Starting phenix.real_space_refine on Thu Aug 6 13:35:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11wp_76138/08_2026/11wp_76138.cif Found real_map, /net/cci-nas-00/data/ceres_data/11wp_76138/08_2026/11wp_76138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11wp_76138/08_2026/11wp_76138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11wp_76138/08_2026/11wp_76138.map" model { file = "/net/cci-nas-00/data/ceres_data/11wp_76138/08_2026/11wp_76138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11wp_76138/08_2026/11wp_76138.cif" } resolution = 3.2 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= 0.013 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 75 5.16 5 C 9582 2.51 5 N 2583 2.21 5 O 2751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4969 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 41, 'TRANS': 596} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'APC': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C Time building chain proxies: 4.89, per 1000 atoms: 0.33 Number of scatterers: 15000 At special positions: 0 Unit cell: (78.26, 139.32, 145.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 9 15.00 O 2751 8.00 N 2583 7.00 C 9582 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: 1.21 Conformation dependent library (CDL) restraints added in 675.3 milliseconds 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 24 sheets defined 36.2% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.657A pdb=" N ASP A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.556A pdb=" N SER A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.769A pdb=" N ILE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 247 through 253 removed outlier: 4.890A pdb=" N ILE A 250 " --> pdb=" O HIS A 247 " (cutoff:3.500A) Proline residue: A 251 - end of helix No H-bonds generated for 'chain 'A' and resid 247 through 253' Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.656A pdb=" N LEU A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 359 Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 399 through 409 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.641A pdb=" N HIS A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 595 Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 646 through 657 Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 31 through 45 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.656A pdb=" N ASP B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.556A pdb=" N SER B 136 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.769A pdb=" N ILE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 247 through 253 removed outlier: 4.890A pdb=" N ILE B 250 " --> pdb=" O HIS B 247 " (cutoff:3.500A) Proline residue: B 251 - end of helix No H-bonds generated for 'chain 'B' and resid 247 through 253' Processing helix chain 'B' and resid 287 through 301 Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.655A pdb=" N LEU B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 399 through 409 Processing helix chain 'B' and resid 491 through 499 Processing helix chain 'B' and resid 539 through 549 removed outlier: 3.640A pdb=" N HIS B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 646 through 657 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.656A pdb=" N ASP C 56 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 120 through 137 removed outlier: 3.556A pdb=" N SER C 136 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 166 removed outlier: 3.769A pdb=" N ILE C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 247 through 253 removed outlier: 4.890A pdb=" N ILE C 250 " --> pdb=" O HIS C 247 " (cutoff:3.500A) Proline residue: C 251 - end of helix No H-bonds generated for 'chain 'C' and resid 247 through 253' Processing helix chain 'C' and resid 287 through 301 Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 326 through 333 removed outlier: 3.656A pdb=" N LEU C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 491 through 499 Processing helix chain 'C' and resid 539 through 549 removed outlier: 3.640A pdb=" N HIS C 549 " --> pdb=" O ALA C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 595 Processing helix chain 'C' and resid 622 through 629 Processing helix chain 'C' and resid 646 through 657 Processing sheet with id=1, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=2, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.977A pdb=" N ARG A 116 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE A 106 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 118 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 104 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 338 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 106 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 168 through 171 removed outlier: 6.466A pdb=" N VAL A 145 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 192 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 196 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 193 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 225 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 198 through 201 Processing sheet with id=5, first strand: chain 'A' and resid 269 through 272 removed outlier: 4.029A pdb=" N PHE A 269 " --> pdb=" O HIS A 285 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 285 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A 486 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 362 through 365 removed outlier: 6.955A pdb=" N TRP A 363 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 391 " --> pdb=" O ALA A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'A' and resid 464 through 465 removed outlier: 4.631A pdb=" N ILE A 456 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP A 510 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N ILE A 476 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR A 508 " --> pdb=" O ILE A 476 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 554 through 561 Processing sheet with id=9, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=10, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.977A pdb=" N ARG B 116 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE B 106 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 118 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 104 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 338 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 106 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.466A pdb=" N VAL B 145 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL B 192 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 196 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 193 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 225 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 198 through 201 Processing sheet with id=13, first strand: chain 'B' and resid 269 through 272 removed outlier: 4.029A pdb=" N PHE B 269 " --> pdb=" O HIS B 285 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 285 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR B 486 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 362 through 365 removed outlier: 6.955A pdb=" N TRP B 363 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 391 " --> pdb=" O ALA B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=14 Processing sheet with id=15, first strand: chain 'B' and resid 464 through 465 removed outlier: 4.632A pdb=" N ILE B 456 " --> pdb=" O ILE B 465 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP B 510 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ILE B 476 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR B 508 " --> pdb=" O ILE B 476 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 554 through 561 Processing sheet with id=17, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=18, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.977A pdb=" N ARG C 116 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE C 106 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 118 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 104 " --> pdb=" O THR C 336 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL C 338 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 106 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 168 through 171 removed outlier: 6.467A pdb=" N VAL C 145 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL C 192 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 196 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 193 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 225 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 198 through 201 Processing sheet with id=21, first strand: chain 'C' and resid 269 through 272 removed outlier: 4.029A pdb=" N PHE C 269 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS C 285 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 486 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 362 through 365 removed outlier: 6.955A pdb=" N TRP C 363 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 391 " --> pdb=" O ALA C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=22 Processing sheet with id=23, first strand: chain 'C' and resid 464 through 465 removed outlier: 4.631A pdb=" N ILE C 456 " --> pdb=" O ILE C 465 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP C 510 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N ILE C 476 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR C 508 " --> pdb=" O ILE C 476 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'C' and resid 554 through 561 531 hydrogen bonds defined for protein. 1557 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: 2.30 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4851 1.35 - 1.47: 3707 1.47 - 1.59: 6706 1.59 - 1.71: 6 1.71 - 1.83: 129 Bond restraints: 15399 Sorted by residual: bond pdb=" C ILE C 250 " pdb=" N PRO C 251 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.78e+00 bond pdb=" C ILE B 250 " pdb=" N PRO B 251 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.76e+00 bond pdb=" C ILE A 250 " pdb=" N PRO A 251 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.58e+00 bond pdb=" C LYS C 576 " pdb=" N PRO C 577 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.28e+00 bond pdb=" CA ASP C 469 " pdb=" CB ASP C 469 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.26e+00 ... (remaining 15394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 20470 1.86 - 3.71: 421 3.71 - 5.57: 70 5.57 - 7.42: 21 7.42 - 9.28: 6 Bond angle restraints: 20988 Sorted by residual: angle pdb=" CA TYR C 656 " pdb=" CB TYR C 656 " pdb=" CG TYR C 656 " ideal model delta sigma weight residual 113.90 121.22 -7.32 1.80e+00 3.09e-01 1.65e+01 angle pdb=" CA TYR B 656 " pdb=" CB TYR B 656 " pdb=" CG TYR B 656 " ideal model delta sigma weight residual 113.90 121.22 -7.32 1.80e+00 3.09e-01 1.65e+01 angle pdb=" CA TYR A 656 " pdb=" CB TYR A 656 " pdb=" CG TYR A 656 " ideal model delta sigma weight residual 113.90 121.21 -7.31 1.80e+00 3.09e-01 1.65e+01 angle pdb=" C ILE B 249 " pdb=" N ILE B 250 " pdb=" CA ILE B 250 " ideal model delta sigma weight residual 120.33 123.25 -2.92 8.00e-01 1.56e+00 1.33e+01 angle pdb=" C ILE A 249 " pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 120.33 123.25 -2.92 8.00e-01 1.56e+00 1.33e+01 ... (remaining 20983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8153 17.76 - 35.51: 832 35.51 - 53.27: 144 53.27 - 71.02: 30 71.02 - 88.78: 18 Dihedral angle restraints: 9177 sinusoidal: 3663 harmonic: 5514 Sorted by residual: dihedral pdb=" CA HIS C 658 " pdb=" C HIS C 658 " pdb=" N GLN C 659 " pdb=" CA GLN C 659 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS B 658 " pdb=" C HIS B 658 " pdb=" N GLN B 659 " pdb=" CA GLN B 659 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS A 658 " pdb=" C HIS A 658 " pdb=" N GLN A 659 " pdb=" CA GLN A 659 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 9174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1533 0.042 - 0.084: 557 0.084 - 0.126: 228 0.126 - 0.169: 8 0.169 - 0.211: 5 Chirality restraints: 2331 Sorted by residual: chirality pdb=" CA HIS C 652 " pdb=" N HIS C 652 " pdb=" C HIS C 652 " pdb=" CB HIS C 652 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA HIS A 652 " pdb=" N HIS A 652 " pdb=" C HIS A 652 " pdb=" CB HIS A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA HIS B 652 " pdb=" N HIS B 652 " pdb=" C HIS B 652 " pdb=" CB HIS B 652 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2328 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 656 " -0.028 2.00e-02 2.50e+03 2.62e-02 1.37e+01 pdb=" CG TYR B 656 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR B 656 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 656 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 656 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 656 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 656 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 656 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 656 " 0.027 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR C 656 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR C 656 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 656 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 656 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 656 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 656 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 656 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 656 " 0.028 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR A 656 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 656 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 656 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 656 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 656 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 656 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 656 " 0.001 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 9008 3.04 - 3.50: 15218 3.50 - 3.97: 23099 3.97 - 4.43: 26823 4.43 - 4.90: 42732 Nonbonded interactions: 116880 Sorted by model distance: nonbonded pdb=" OD1 ASP B 308 " pdb=" OG1 THR B 361 " model vdw 2.571 3.040 nonbonded pdb=" OD1 ASP C 308 " pdb=" OG1 THR C 361 " model vdw 2.571 3.040 nonbonded pdb=" OD1 ASP A 308 " pdb=" OG1 THR A 361 " model vdw 2.572 3.040 nonbonded pdb=" N ASP A 347 " pdb=" O ASP A 347 " model vdw 2.588 2.496 nonbonded pdb=" O2' APC B 701 " pdb=" O3' APC B 701 " model vdw 2.588 2.432 ... (remaining 116875 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.370 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 : 0.003 0.028 15399 Z= 0.147 Angle : 0.666 9.279 20988 Z= 0.368 Chirality : 0.048 0.211 2331 Planarity : 0.005 0.059 2664 Dihedral : 14.856 88.781 5649 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 0.95 % Allowed : 12.22 % Favored : 86.83 % 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 (0.20), residues: 1896 helix: 1.39 (0.21), residues: 606 sheet: -0.41 (0.29), residues: 300 loop : -1.19 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 625 TYR 0.065 0.002 TYR B 656 PHE 0.007 0.001 PHE C 49 TRP 0.009 0.001 TRP B 246 HIS 0.024 0.002 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (15399) covalent geometry : angle 0.66616 / 0.37 (20988) hydrogen bonds : bond 0.17023 / 11.92 ( 531) hydrogen bonds : angle 6.89568 / 4.80 ( 1557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9113 (mtm) cc_final: 0.8525 (mtm) REVERT: A 574 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8279 (mm) REVERT: C 440 MET cc_start: 0.7886 (mtm) cc_final: 0.7618 (mtm) outliers start: 15 outliers final: 11 residues processed: 115 average time/residue: 0.1095 time to fit residues: 18.9055 Evaluate side-chains 82 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 561 HIS Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 574 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.152840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077973 restraints weight = 37926.304| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 6.22 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15399 Z= 0.138 Angle : 0.600 11.376 20988 Z= 0.310 Chirality : 0.047 0.165 2331 Planarity : 0.004 0.057 2664 Dihedral : 6.901 84.028 2214 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 2.46 % Allowed : 11.03 % 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 are not related in a simple way. whole: -0.23 (0.20), residues: 1896 helix: 1.43 (0.21), residues: 624 sheet: -0.37 (0.30), residues: 297 loop : -1.16 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 375 TYR 0.012 0.001 TYR B 406 PHE 0.015 0.001 PHE B 49 TRP 0.010 0.001 TRP A 246 HIS 0.016 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (15399) covalent geometry : angle 0.59972 / 0.31 (20988) hydrogen bonds : bond 0.04499 / 3.14 ( 531) hydrogen bonds : angle 5.71498 / 4.01 ( 1557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 72 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9260 (mtm) cc_final: 0.8543 (mtm) REVERT: A 308 ASP cc_start: 0.8238 (t0) cc_final: 0.7930 (t0) REVERT: A 465 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8784 (pt) REVERT: B 406 TYR cc_start: 0.9210 (t80) cc_final: 0.8906 (t80) REVERT: B 573 ILE cc_start: -0.3438 (OUTLIER) cc_final: -0.3648 (tp) REVERT: C 38 MET cc_start: 0.9267 (mmp) cc_final: 0.8882 (mtp) REVERT: C 404 MET cc_start: 0.9028 (mmm) cc_final: 0.8780 (mmm) outliers start: 39 outliers final: 9 residues processed: 108 average time/residue: 0.0929 time to fit residues: 15.9784 Evaluate side-chains 81 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 650 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 123 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 HIS B 213 ASN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 HIS ** 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 = 0.4246 r_free = 0.4246 target = 0.151710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.074789 restraints weight = 38008.391| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 6.37 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15399 Z= 0.171 Angle : 0.581 7.362 20988 Z= 0.300 Chirality : 0.047 0.171 2331 Planarity : 0.005 0.057 2664 Dihedral : 6.603 84.797 2200 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.15 % Rotamer: Outliers : 1.83 % Allowed : 11.97 % Favored : 86.20 % 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: -0.18 (0.20), residues: 1896 helix: 1.47 (0.22), residues: 621 sheet: -0.29 (0.30), residues: 297 loop : -1.13 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.019 0.001 TYR C 656 PHE 0.009 0.001 PHE B 49 TRP 0.012 0.001 TRP A 246 HIS 0.016 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15399) covalent geometry : angle 0.58110 / 0.30 (20988) hydrogen bonds : bond 0.04357 / 3.03 ( 531) hydrogen bonds : angle 5.46350 / 3.86 ( 1557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ASP cc_start: 0.8427 (t0) cc_final: 0.8213 (t0) REVERT: A 465 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8805 (pt) REVERT: B 406 TYR cc_start: 0.9206 (t80) cc_final: 0.8935 (t80) REVERT: B 440 MET cc_start: 0.3638 (mpp) cc_final: 0.3385 (mpp) REVERT: B 573 ILE cc_start: -0.2846 (OUTLIER) cc_final: -0.3524 (tp) REVERT: C 38 MET cc_start: 0.9248 (mmp) cc_final: 0.9032 (mmp) REVERT: C 404 MET cc_start: 0.9152 (mmm) cc_final: 0.8828 (mmm) outliers start: 29 outliers final: 13 residues processed: 94 average time/residue: 0.1059 time to fit residues: 16.3354 Evaluate side-chains 84 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 650 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 83 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 177 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 175 optimal weight: 0.0040 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 HIS B 378 ASN C 200 HIS ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.153288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.076597 restraints weight = 37360.807| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 6.22 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15399 Z= 0.097 Angle : 0.536 15.122 20988 Z= 0.273 Chirality : 0.046 0.138 2331 Planarity : 0.004 0.054 2664 Dihedral : 6.465 82.576 2198 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 1.95 % Allowed : 11.91 % Favored : 86.14 % 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: -0.14 (0.20), residues: 1896 helix: 1.57 (0.22), residues: 600 sheet: -0.44 (0.29), residues: 330 loop : -1.06 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 621 TYR 0.023 0.001 TYR C 656 PHE 0.010 0.001 PHE B 49 TRP 0.008 0.001 TRP C 246 HIS 0.018 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (15399) covalent geometry : angle 0.53639 / 0.27 (20988) hydrogen bonds : bond 0.03388 / 2.35 ( 531) hydrogen bonds : angle 5.23202 / 3.69 ( 1557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9247 (mtm) cc_final: 0.8477 (mtm) REVERT: A 308 ASP cc_start: 0.8432 (t0) cc_final: 0.8120 (t0) REVERT: B 151 MET cc_start: 0.8021 (mmm) cc_final: 0.7729 (tpp) REVERT: B 257 CYS cc_start: 0.8874 (t) cc_final: 0.8343 (p) REVERT: B 406 TYR cc_start: 0.9233 (t80) cc_final: 0.8970 (t80) REVERT: B 440 MET cc_start: 0.3717 (mpp) cc_final: 0.3439 (mpp) REVERT: B 573 ILE cc_start: -0.2868 (OUTLIER) cc_final: -0.3490 (tp) REVERT: C 38 MET cc_start: 0.9234 (mmp) cc_final: 0.9017 (mmp) REVERT: C 404 MET cc_start: 0.9210 (mmm) cc_final: 0.8836 (mmm) outliers start: 31 outliers final: 15 residues processed: 100 average time/residue: 0.1056 time to fit residues: 17.1793 Evaluate side-chains 86 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 622 ARG Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 650 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 108 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 HIS B 200 HIS B 378 ASN B 423 GLN C 113 ASN C 200 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.152838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.075132 restraints weight = 37605.657| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 6.44 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15399 Z= 0.105 Angle : 0.521 6.750 20988 Z= 0.266 Chirality : 0.046 0.234 2331 Planarity : 0.004 0.052 2664 Dihedral : 6.310 83.164 2196 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.64 % Allowed : 13.17 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1896 helix: 1.65 (0.22), residues: 600 sheet: -0.26 (0.30), residues: 318 loop : -1.06 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 621 TYR 0.024 0.001 TYR A 656 PHE 0.009 0.001 PHE B 49 TRP 0.008 0.001 TRP A 246 HIS 0.016 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (15399) covalent geometry : angle 0.52129 / 0.27 (20988) hydrogen bonds : bond 0.03317 / 2.31 ( 531) hydrogen bonds : angle 5.05445 / 3.56 ( 1557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9196 (mtm) cc_final: 0.8412 (mtm) REVERT: A 308 ASP cc_start: 0.8462 (t0) cc_final: 0.8047 (t0) REVERT: A 465 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8918 (pt) REVERT: A 523 ARG cc_start: 0.8353 (ptm-80) cc_final: 0.7576 (ptm160) REVERT: B 257 CYS cc_start: 0.8845 (t) cc_final: 0.8263 (p) REVERT: B 440 MET cc_start: 0.3318 (mpp) cc_final: 0.3111 (mpp) REVERT: B 573 ILE cc_start: -0.2739 (OUTLIER) cc_final: -0.3423 (tp) REVERT: C 38 MET cc_start: 0.9232 (mmp) cc_final: 0.9030 (mmp) REVERT: C 404 MET cc_start: 0.9287 (mmm) cc_final: 0.8891 (mmm) outliers start: 26 outliers final: 13 residues processed: 95 average time/residue: 0.1247 time to fit residues: 18.3302 Evaluate side-chains 85 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 539 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 HIS B 200 HIS C 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.151098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.072755 restraints weight = 37412.386| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 6.33 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15399 Z= 0.160 Angle : 0.540 6.564 20988 Z= 0.277 Chirality : 0.046 0.161 2331 Planarity : 0.004 0.054 2664 Dihedral : 6.368 84.163 2196 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.64 % Allowed : 13.93 % Favored : 84.44 % 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: 0.01 (0.20), residues: 1896 helix: 1.59 (0.22), residues: 621 sheet: -0.05 (0.31), residues: 279 loop : -1.02 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 604 TYR 0.025 0.001 TYR C 656 PHE 0.010 0.001 PHE B 49 TRP 0.013 0.001 TRP A 246 HIS 0.014 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15399) covalent geometry : angle 0.54032 / 0.28 (20988) hydrogen bonds : bond 0.03751 / 2.59 ( 531) hydrogen bonds : angle 4.97107 / 3.51 ( 1557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9216 (mtm) cc_final: 0.8490 (mtm) REVERT: A 308 ASP cc_start: 0.8465 (t0) cc_final: 0.8055 (t0) REVERT: A 465 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8857 (pt) REVERT: A 523 ARG cc_start: 0.8453 (ptm-80) cc_final: 0.7629 (ptm160) REVERT: B 257 CYS cc_start: 0.8815 (t) cc_final: 0.8293 (p) REVERT: B 573 ILE cc_start: -0.2779 (OUTLIER) cc_final: -0.3284 (tp) REVERT: B 620 MET cc_start: 0.0154 (tpt) cc_final: -0.2581 (mpp) REVERT: C 38 MET cc_start: 0.9214 (mmp) cc_final: 0.8995 (mmp) REVERT: C 310 MET cc_start: 0.7488 (tpp) cc_final: 0.6537 (tmm) outliers start: 26 outliers final: 13 residues processed: 91 average time/residue: 0.1098 time to fit residues: 16.2208 Evaluate side-chains 83 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 539 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 12 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS B 378 ASN C 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.151765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081755 restraints weight = 36971.089| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 6.65 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15399 Z= 0.106 Angle : 0.526 11.575 20988 Z= 0.266 Chirality : 0.046 0.296 2331 Planarity : 0.004 0.053 2664 Dihedral : 6.336 82.781 2196 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.51 % Allowed : 14.24 % Favored : 84.25 % 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 (0.20), residues: 1896 helix: 1.60 (0.22), residues: 621 sheet: -0.21 (0.30), residues: 315 loop : -0.97 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 622 TYR 0.025 0.001 TYR C 656 PHE 0.013 0.001 PHE B 49 TRP 0.009 0.001 TRP A 246 HIS 0.013 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (15399) covalent geometry : angle 0.52592 / 0.27 (20988) hydrogen bonds : bond 0.03239 / 2.25 ( 531) hydrogen bonds : angle 4.89093 / 3.44 ( 1557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9246 (mtm) cc_final: 0.8520 (mtm) REVERT: A 308 ASP cc_start: 0.8441 (t0) cc_final: 0.8017 (t0) REVERT: A 465 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8918 (pt) REVERT: A 523 ARG cc_start: 0.8363 (ptm-80) cc_final: 0.7481 (ptm160) REVERT: B 573 ILE cc_start: -0.1233 (OUTLIER) cc_final: -0.1952 (tp) REVERT: B 620 MET cc_start: 0.0298 (tpt) cc_final: -0.2559 (mpp) REVERT: C 57 MET cc_start: 0.7991 (mmm) cc_final: 0.7746 (ttm) REVERT: C 404 MET cc_start: 0.9367 (mmm) cc_final: 0.9083 (mmm) outliers start: 24 outliers final: 12 residues processed: 91 average time/residue: 0.0963 time to fit residues: 14.5033 Evaluate side-chains 82 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 650 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 140 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 HIS B 200 HIS B 378 ASN C 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.151769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.074382 restraints weight = 36924.018| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 6.14 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15399 Z= 0.105 Angle : 0.525 9.520 20988 Z= 0.266 Chirality : 0.046 0.310 2331 Planarity : 0.004 0.052 2664 Dihedral : 6.280 82.607 2194 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.32 % Allowed : 14.62 % Favored : 84.06 % 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: 0.05 (0.20), residues: 1896 helix: 1.70 (0.22), residues: 603 sheet: -0.15 (0.30), residues: 300 loop : -0.97 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 622 TYR 0.027 0.001 TYR A 656 PHE 0.011 0.001 PHE B 49 TRP 0.008 0.001 TRP A 246 HIS 0.013 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (15399) covalent geometry : angle 0.52537 / 0.27 (20988) hydrogen bonds : bond 0.03146 / 2.20 ( 531) hydrogen bonds : angle 4.82892 / 3.41 ( 1557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9232 (mtm) cc_final: 0.8517 (mtm) REVERT: A 308 ASP cc_start: 0.8484 (t0) cc_final: 0.8032 (t0) REVERT: A 465 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8887 (pt) REVERT: A 523 ARG cc_start: 0.8364 (ptm-80) cc_final: 0.7498 (ptm160) REVERT: B 573 ILE cc_start: -0.2624 (OUTLIER) cc_final: -0.3751 (pt) REVERT: B 620 MET cc_start: -0.0084 (tpt) cc_final: -0.2717 (mpp) REVERT: C 404 MET cc_start: 0.9319 (mmm) cc_final: 0.8728 (mmm) outliers start: 21 outliers final: 15 residues processed: 85 average time/residue: 0.0846 time to fit residues: 11.7542 Evaluate side-chains 83 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 547 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 85 optimal weight: 0.3980 chunk 181 optimal weight: 50.0000 chunk 17 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 63 optimal weight: 30.0000 chunk 177 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 HIS B 378 ASN C 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.150953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072180 restraints weight = 37234.697| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 6.46 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15399 Z= 0.172 Angle : 0.552 9.684 20988 Z= 0.281 Chirality : 0.047 0.259 2331 Planarity : 0.004 0.054 2664 Dihedral : 6.357 84.121 2194 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.20 % Allowed : 14.87 % Favored : 83.93 % 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: 0.06 (0.20), residues: 1896 helix: 1.65 (0.22), residues: 621 sheet: 0.04 (0.31), residues: 267 loop : -1.02 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 622 TYR 0.025 0.001 TYR A 656 PHE 0.012 0.001 PHE B 49 TRP 0.014 0.001 TRP A 246 HIS 0.013 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (15399) covalent geometry : angle 0.55159 / 0.28 (20988) hydrogen bonds : bond 0.03688 / 2.55 ( 531) hydrogen bonds : angle 4.87804 / 3.44 ( 1557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9239 (mtm) cc_final: 0.8516 (mtm) REVERT: A 308 ASP cc_start: 0.8482 (t0) cc_final: 0.8036 (t0) REVERT: A 465 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8831 (pt) REVERT: B 573 ILE cc_start: -0.2507 (OUTLIER) cc_final: -0.3590 (pt) REVERT: B 620 MET cc_start: 0.0473 (tpt) cc_final: -0.2273 (mpp) REVERT: C 38 MET cc_start: 0.9584 (mtp) cc_final: 0.9103 (mmp) REVERT: C 404 MET cc_start: 0.9313 (mmm) cc_final: 0.8719 (mmm) outliers start: 19 outliers final: 14 residues processed: 86 average time/residue: 0.0944 time to fit residues: 12.8840 Evaluate side-chains 81 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 650 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 77 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 71 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.151199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.081408 restraints weight = 37258.048| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 6.56 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15399 Z= 0.144 Angle : 0.540 9.702 20988 Z= 0.275 Chirality : 0.046 0.255 2331 Planarity : 0.004 0.055 2664 Dihedral : 6.341 82.906 2194 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.13 % Allowed : 15.19 % Favored : 83.68 % 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: 0.05 (0.20), residues: 1896 helix: 1.64 (0.22), residues: 618 sheet: -0.06 (0.31), residues: 273 loop : -0.98 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 622 TYR 0.026 0.001 TYR A 656 PHE 0.014 0.001 PHE C 450 TRP 0.011 0.001 TRP A 246 HIS 0.012 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (15399) covalent geometry : angle 0.54015 / 0.28 (20988) hydrogen bonds : bond 0.03360 / 2.33 ( 531) hydrogen bonds : angle 4.82975 / 3.41 ( 1557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9221 (mtm) cc_final: 0.8522 (mtm) REVERT: A 308 ASP cc_start: 0.8447 (t0) cc_final: 0.8002 (t0) REVERT: A 465 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8799 (pt) REVERT: B 573 ILE cc_start: -0.0890 (OUTLIER) cc_final: -0.2060 (pt) REVERT: B 620 MET cc_start: 0.0333 (tpt) cc_final: -0.2223 (mpp) REVERT: C 38 MET cc_start: 0.9404 (mtp) cc_final: 0.9102 (mmp) REVERT: C 404 MET cc_start: 0.9369 (mmm) cc_final: 0.9083 (mmm) outliers start: 18 outliers final: 12 residues processed: 82 average time/residue: 0.0979 time to fit residues: 13.3493 Evaluate side-chains 78 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 106 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.151330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.072772 restraints weight = 36664.663| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 6.36 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15399 Z= 0.127 Angle : 0.536 9.697 20988 Z= 0.273 Chirality : 0.046 0.240 2331 Planarity : 0.005 0.081 2664 Dihedral : 6.367 82.705 2194 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.07 % Allowed : 15.31 % Favored : 83.62 % 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: 0.13 (0.20), residues: 1896 helix: 1.63 (0.22), residues: 618 sheet: -0.15 (0.28), residues: 327 loop : -0.86 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 371 TYR 0.026 0.001 TYR A 656 PHE 0.011 0.001 PHE B 49 TRP 0.010 0.001 TRP A 246 HIS 0.012 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15399) covalent geometry : angle 0.53616 / 0.27 (20988) hydrogen bonds : bond 0.03271 / 2.28 ( 531) hydrogen bonds : angle 4.78698 / 3.38 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.98 seconds wall clock time: 68 minutes 26.54 seconds (4106.54 seconds total)