Starting phenix.real_space_refine on Wed Sep 17 18:05:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e2p_47460/09_2025/9e2p_47460.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e2p_47460/09_2025/9e2p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9e2p_47460/09_2025/9e2p_47460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e2p_47460/09_2025/9e2p_47460.map" model { file = "/net/cci-nas-00/data/ceres_data/9e2p_47460/09_2025/9e2p_47460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e2p_47460/09_2025/9e2p_47460.cif" } 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-2.0-5805/lib/python3.9/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, 67 Unusual residues: {' CA': 2, ' MG': 1, 'GTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: C, D Time building chain proxies: 3.71, 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: 0.87 Conformation dependent library (CDL) restraints added in 390.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.33 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: 1.22 Time building geometry restraints manager: 1.13 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: 0.010 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.900 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 aren 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 covalent geometry : bond 0.01717 (10516) covalent geometry : angle 1.60186 (14312) hydrogen bonds : bond 0.24294 ( 344) hydrogen bonds : angle 8.63153 ( 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 : 0.473 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: 0.1067 time to fit residues: 19.4194 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 : 0.435 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.155395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107838 restraints weight = 16043.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110165 restraints weight = 12405.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110376 restraints weight = 9906.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110860 restraints weight = 9002.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111341 restraints weight = 8250.634| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10516 Z= 0.138 Angle : 0.643 12.098 14312 Z= 0.319 Chirality : 0.044 0.141 1612 Planarity : 0.005 0.055 1818 Dihedral : 16.110 163.006 1420 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.13 % Allowed : 6.17 % Favored : 92.70 % 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 aren not related in a simple way. whole: -1.81 (0.22), residues: 1254 helix: -1.67 (0.18), residues: 548 sheet: 1.26 (0.43), residues: 164 loop : -1.34 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 416 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 covalent geometry : bond 0.00326 (10516) covalent geometry : angle 0.64296 (14312) hydrogen bonds : bond 0.04924 ( 344) hydrogen bonds : angle 5.13934 ( 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 114 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.412 Fit side-chains REVERT: A 22 MET cc_start: 0.8485 (mmt) cc_final: 0.8016 (mmt) REVERT: C 22 MET cc_start: 0.8561 (mmt) cc_final: 0.8304 (mmm) REVERT: C 488 ILE cc_start: 0.8935 (mm) cc_final: 0.8722 (tt) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.0938 time to fit residues: 15.1061 Evaluate side-chains 96 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 492 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 492 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: 0.0030 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 overall best weight: 0.5252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 200 ASN C 168 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 = 0.3877 r_free = 0.3877 target = 0.156353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108865 restraints weight = 15907.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110957 restraints weight = 12254.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111286 restraints weight = 10528.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112035 restraints weight = 8968.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112183 restraints weight = 8423.623| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10516 Z= 0.094 Angle : 0.534 8.999 14312 Z= 0.261 Chirality : 0.042 0.138 1612 Planarity : 0.005 0.045 1818 Dihedral : 15.846 162.499 1420 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.22 % Allowed : 7.83 % Favored : 90.96 % 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 aren not related in a simple way. whole: -0.99 (0.23), residues: 1254 helix: -0.69 (0.21), residues: 560 sheet: 1.15 (0.42), residues: 166 loop : -1.10 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.018 0.001 TYR C 506 PHE 0.037 0.001 PHE C 504 TRP 0.007 0.001 TRP B 589 HIS 0.003 0.000 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00203 (10516) covalent geometry : angle 0.53425 (14312) hydrogen bonds : bond 0.03807 ( 344) hydrogen bonds : angle 4.64814 ( 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 117 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.418 Fit side-chains REVERT: C 23 SER cc_start: 0.8936 (m) cc_final: 0.8685 (p) outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 0.0982 time to fit residues: 16.2025 Evaluate side-chains 104 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 492 VAL Chi-restraints excluded: chain A residue 514 HIS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain C residue 56 VAL 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: 0.8980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN C 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101828 restraints weight = 16000.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103726 restraints weight = 13319.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103951 restraints weight = 10700.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104559 restraints weight = 9640.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104707 restraints weight = 9238.645| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10516 Z= 0.165 Angle : 0.573 8.736 14312 Z= 0.281 Chirality : 0.045 0.154 1612 Planarity : 0.004 0.044 1818 Dihedral : 15.675 165.995 1420 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.83 % Allowed : 9.39 % Favored : 88.78 % 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 aren not related in a simple way. whole: -0.55 (0.23), residues: 1254 helix: -0.23 (0.22), residues: 548 sheet: 1.81 (0.43), residues: 150 loop : -1.05 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 320 TYR 0.014 0.001 TYR C 506 PHE 0.027 0.002 PHE C 504 TRP 0.008 0.001 TRP D 589 HIS 0.003 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00397 (10516) covalent geometry : angle 0.57277 (14312) hydrogen bonds : bond 0.04746 ( 344) hydrogen bonds : angle 4.62741 ( 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 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.498 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 0.1046 time to fit residues: 18.5962 Evaluate side-chains 115 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 130 THR 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 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: 0.9980 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.0000 chunk 53 optimal weight: 8.9990 chunk 44 optimal weight: 0.0170 chunk 115 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3838 r_free = 0.3838 target = 0.153120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104058 restraints weight = 16019.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106163 restraints weight = 12926.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106370 restraints weight = 10449.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106990 restraints weight = 9461.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107104 restraints weight = 9044.592| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2496 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 8.456 14312 Z= 0.257 Chirality : 0.043 0.136 1612 Planarity : 0.004 0.064 1818 Dihedral : 15.500 167.237 1420 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.00 % Allowed : 11.22 % Favored : 86.78 % 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 aren not related in a simple way. whole: -0.27 (0.24), residues: 1254 helix: 0.13 (0.23), residues: 548 sheet: 1.83 (0.43), residues: 150 loop : -1.02 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 320 TYR 0.018 0.001 TYR C 506 PHE 0.023 0.001 PHE C 504 TRP 0.007 0.001 TRP B 589 HIS 0.002 0.000 HIS C 453 Details of bonding type rmsd covalent geometry : bond 0.00258 (10516) covalent geometry : angle 0.52783 (14312) hydrogen bonds : bond 0.03835 ( 344) hydrogen bonds : angle 4.37946 ( 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 122 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.420 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 118 average time/residue: 0.1058 time to fit residues: 18.2012 Evaluate side-chains 114 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 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 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=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: 5.9990 chunk 75 optimal weight: 7.9990 chunk 96 optimal weight: 0.0770 chunk 15 optimal weight: 0.0040 chunk 63 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104650 restraints weight = 16233.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.106046 restraints weight = 13958.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106837 restraints weight = 12786.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107459 restraints weight = 10285.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107716 restraints weight = 9749.084| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10516 Z= 0.136 Angle : 0.541 9.022 14312 Z= 0.263 Chirality : 0.044 0.136 1612 Planarity : 0.004 0.050 1818 Dihedral : 15.354 170.436 1420 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.91 % Allowed : 11.57 % Favored : 86.52 % 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 aren not related in a simple way. whole: -0.15 (0.24), residues: 1254 helix: 0.27 (0.23), residues: 548 sheet: 1.77 (0.43), residues: 150 loop : -0.97 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 509 TYR 0.016 0.001 TYR C 506 PHE 0.013 0.001 PHE C 504 TRP 0.008 0.001 TRP D 589 HIS 0.002 0.000 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00328 (10516) covalent geometry : angle 0.54089 (14312) hydrogen bonds : bond 0.04081 ( 344) hydrogen bonds : angle 4.35229 ( 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 123 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.421 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 116 average time/residue: 0.1110 time to fit residues: 18.5971 Evaluate side-chains 117 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 91 ASP 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 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: 9.9990 chunk 75 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3806 r_free = 0.3806 target = 0.150891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103109 restraints weight = 16019.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104787 restraints weight = 13541.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104964 restraints weight = 11980.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105664 restraints weight = 10266.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105720 restraints weight = 9627.566| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10516 Z= 0.133 Angle : 0.535 8.509 14312 Z= 0.260 Chirality : 0.044 0.138 1612 Planarity : 0.004 0.043 1818 Dihedral : 15.177 172.752 1420 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.83 % Allowed : 12.09 % Favored : 86.09 % 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 aren not related in a simple way. whole: 0.05 (0.24), residues: 1254 helix: 0.47 (0.23), residues: 538 sheet: 1.41 (0.41), residues: 170 loop : -0.81 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.015 0.001 TYR C 506 PHE 0.011 0.001 PHE C 504 TRP 0.007 0.001 TRP B 589 HIS 0.004 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00320 (10516) covalent geometry : angle 0.53497 (14312) hydrogen bonds : bond 0.03972 ( 344) hydrogen bonds : angle 4.31641 ( 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 119 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 113 average time/residue: 0.1075 time to fit residues: 17.4719 Evaluate side-chains 110 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 41 optimal weight: 3.9990 chunk 117 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 0.0670 chunk 71 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.0020 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3847 r_free = 0.3847 target = 0.154403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107785 restraints weight = 16110.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109338 restraints weight = 13364.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109568 restraints weight = 11834.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110015 restraints weight = 10382.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110461 restraints weight = 9405.465| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2931 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= 0.087 Angle : 0.510 8.896 14312 Z= 0.244 Chirality : 0.042 0.141 1612 Planarity : 0.004 0.041 1818 Dihedral : 14.995 174.815 1420 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.57 % Allowed : 12.78 % Favored : 85.65 % 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 aren not related in a simple way. whole: 0.40 (0.24), residues: 1254 helix: 0.83 (0.23), residues: 534 sheet: 1.77 (0.42), residues: 160 loop : -0.71 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.021 0.001 TYR C 506 PHE 0.009 0.001 PHE C 211 TRP 0.008 0.001 TRP B 589 HIS 0.001 0.000 HIS C 581 Details of bonding type rmsd covalent geometry : bond 0.00202 (10516) covalent geometry : angle 0.50997 (14312) hydrogen bonds : bond 0.02961 ( 344) hydrogen bonds : angle 4.06233 ( 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 122 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.456 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.1033 time to fit residues: 17.8349 Evaluate side-chains 110 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 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 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 570 LEU 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: 0.0010 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 117 optimal weight: 0.0070 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3850 r_free = 0.3850 target = 0.154734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108049 restraints weight = 16155.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109456 restraints weight = 13431.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109769 restraints weight = 12010.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110246 restraints weight = 10483.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110671 restraints weight = 9498.023| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10516 Z= 0.087 Angle : 0.512 9.066 14312 Z= 0.244 Chirality : 0.042 0.139 1612 Planarity : 0.004 0.063 1818 Dihedral : 14.880 176.112 1420 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.48 % Allowed : 13.22 % Favored : 85.30 % 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 aren not related in a simple way. whole: 0.57 (0.24), residues: 1254 helix: 1.05 (0.23), residues: 532 sheet: 1.59 (0.41), residues: 170 loop : -0.64 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 509 TYR 0.019 0.001 TYR C 506 PHE 0.008 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 covalent geometry : bond 0.00202 (10516) covalent geometry : angle 0.51178 (14312) hydrogen bonds : bond 0.02941 ( 344) hydrogen bonds : angle 3.95768 ( 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 116 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.429 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.1022 time to fit residues: 16.2794 Evaluate side-chains 112 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 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 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 569 ILE Chi-restraints excluded: chain D residue 570 LEU 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: 3.9990 chunk 33 optimal weight: 0.0170 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3815 r_free = 0.3815 target = 0.151771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104576 restraints weight = 15989.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105923 restraints weight = 13556.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106213 restraints weight = 12164.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106628 restraints weight = 10515.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107022 restraints weight = 9619.274| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10516 Z= 0.149 Angle : 0.550 9.009 14312 Z= 0.267 Chirality : 0.045 0.211 1612 Planarity : 0.004 0.067 1818 Dihedral : 14.789 176.084 1420 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.39 % Allowed : 13.74 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.24), residues: 1254 helix: 0.82 (0.23), residues: 534 sheet: 1.45 (0.41), residues: 170 loop : -0.68 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 509 TYR 0.019 0.001 TYR C 506 PHE 0.013 0.001 PHE A 504 TRP 0.007 0.001 TRP D 589 HIS 0.003 0.001 HIS C 581 Details of bonding type rmsd covalent geometry : bond 0.00361 (10516) covalent geometry : angle 0.55014 (14312) hydrogen bonds : bond 0.04110 ( 344) hydrogen bonds : angle 4.24290 ( 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 117 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.444 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 114 average time/residue: 0.0998 time to fit residues: 16.7261 Evaluate side-chains 112 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 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 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 570 LEU 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: 0.8980 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3808 r_free = 0.3808 target = 0.151352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103295 restraints weight = 16006.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104983 restraints weight = 13474.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105222 restraints weight = 11465.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105855 restraints weight = 10091.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105862 restraints weight = 9623.370| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10516 Z= 0.135 Angle : 0.540 9.008 14312 Z= 0.261 Chirality : 0.044 0.138 1612 Planarity : 0.004 0.063 1818 Dihedral : 14.655 175.206 1420 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.83 % Allowed : 13.65 % Favored : 84.52 % 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 aren not related in a simple way. whole: 0.31 (0.24), residues: 1254 helix: 0.82 (0.23), residues: 532 sheet: 1.36 (0.41), residues: 166 loop : -0.71 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.019 0.001 TYR C 506 PHE 0.009 0.001 PHE A 504 TRP 0.007 0.001 TRP B 589 HIS 0.002 0.000 HIS C 581 Details of bonding type rmsd covalent geometry : bond 0.00328 (10516) covalent geometry : angle 0.54012 (14312) hydrogen bonds : bond 0.03885 ( 344) hydrogen bonds : angle 4.22076 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.53 seconds wall clock time: 29 minutes 5.78 seconds (1745.78 seconds total)