 (mm) cc_final: 0.8484 (tt) REVERT: C 550 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8747 (ttpp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0795 time to fit residues: 14.4993 Evaluate side-chains 89 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.0870 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108820 restraints weight = 16020.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105385 restraints weight = 11258.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106615 restraints weight = 12575.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107194 restraints weight = 10094.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108092 restraints weight = 9397.238| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10516 Z= 0.138 Angle : 0.645 11.788 14312 Z= 0.321 Chirality : 0.045 0.144 1612 Planarity : 0.006 0.055 1818 Dihedral : 16.144 163.052 1420 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.04 % Allowed : 6.00 % Favored : 92.96 % 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: -1.86 (0.21), residues: 1254 helix: -1.77 (0.18), residues: 544 sheet: 1.28 (0.43), residues: 164 loop : -1.32 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 320 TYR 0.012 0.001 TYR C 359 PHE 0.010 0.001 PHE C 211 TRP 0.007 0.001 TRP B 589 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10516) covalent geometry : angle 0.64477 / 0.32 (14312) hydrogen bonds : bond 0.05370 / 3.49 ( 344) hydrogen bonds : angle 5.22852 / 3.63 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.238 Fit side-chains REVERT: A 22 MET cc_start: 0.8480 (mmt) cc_final: 0.8025 (mmt) REVERT: C 22 MET cc_start: 0.8555 (mmt) cc_final: 0.8285 (mmm) REVERT: C 231 ASN cc_start: 0.8880 (m-40) cc_final: 0.8675 (t0) REVERT: C 488 ILE cc_start: 0.8884 (mm) cc_final: 0.8684 (tt) REVERT: C 550 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8799 (tttp) outliers start: 12 outliers final: 8 residues processed: 107 average time/residue: 0.0855 time to fit residues: 13.3806 Evaluate side-chains 96 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 24 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 200 ASN A 303 HIS C 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.149522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100238 restraints weight = 15980.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.101952 restraints weight = 13116.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102394 restraints weight = 10762.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.102932 restraints weight = 9452.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103112 restraints weight = 8994.794| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10516 Z= 0.223 Angle : 0.638 8.955 14312 Z= 0.320 Chirality : 0.047 0.135 1612 Planarity : 0.005 0.049 1818 Dihedral : 15.960 161.619 1420 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.57 % Allowed : 9.13 % Favored : 89.30 % 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: -1.19 (0.22), residues: 1254 helix: -0.90 (0.21), residues: 548 sheet: 1.59 (0.43), residues: 150 loop : -1.26 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 320 TYR 0.011 0.001 TYR C 276 PHE 0.037 0.002 PHE C 504 TRP 0.010 0.002 TRP D 589 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (10516) covalent geometry : angle 0.63812 / 0.32 (14312) hydrogen bonds : bond 0.05941 / 3.92 ( 344) hydrogen bonds : angle 4.93680 / 3.42 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.357 Fit side-chains REVERT: A 22 MET cc_start: 0.8522 (mmt) cc_final: 0.8227 (mmt) REVERT: C 23 SER cc_start: 0.8995 (m) cc_final: 0.8763 (p) REVERT: C 488 ILE cc_start: 0.8902 (mm) cc_final: 0.8669 (tt) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.0807 time to fit residues: 14.4172 Evaluate side-chains 115 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.152197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104959 restraints weight = 15968.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107181 restraints weight = 13659.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107160 restraints weight = 11338.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107565 restraints weight = 10204.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107923 restraints weight = 9306.156| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10516 Z= 0.113 Angle : 0.538 8.291 14312 Z= 0.264 Chirality : 0.044 0.138 1612 Planarity : 0.004 0.044 1818 Dihedral : 15.717 162.742 1420 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.74 % Allowed : 11.30 % Favored : 86.96 % 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: -0.68 (0.23), residues: 1254 helix: -0.20 (0.22), residues: 548 sheet: 1.64 (0.44), residues: 150 loop : -1.25 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.012 0.001 TYR A 496 PHE 0.026 0.001 PHE C 504 TRP 0.008 0.001 TRP B 589 HIS 0.003 0.000 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10516) covalent geometry : angle 0.53771 / 0.26 (14312) hydrogen bonds : bond 0.04049 / 2.61 ( 344) hydrogen bonds : angle 4.55679 / 3.14 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.412 Fit side-chains REVERT: A 22 MET cc_start: 0.8488 (mmt) cc_final: 0.8199 (mmt) REVERT: C 488 ILE cc_start: 0.8920 (mm) cc_final: 0.8686 (tt) outliers start: 20 outliers final: 14 residues processed: 114 average time/residue: 0.0861 time to fit residues: 14.5680 Evaluate side-chains 108 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** 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 = 0.3830 r_free = 0.3830 target = 0.152450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103363 restraints weight = 15992.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105483 restraints weight = 12666.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105671 restraints weight = 10240.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106362 restraints weight = 9236.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106420 restraints weight = 8791.552| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10516 Z= 0.111 Angle : 0.528 8.851 14312 Z= 0.256 Chirality : 0.043 0.136 1612 Planarity : 0.005 0.062 1818 Dihedral : 15.486 167.202 1420 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.00 % Allowed : 11.65 % Favored : 86.35 % 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: -0.31 (0.24), residues: 1254 helix: 0.13 (0.23), residues: 548 sheet: 1.70 (0.43), residues: 150 loop : -1.04 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.013 0.001 TYR A 496 PHE 0.023 0.001 PHE C 504 TRP 0.008 0.001 TRP D 589 HIS 0.002 0.000 HIS C 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10516) covalent geometry : angle 0.52755 / 0.26 (14312) hydrogen bonds : bond 0.03856 / 2.50 ( 344) hydrogen bonds : angle 4.33183 / 2.98 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.393 Fit side-chains REVERT: A 22 MET cc_start: 0.8492 (mmt) cc_final: 0.8234 (mmt) REVERT: B 591 GLN cc_start: 0.8950 (tp40) cc_final: 0.8586 (tp40) REVERT: C 488 ILE cc_start: 0.8895 (mm) cc_final: 0.8670 (tt) outliers start: 23 outliers final: 16 residues processed: 119 average time/residue: 0.0918 time to fit residues: 15.7865 Evaluate side-chains 113 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 93 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** 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 = 0.3817 r_free = 0.3817 target = 0.151625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103495 restraints weight = 16293.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104655 restraints weight = 14649.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104824 restraints weight = 12404.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105502 restraints weight = 11158.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107543 restraints weight = 10643.998| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10516 Z= 0.129 Angle : 0.533 8.575 14312 Z= 0.261 Chirality : 0.044 0.140 1612 Planarity : 0.004 0.052 1818 Dihedral : 15.349 169.263 1420 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.83 % Allowed : 12.70 % Favored : 85.48 % 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: -0.21 (0.24), residues: 1254 helix: 0.28 (0.23), residues: 546 sheet: 1.72 (0.43), residues: 150 loop : -1.06 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 509 TYR 0.011 0.001 TYR A 496 PHE 0.011 0.001 PHE C 504 TRP 0.008 0.001 TRP B 589 HIS 0.002 0.000 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (10516) covalent geometry : angle 0.53311 / 0.26 (14312) hydrogen bonds : bond 0.03974 / 2.59 ( 344) hydrogen bonds : angle 4.34254 / 2.98 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.386 Fit side-chains REVERT: B 591 GLN cc_start: 0.8973 (tp40) cc_final: 0.8611 (tp40) REVERT: C 488 ILE cc_start: 0.8948 (mm) cc_final: 0.8697 (tt) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.0788 time to fit residues: 13.5012 Evaluate side-chains 112 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103801 restraints weight = 16083.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105697 restraints weight = 14052.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105834 restraints weight = 12142.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106453 restraints weight = 10484.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106434 restraints weight = 9959.175| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10516 Z= 0.135 Angle : 0.540 8.355 14312 Z= 0.263 Chirality : 0.044 0.140 1612 Planarity : 0.004 0.043 1818 Dihedral : 15.194 171.842 1420 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.00 % Allowed : 13.22 % Favored : 84.78 % 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: -0.03 (0.24), residues: 1254 helix: 0.48 (0.23), residues: 534 sheet: 1.39 (0.41), residues: 170 loop : -0.93 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.010 0.001 TYR A 496 PHE 0.013 0.001 PHE C 504 TRP 0.008 0.001 TRP D 589 HIS 0.002 0.000 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (10516) covalent geometry : angle 0.53954 / 0.26 (14312) hydrogen bonds : bond 0.04072 / 2.66 ( 344) hydrogen bonds : angle 4.33617 / 2.97 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.378 Fit side-chains REVERT: B 591 GLN cc_start: 0.8993 (tp40) cc_final: 0.8610 (tp40) REVERT: C 488 ILE cc_start: 0.8954 (mm) cc_final: 0.8713 (tt) outliers start: 23 outliers final: 17 residues processed: 118 average time/residue: 0.0821 time to fit residues: 14.4351 Evaluate side-chains 112 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** 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 = 0.3782 r_free = 0.3782 target = 0.148708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101212 restraints weight = 16204.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103147 restraints weight = 14331.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103758 restraints weight = 12889.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104293 restraints weight = 10053.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104560 restraints weight = 9572.036| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10516 Z= 0.202 Angle : 0.596 7.929 14312 Z= 0.294 Chirality : 0.046 0.150 1612 Planarity : 0.004 0.043 1818 Dihedral : 15.159 172.893 1420 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.83 % Allowed : 14.17 % Favored : 84.00 % 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: -0.23 (0.24), residues: 1254 helix: 0.31 (0.23), residues: 534 sheet: 1.22 (0.41), residues: 170 loop : -1.01 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.010 0.001 TYR C 161 PHE 0.012 0.002 PHE A 336 TRP 0.008 0.001 TRP B 589 HIS 0.002 0.001 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 (10516) covalent geometry : angle 0.59570 / 0.29 (14312) hydrogen bonds : bond 0.05034 / 3.33 ( 344) hydrogen bonds : angle 4.61149 / 3.15 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.362 Fit side-chains REVERT: B 591 GLN cc_start: 0.9025 (tp40) cc_final: 0.8671 (tp40) REVERT: C 488 ILE cc_start: 0.8933 (mm) cc_final: 0.8675 (tt) outliers start: 21 outliers final: 18 residues processed: 117 average time/residue: 0.0849 time to fit residues: 14.6656 Evaluate side-chains 116 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.147721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.098293 restraints weight = 16113.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101141 restraints weight = 13760.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101028 restraints weight = 10416.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101648 restraints weight = 9461.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101751 restraints weight = 8970.463| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10516 Z= 0.201 Angle : 0.587 8.186 14312 Z= 0.289 Chirality : 0.046 0.152 1612 Planarity : 0.004 0.043 1818 Dihedral : 15.096 172.974 1420 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.91 % Allowed : 14.87 % Favored : 83.22 % 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: -0.32 (0.24), residues: 1254 helix: 0.28 (0.23), residues: 532 sheet: 1.09 (0.41), residues: 166 loop : -1.05 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.014 0.001 TYR A 496 PHE 0.012 0.001 PHE A 336 TRP 0.008 0.001 TRP B 589 HIS 0.003 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 (10516) covalent geometry : angle 0.58675 / 0.29 (14312) hydrogen bonds : bond 0.04858 / 3.20 ( 344) hydrogen bonds : angle 4.59722 / 3.14 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.334 Fit side-chains REVERT: B 591 GLN cc_start: 0.9018 (tp40) cc_final: 0.8659 (tp40) REVERT: C 488 ILE cc_start: 0.8922 (mm) cc_final: 0.8650 (tt) outliers start: 22 outliers final: 19 residues processed: 114 average time/residue: 0.0907 time to fit residues: 14.9850 Evaluate side-chains 112 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 0.0050 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS ** C 213 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.151341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102816 restraints weight = 15898.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105054 restraints weight = 12792.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105201 restraints weight = 10236.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105889 restraints weight = 9243.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105889 restraints weight = 8732.464| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10516 Z= 0.104 Angle : 0.529 8.406 14312 Z= 0.257 Chirality : 0.043 0.147 1612 Planarity : 0.004 0.042 1818 Dihedral : 14.919 173.720 1420 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.74 % Allowed : 15.04 % Favored : 83.22 % 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: -0.02 (0.24), residues: 1254 helix: 0.54 (0.23), residues: 534 sheet: 1.21 (0.41), residues: 166 loop : -0.90 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 509 TYR 0.014 0.001 TYR A 496 PHE 0.010 0.001 PHE A 159 TRP 0.009 0.001 TRP B 589 HIS 0.002 0.001 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 (10516) covalent geometry : angle 0.52854 / 0.26 (14312) hydrogen bonds : bond 0.03629 / 2.34 ( 344) hydrogen bonds : angle 4.27856 / 2.92 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.292 Fit side-chains REVERT: A 551 MET cc_start: 0.6690 (mtp) cc_final: 0.6465 (mtp) REVERT: C 488 ILE cc_start: 0.8910 (mm) cc_final: 0.8670 (tt) outliers start: 20 outliers final: 16 residues processed: 118 average time/residue: 0.0860 time to fit residues: 14.8157 Evaluate side-chains 110 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 65 optimal weight: 0.0970 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 GLN ** 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 = 0.3823 r_free = 0.3823 target = 0.152752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104294 restraints weight = 16091.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106701 restraints weight = 12561.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.106855 restraints weight = 10243.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107574 restraints weight = 9191.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107519 restraints weight = 8683.657| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10516 Z= 0.093 Angle : 0.527 8.548 14312 Z= 0.253 Chirality : 0.043 0.145 1612 Planarity : 0.004 0.042 1818 Dihedral : 14.740 174.982 1420 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.48 % Allowed : 15.48 % Favored : 83.04 % 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: 0.20 (0.24), residues: 1254 helix: 0.72 (0.23), residues: 534 sheet: 1.35 (0.42), residues: 166 loop : -0.79 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 509 TYR 0.014 0.001 TYR A 496 PHE 0.026 0.001 PHE A 504 TRP 0.009 0.001 TRP B 589 HIS 0.002 0.000 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (10516) covalent geometry : angle 0.52654 / 0.25 (14312) hydrogen bonds : bond 0.03196 / 2.04 ( 344) hydrogen bonds : angle 4.10024 / 2.80 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.72 seconds wall clock time: 25 minutes 27.51 seconds (1527.51 seconds total)