Starting phenix.real_space_refine on Fri Mar 15 11:33:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/03_2024/6out_20205.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/03_2024/6out_20205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/03_2024/6out_20205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/03_2024/6out_20205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/03_2024/6out_20205.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/03_2024/6out_20205.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.060 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7203 2.51 5 N 1904 2.21 5 O 2344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3721 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 51, 'TRANS': 440} Chain: "B" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3843 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 52, 'TRANS': 458} Chain: "C" Number of atoms: 3715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3715 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 51, 'TRANS': 439} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 6.15, per 1000 atoms: 0.53 Number of scatterers: 11505 At special positions: 0 Unit cell: (97.37, 110.21, 104.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2344 8.00 N 1904 7.00 C 7203 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 - 3.50 Amino acid : False - 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: 4.13 Conformation dependent library (CDL) restraints added in 2.4 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 19 sheets defined 11.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.813A pdb=" N THR A 228 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 229' Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.564A pdb=" N HIS A 286 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.640A pdb=" N GLN A 494 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.707A pdb=" N THR B 41 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.771A pdb=" N ILE B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN B 58 " --> pdb=" O PRO B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 58' Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.518A pdb=" N LEU B 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.574A pdb=" N PHE B 145 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.783A pdb=" N THR B 228 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.585A pdb=" N HIS B 286 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 491 through 495 removed outlier: 3.654A pdb=" N GLN B 494 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 43 removed outlier: 3.844A pdb=" N THR C 41 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 43 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.561A pdb=" N THR C 228 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 229' Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.578A pdb=" N HIS C 286 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.635A pdb=" N LEU C 495 " --> pdb=" O PRO C 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 70 removed outlier: 12.482A pdb=" N GLN A 62 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N THR A 208 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY A 66 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 203 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 84 removed outlier: 7.289A pdb=" N VAL A 79 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU A 186 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 81 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 255 removed outlier: 4.189A pdb=" N TYR A 431 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 255 removed outlier: 4.808A pdb=" N LEU A 481 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 480 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 461 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A 472 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 459 " --> pdb=" O GLU A 472 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 474 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 457 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 456 " --> pdb=" O TRP A 506 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TRP A 506 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 458 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 344 removed outlier: 4.092A pdb=" N TRP A 375 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN A 331 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU A 373 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR A 333 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY A 371 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.040A pdb=" N ALA C 120 " --> pdb=" O PRO C 189 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS C 122 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 182 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP C 82 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS C 184 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 70 removed outlier: 12.625A pdb=" N GLN B 62 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N THR B 208 " --> pdb=" O PRO B 64 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY B 66 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.750A pdb=" N CYS B 184 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 82 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 182 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS B 122 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA B 120 " --> pdb=" O PRO B 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 removed outlier: 4.305A pdb=" N TYR B 431 " --> pdb=" O MET B 425 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 4.846A pdb=" N LEU B 481 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 480 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 471 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 456 " --> pdb=" O TRP B 506 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP B 506 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 458 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 341 through 344 removed outlier: 7.616A pdb=" N HIS B 329 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 374 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 70 removed outlier: 12.667A pdb=" N GLN C 62 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N THR C 208 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY C 66 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 203 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 171 through 172 removed outlier: 3.541A pdb=" N TRP C 103 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 250 through 254 removed outlier: 7.946A pdb=" N ILE C 250 " --> pdb=" O LYS C 424 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS C 424 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR C 431 " --> pdb=" O MET C 425 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 250 through 254 removed outlier: 7.946A pdb=" N ILE C 250 " --> pdb=" O LYS C 424 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS C 424 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU C 481 " --> pdb=" O VAL C 419 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 480 " --> pdb=" O TYR C 476 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TYR C 461 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 472 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 459 " --> pdb=" O GLU C 472 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS C 474 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA C 457 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 456 " --> pdb=" O VAL C 507 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 505 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N HIS C 460 " --> pdb=" O PHE C 503 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE C 503 " --> pdb=" O HIS C 460 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 462 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE C 501 " --> pdb=" O VAL C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 343 removed outlier: 7.508A pdb=" N HIS C 329 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER C 374 " --> pdb=" O HIS C 329 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 705 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: 3.66 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3470 1.33 - 1.45: 1808 1.45 - 1.57: 6257 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 11622 Sorted by residual: bond pdb=" C ALA B 475 " pdb=" N TYR B 476 " ideal model delta sigma weight residual 1.327 1.282 0.045 1.39e-02 5.18e+03 1.03e+01 bond pdb=" C HIS A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.335 1.370 -0.034 1.30e-02 5.92e+03 7.00e+00 bond pdb=" C HIS B 381 " pdb=" N PRO B 382 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.81e+00 bond pdb=" C HIS C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.46e+00 bond pdb=" CA ILE A 392 " pdb=" C ILE A 392 " ideal model delta sigma weight residual 1.524 1.499 0.026 1.05e-02 9.07e+03 5.98e+00 ... (remaining 11617 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.68: 499 105.68 - 112.78: 6017 112.78 - 119.88: 3823 119.88 - 126.98: 5407 126.98 - 134.08: 198 Bond angle restraints: 15944 Sorted by residual: angle pdb=" C ILE A 392 " pdb=" N PRO A 393 " pdb=" CA PRO A 393 " ideal model delta sigma weight residual 119.78 128.40 -8.62 1.03e+00 9.43e-01 7.01e+01 angle pdb=" N PRO A 382 " pdb=" CA PRO A 382 " pdb=" C PRO A 382 " ideal model delta sigma weight residual 113.47 122.55 -9.08 1.43e+00 4.89e-01 4.04e+01 angle pdb=" N THR B 348 " pdb=" CA THR B 348 " pdb=" C THR B 348 " ideal model delta sigma weight residual 113.16 120.82 -7.66 1.42e+00 4.96e-01 2.91e+01 angle pdb=" N GLY A 396 " pdb=" CA GLY A 396 " pdb=" C GLY A 396 " ideal model delta sigma weight residual 111.36 117.28 -5.92 1.17e+00 7.31e-01 2.56e+01 angle pdb=" N GLY B 19 " pdb=" CA GLY B 19 " pdb=" C GLY B 19 " ideal model delta sigma weight residual 115.30 121.63 -6.33 1.39e+00 5.18e-01 2.08e+01 ... (remaining 15939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6317 17.85 - 35.70: 448 35.70 - 53.55: 70 53.55 - 71.40: 8 71.40 - 89.25: 6 Dihedral angle restraints: 6849 sinusoidal: 2625 harmonic: 4224 Sorted by residual: dihedral pdb=" CA THR B 223 " pdb=" C THR B 223 " pdb=" N VAL B 224 " pdb=" CA VAL B 224 " ideal model delta harmonic sigma weight residual -180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP B 198 " pdb=" C ASP B 198 " pdb=" N SER B 199 " pdb=" CA SER B 199 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA HIS A 329 " pdb=" C HIS A 329 " pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1517 0.082 - 0.165: 249 0.165 - 0.247: 18 0.247 - 0.329: 2 0.329 - 0.412: 1 Chirality restraints: 1787 Sorted by residual: chirality pdb=" CB VAL A 220 " pdb=" CA VAL A 220 " pdb=" CG1 VAL A 220 " pdb=" CG2 VAL A 220 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA GLN B 20 " pdb=" N GLN B 20 " pdb=" C GLN B 20 " pdb=" CB GLN B 20 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA PRO A 382 " pdb=" N PRO A 382 " pdb=" C PRO A 382 " pdb=" CB PRO A 382 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1784 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 63 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO A 64 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 377 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 378 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 211 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO C 212 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.034 5.00e-02 4.00e+02 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 215 2.66 - 3.22: 9398 3.22 - 3.78: 17367 3.78 - 4.34: 25308 4.34 - 4.90: 41012 Nonbonded interactions: 93300 Sorted by model distance: nonbonded pdb=" O GLN C 264 " pdb=" CG2 ILE C 392 " model vdw 2.099 3.460 nonbonded pdb=" O PRO A 249 " pdb=" O HOH A 601 " model vdw 2.203 2.440 nonbonded pdb=" O ASP A 478 " pdb=" O HOH A 602 " model vdw 2.207 2.440 nonbonded pdb=" OE1 GLN A 264 " pdb=" O HOH A 603 " model vdw 2.230 2.440 nonbonded pdb=" O THR B 179 " pdb=" O HOH B 601 " model vdw 2.240 2.440 ... (remaining 93295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 29 through 519) selection = (chain 'B' and resid 29 through 519) 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: 0.100 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: 0.010 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 33.380 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 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:15.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.007 0.070 11622 Z= 0.427 Angle : 0.926 11.843 15944 Z= 0.532 Chirality : 0.061 0.412 1787 Planarity : 0.010 0.065 2123 Dihedral : 12.598 89.251 4149 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.18), residues: 1488 helix: -2.80 (0.42), residues: 76 sheet: 0.09 (0.24), residues: 382 loop : -2.02 (0.15), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 328 HIS 0.009 0.001 HIS A 329 PHE 0.027 0.003 PHE A 200 TYR 0.014 0.002 TYR A 369 ARG 0.008 0.001 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8320 (mtt) cc_final: 0.7910 (mtp) REVERT: A 416 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8172 (mt-10) REVERT: A 440 GLU cc_start: 0.8612 (mp0) cc_final: 0.8339 (mp0) REVERT: C 227 LYS cc_start: 0.8891 (mttt) cc_final: 0.8491 (mmtt) REVERT: C 282 VAL cc_start: 0.8914 (m) cc_final: 0.8654 (t) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 1.2486 time to fit residues: 298.7461 Evaluate side-chains 164 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 135 optimal weight: 0.0870 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 74 ASN A 106 ASN A 172 ASN A 259 ASN A 266 GLN A 386 GLN B 58 ASN B 74 ASN B 95 HIS B 171 HIS B 355 HIS B 460 HIS B 512 GLN C 50 ASN C 171 HIS C 173 ASN C 177 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11622 Z= 0.291 Angle : 0.657 8.827 15944 Z= 0.336 Chirality : 0.049 0.150 1787 Planarity : 0.007 0.053 2123 Dihedral : 5.733 22.431 1569 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 2.84 % Allowed : 9.16 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1488 helix: -1.45 (0.53), residues: 82 sheet: 0.42 (0.25), residues: 374 loop : -1.41 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 328 HIS 0.006 0.001 HIS B 329 PHE 0.025 0.002 PHE A 200 TYR 0.011 0.002 TYR A 476 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.335 Fit side-chains REVERT: A 185 MET cc_start: 0.8317 (mtt) cc_final: 0.7967 (mtp) REVERT: B 99 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8323 (mtm) REVERT: B 468 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7566 (ttp-170) REVERT: C 227 LYS cc_start: 0.8906 (mttt) cc_final: 0.8637 (mtpt) REVERT: C 259 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7711 (p0) REVERT: C 273 ASP cc_start: 0.7669 (m-30) cc_final: 0.7355 (m-30) REVERT: C 302 THR cc_start: 0.7873 (p) cc_final: 0.7373 (t) REVERT: C 449 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7154 (mm110) outliers start: 36 outliers final: 15 residues processed: 196 average time/residue: 1.2714 time to fit residues: 271.2207 Evaluate side-chains 189 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 449 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 40.0000 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 0.0470 chunk 146 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 46 optimal weight: 0.0170 chunk 108 optimal weight: 10.0000 overall best weight: 3.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 58 ASN B 116 ASN C 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11622 Z= 0.185 Angle : 0.565 6.721 15944 Z= 0.285 Chirality : 0.046 0.133 1787 Planarity : 0.006 0.046 2123 Dihedral : 5.188 21.063 1569 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.45 % Allowed : 10.74 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1488 helix: -0.81 (0.56), residues: 83 sheet: 0.55 (0.25), residues: 382 loop : -1.02 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 328 HIS 0.005 0.001 HIS C 355 PHE 0.017 0.001 PHE A 200 TYR 0.011 0.001 TYR C 431 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.097 Fit side-chains REVERT: B 295 ASN cc_start: 0.7673 (t0) cc_final: 0.7393 (p0) REVERT: B 468 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7510 (ttp-170) REVERT: C 33 MET cc_start: 0.8852 (mtp) cc_final: 0.8518 (mtp) REVERT: C 227 LYS cc_start: 0.8895 (mttt) cc_final: 0.8444 (mmtt) REVERT: C 259 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7638 (p0) REVERT: C 273 ASP cc_start: 0.7615 (m-30) cc_final: 0.7301 (m-30) REVERT: C 282 VAL cc_start: 0.9001 (m) cc_final: 0.8732 (t) REVERT: C 302 THR cc_start: 0.7785 (p) cc_final: 0.7426 (t) outliers start: 31 outliers final: 17 residues processed: 198 average time/residue: 1.1910 time to fit residues: 256.0035 Evaluate side-chains 196 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 116 ASN C 177 GLN C 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11622 Z= 0.329 Angle : 0.670 10.123 15944 Z= 0.340 Chirality : 0.050 0.162 1787 Planarity : 0.007 0.052 2123 Dihedral : 5.527 24.805 1569 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 3.48 % Allowed : 11.45 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1488 helix: -0.61 (0.57), residues: 82 sheet: 0.58 (0.25), residues: 377 loop : -0.96 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 328 HIS 0.006 0.001 HIS C 355 PHE 0.026 0.002 PHE A 200 TYR 0.016 0.002 TYR B 343 ARG 0.005 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 1.284 Fit side-chains REVERT: A 261 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: A 329 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.6971 (p-80) REVERT: B 295 ASN cc_start: 0.7719 (t0) cc_final: 0.7434 (p0) REVERT: B 329 HIS cc_start: 0.6932 (OUTLIER) cc_final: 0.5980 (p-80) REVERT: B 468 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7534 (ttp-170) REVERT: C 33 MET cc_start: 0.8837 (mtp) cc_final: 0.8532 (mtp) REVERT: C 227 LYS cc_start: 0.8916 (mttt) cc_final: 0.8455 (mmtt) REVERT: C 259 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7712 (p0) REVERT: C 273 ASP cc_start: 0.7633 (m-30) cc_final: 0.7299 (m-30) REVERT: C 302 THR cc_start: 0.7784 (p) cc_final: 0.7415 (t) outliers start: 44 outliers final: 26 residues processed: 205 average time/residue: 1.1669 time to fit residues: 259.7007 Evaluate side-chains 194 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 497 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 329 HIS B 58 ASN C 135 HIS C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11622 Z= 0.326 Angle : 0.664 10.001 15944 Z= 0.337 Chirality : 0.050 0.161 1787 Planarity : 0.007 0.052 2123 Dihedral : 5.522 24.427 1569 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.79 % Allowed : 11.93 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1488 helix: -0.31 (0.60), residues: 76 sheet: 0.59 (0.25), residues: 378 loop : -0.87 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 328 HIS 0.005 0.001 HIS C 355 PHE 0.025 0.002 PHE A 200 TYR 0.012 0.002 TYR B 343 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 165 time to evaluate : 1.479 Fit side-chains REVERT: A 261 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: A 329 HIS cc_start: 0.7700 (OUTLIER) cc_final: 0.6749 (p90) REVERT: B 116 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8543 (m-40) REVERT: B 295 ASN cc_start: 0.7725 (t0) cc_final: 0.7410 (p0) REVERT: B 329 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6129 (p-80) REVERT: B 468 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7520 (ttp-170) REVERT: B 509 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7551 (ttm-80) REVERT: C 33 MET cc_start: 0.8827 (mtp) cc_final: 0.8515 (mtp) REVERT: C 227 LYS cc_start: 0.8929 (mttt) cc_final: 0.8649 (mtpt) REVERT: C 259 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7697 (p0) REVERT: C 273 ASP cc_start: 0.7643 (m-30) cc_final: 0.7313 (m-30) REVERT: C 302 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7424 (t) REVERT: C 449 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7160 (mm110) REVERT: C 455 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7463 (tt0) outliers start: 48 outliers final: 25 residues processed: 193 average time/residue: 1.2304 time to fit residues: 258.2974 Evaluate side-chains 199 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 455 GLU Chi-restraints excluded: chain C residue 497 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 84 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 50 ASN B 58 ASN B 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11622 Z= 0.159 Angle : 0.543 6.099 15944 Z= 0.274 Chirality : 0.046 0.146 1787 Planarity : 0.006 0.046 2123 Dihedral : 5.036 22.238 1569 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.69 % Allowed : 13.51 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1488 helix: -0.06 (0.61), residues: 78 sheet: 0.81 (0.26), residues: 366 loop : -0.64 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 375 HIS 0.015 0.001 HIS A 329 PHE 0.013 0.001 PHE A 81 TYR 0.013 0.001 TYR B 343 ARG 0.003 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.169 Fit side-chains REVERT: A 261 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: B 329 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6062 (p-80) REVERT: B 468 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7506 (ttp-170) REVERT: C 33 MET cc_start: 0.8814 (mtp) cc_final: 0.8496 (mtp) REVERT: C 227 LYS cc_start: 0.8914 (mttt) cc_final: 0.8465 (mmtt) REVERT: C 259 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7744 (p0) REVERT: C 273 ASP cc_start: 0.7604 (m-30) cc_final: 0.7231 (m-30) REVERT: C 329 HIS cc_start: 0.5911 (OUTLIER) cc_final: 0.5561 (p-80) REVERT: C 468 ARG cc_start: 0.7597 (ttm170) cc_final: 0.7393 (ttt-90) outliers start: 34 outliers final: 17 residues processed: 189 average time/residue: 1.1852 time to fit residues: 243.5047 Evaluate side-chains 192 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 329 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 329 HIS B 58 ASN B 116 ASN B 360 GLN C 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11622 Z= 0.255 Angle : 0.610 8.037 15944 Z= 0.309 Chirality : 0.048 0.160 1787 Planarity : 0.006 0.049 2123 Dihedral : 5.191 23.603 1569 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.16 % Allowed : 13.35 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1488 helix: 0.08 (0.61), residues: 76 sheet: 0.72 (0.26), residues: 375 loop : -0.64 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 375 HIS 0.004 0.001 HIS C 355 PHE 0.027 0.002 PHE B 312 TYR 0.011 0.002 TYR C 431 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.316 Fit side-chains REVERT: A 261 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7563 (mt0) REVERT: B 329 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6110 (p-80) REVERT: B 468 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7515 (ttp-170) REVERT: C 33 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8495 (mtp) REVERT: C 227 LYS cc_start: 0.8910 (mttt) cc_final: 0.8463 (mmtt) REVERT: C 259 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7759 (p0) REVERT: C 273 ASP cc_start: 0.7626 (m-30) cc_final: 0.7258 (m-30) REVERT: C 313 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5853 (mm-30) REVERT: C 455 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: C 468 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7367 (ttt-90) outliers start: 40 outliers final: 22 residues processed: 194 average time/residue: 1.2069 time to fit residues: 253.4759 Evaluate side-chains 198 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 116 ASN B 360 GLN C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11622 Z= 0.208 Angle : 0.580 6.917 15944 Z= 0.292 Chirality : 0.047 0.155 1787 Planarity : 0.006 0.048 2123 Dihedral : 5.071 23.166 1569 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.61 % Allowed : 13.82 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1488 helix: 0.21 (0.61), residues: 76 sheet: 0.84 (0.26), residues: 366 loop : -0.56 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 375 HIS 0.007 0.001 HIS A 329 PHE 0.028 0.001 PHE B 312 TYR 0.016 0.001 TYR B 343 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.433 Fit side-chains REVERT: A 261 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: B 329 HIS cc_start: 0.6995 (OUTLIER) cc_final: 0.6081 (p-80) REVERT: B 468 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7510 (ttp-170) REVERT: C 33 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8483 (mtp) REVERT: C 227 LYS cc_start: 0.8904 (mttt) cc_final: 0.8462 (mmtt) REVERT: C 259 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7818 (p0) REVERT: C 273 ASP cc_start: 0.7647 (m-30) cc_final: 0.7271 (m-30) REVERT: C 329 HIS cc_start: 0.6064 (OUTLIER) cc_final: 0.5720 (p-80) REVERT: C 455 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7377 (tt0) outliers start: 33 outliers final: 20 residues processed: 195 average time/residue: 1.1892 time to fit residues: 251.3487 Evaluate side-chains 194 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 58 ASN B 116 ASN B 360 GLN C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11622 Z= 0.226 Angle : 0.590 7.174 15944 Z= 0.299 Chirality : 0.047 0.162 1787 Planarity : 0.006 0.054 2123 Dihedral : 5.101 23.434 1569 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.53 % Allowed : 14.30 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1488 helix: 0.19 (0.61), residues: 76 sheet: 0.83 (0.26), residues: 366 loop : -0.55 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 375 HIS 0.004 0.001 HIS B 329 PHE 0.030 0.001 PHE B 312 TYR 0.013 0.002 TYR C 431 ARG 0.006 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.268 Fit side-chains REVERT: A 261 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: B 329 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6109 (p-80) REVERT: B 509 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7526 (ttm-80) REVERT: C 33 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8459 (mtp) REVERT: C 227 LYS cc_start: 0.8908 (mttt) cc_final: 0.8468 (mmtt) REVERT: C 259 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7844 (p0) REVERT: C 273 ASP cc_start: 0.7615 (m-30) cc_final: 0.7236 (m-30) REVERT: C 313 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5863 (mm-30) REVERT: C 329 HIS cc_start: 0.5977 (OUTLIER) cc_final: 0.5605 (p-80) REVERT: C 455 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7378 (tt0) outliers start: 32 outliers final: 20 residues processed: 184 average time/residue: 1.1989 time to fit residues: 238.7009 Evaluate side-chains 189 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 58 ASN B 116 ASN B 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11622 Z= 0.262 Angle : 0.616 8.126 15944 Z= 0.313 Chirality : 0.048 0.163 1787 Planarity : 0.006 0.060 2123 Dihedral : 5.214 24.142 1569 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.45 % Allowed : 14.38 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1488 helix: 0.10 (0.61), residues: 76 sheet: 0.70 (0.26), residues: 375 loop : -0.57 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 375 HIS 0.004 0.001 HIS B 329 PHE 0.031 0.002 PHE B 312 TYR 0.020 0.002 TYR B 343 ARG 0.005 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.323 Fit side-chains REVERT: A 261 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: B 313 GLU cc_start: 0.7582 (pm20) cc_final: 0.7345 (pm20) REVERT: B 329 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6150 (p-80) REVERT: B 468 ARG cc_start: 0.7804 (mtm180) cc_final: 0.7470 (ttp-170) REVERT: B 509 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7526 (ttm-80) REVERT: C 33 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: C 227 LYS cc_start: 0.8930 (mttt) cc_final: 0.8479 (mmtt) REVERT: C 259 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7850 (p0) REVERT: C 273 ASP cc_start: 0.7618 (m-30) cc_final: 0.7242 (m-30) REVERT: C 455 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7434 (tt0) outliers start: 31 outliers final: 20 residues processed: 182 average time/residue: 1.2394 time to fit residues: 244.2677 Evaluate side-chains 186 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 375 TRP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 455 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 108 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 58 ASN B 116 ASN B 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109849 restraints weight = 13642.537| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.98 r_work: 0.3116 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11622 Z= 0.227 Angle : 0.594 7.043 15944 Z= 0.301 Chirality : 0.048 0.165 1787 Planarity : 0.006 0.069 2123 Dihedral : 5.129 23.597 1569 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.45 % Allowed : 14.45 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1488 helix: 0.18 (0.61), residues: 76 sheet: 0.79 (0.26), residues: 370 loop : -0.52 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 375 HIS 0.004 0.001 HIS B 329 PHE 0.018 0.001 PHE A 200 TYR 0.015 0.002 TYR C 431 ARG 0.006 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4510.78 seconds wall clock time: 80 minutes 11.16 seconds (4811.16 seconds total)