Starting phenix.real_space_refine on Wed Sep 25 20:09:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/09_2024/6out_20205.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/09_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_20205/09_2024/6out_20205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/09_2024/6out_20205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/09_2024/6out_20205.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6out_20205/09_2024/6out_20205.cif" } 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. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.45, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.6 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: 1.48 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: 3.62 Time building geometry restraints manager: 3.43 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: 0.00 - 2.37: 15472 2.37 - 4.74: 415 4.74 - 7.11: 44 7.11 - 9.47: 12 9.47 - 11.84: 1 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 3.040 nonbonded pdb=" O ASP A 478 " pdb=" O HOH A 602 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLN A 264 " pdb=" O HOH A 603 " model vdw 2.230 3.040 nonbonded pdb=" O THR B 179 " pdb=" O HOH B 601 " model vdw 2.240 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.130 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.160 Find NCS groups from input model: 0.480 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.090 ------------------------------------------------------------------------------- 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 : 1.257 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: 1.2247 time to fit residues: 292.9729 Evaluate side-chains 164 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 0.0970 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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 259 ASN A 266 GLN B 58 ASN B 74 ASN B 95 HIS B 171 HIS B 355 HIS B 460 HIS B 469 ASN B 512 GLN C 171 HIS C 177 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1270 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= 0.223 Angle : 0.617 7.796 15944 Z= 0.317 Chirality : 0.048 0.147 1787 Planarity : 0.007 0.051 2123 Dihedral : 5.566 21.984 1569 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 2.37 % Allowed : 9.48 % Favored : 88.15 % 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: -1.29 (0.19), residues: 1488 helix: -1.47 (0.54), residues: 82 sheet: 0.42 (0.25), residues: 385 loop : -1.40 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 328 HIS 0.006 0.001 HIS C 355 PHE 0.021 0.001 PHE A 200 TYR 0.011 0.002 TYR A 476 ARG 0.003 0.000 ARG B 191 *********************** 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 218 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.213 Fit side-chains REVERT: A 185 MET cc_start: 0.8320 (mtt) cc_final: 0.8023 (mtp) REVERT: A 416 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 227 LYS cc_start: 0.7965 (tttt) cc_final: 0.7702 (tttt) REVERT: B 468 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7487 (ttp-170) REVERT: C 227 LYS cc_start: 0.8889 (mttt) cc_final: 0.8445 (mmtt) REVERT: C 273 ASP cc_start: 0.7618 (m-30) cc_final: 0.7307 (m-30) REVERT: C 282 VAL cc_start: 0.9077 (m) cc_final: 0.8838 (t) REVERT: C 302 THR cc_start: 0.7863 (p) cc_final: 0.7391 (t) REVERT: C 449 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7119 (mm110) outliers start: 30 outliers final: 11 residues processed: 199 average time/residue: 1.2264 time to fit residues: 264.8155 Evaluate side-chains 182 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 263 VAL 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 277 VAL Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 497 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 chunk 135 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 chunk 46 optimal weight: 0.0870 chunk 108 optimal weight: 6.9990 overall best weight: 3.4342 ------------------------------------------------------------------------------- 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: 0.8425 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11622 Z= 0.199 Angle : 0.584 7.019 15944 Z= 0.297 Chirality : 0.047 0.161 1787 Planarity : 0.006 0.049 2123 Dihedral : 5.245 22.002 1569 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.53 % Allowed : 10.43 % Favored : 87.05 % 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: -0.92 (0.20), residues: 1488 helix: -0.90 (0.57), residues: 82 sheet: 0.53 (0.25), residues: 385 loop : -1.10 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 328 HIS 0.005 0.001 HIS C 355 PHE 0.018 0.001 PHE A 200 TYR 0.013 0.001 TYR C 431 ARG 0.002 0.000 ARG A 166 *********************** 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 196 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.274 Fit side-chains REVERT: A 416 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 227 LYS cc_start: 0.7958 (tttt) cc_final: 0.7718 (tttt) REVERT: B 295 ASN cc_start: 0.7690 (t0) cc_final: 0.7372 (p0) REVERT: B 468 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7492 (ttp-170) REVERT: C 33 MET cc_start: 0.8831 (mtp) cc_final: 0.8553 (mtp) REVERT: C 227 LYS cc_start: 0.8903 (mttt) cc_final: 0.8449 (mmtt) REVERT: C 273 ASP cc_start: 0.7624 (m-30) cc_final: 0.7306 (m-30) REVERT: C 302 THR cc_start: 0.7812 (p) cc_final: 0.7418 (t) outliers start: 32 outliers final: 18 residues processed: 182 average time/residue: 1.1630 time to fit residues: 230.7572 Evaluate side-chains 189 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 518 THR 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 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 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 409 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 50.0000 chunk 101 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 C 177 GLN C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1664 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= 0.171 Angle : 0.554 6.420 15944 Z= 0.280 Chirality : 0.046 0.141 1787 Planarity : 0.006 0.047 2123 Dihedral : 5.004 21.852 1569 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 2.53 % Allowed : 11.37 % Favored : 86.10 % 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: -0.61 (0.20), residues: 1488 helix: -0.60 (0.58), residues: 82 sheet: 0.73 (0.25), residues: 375 loop : -0.87 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 375 HIS 0.004 0.001 HIS C 355 PHE 0.015 0.001 PHE A 200 TYR 0.010 0.001 TYR C 431 ARG 0.004 0.000 ARG A 509 *********************** 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 208 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 1.305 Fit side-chains REVERT: A 416 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8018 (mt-10) REVERT: B 227 LYS cc_start: 0.7935 (tttt) cc_final: 0.7710 (tttt) REVERT: B 468 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7472 (ttp-170) REVERT: C 33 MET cc_start: 0.8855 (mtp) cc_final: 0.8477 (mtp) REVERT: C 181 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7349 (ptm-80) REVERT: C 227 LYS cc_start: 0.8912 (mttt) cc_final: 0.8473 (mmtt) REVERT: C 273 ASP cc_start: 0.7618 (m-30) cc_final: 0.7287 (m-30) REVERT: C 275 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7862 (mtm-85) REVERT: C 302 THR cc_start: 0.7754 (p) cc_final: 0.7525 (t) outliers start: 32 outliers final: 15 residues processed: 196 average time/residue: 1.2257 time to fit residues: 260.1142 Evaluate side-chains 189 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 329 HIS 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 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 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 409 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN C 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11622 Z= 0.157 Angle : 0.533 6.112 15944 Z= 0.268 Chirality : 0.046 0.149 1787 Planarity : 0.005 0.046 2123 Dihedral : 4.764 20.329 1569 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.53 % Allowed : 11.85 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.21), residues: 1488 helix: -0.40 (0.59), residues: 83 sheet: 0.82 (0.26), residues: 374 loop : -0.68 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 375 HIS 0.004 0.001 HIS C 355 PHE 0.016 0.001 PHE B 312 TYR 0.009 0.001 TYR C 431 ARG 0.003 0.000 ARG A 509 *********************** 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 207 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 1.299 Fit side-chains REVERT: A 416 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 329 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.5614 (p-80) REVERT: B 468 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7531 (ttp-170) REVERT: C 33 MET cc_start: 0.8846 (mtp) cc_final: 0.8540 (mtp) REVERT: C 227 LYS cc_start: 0.8907 (mttt) cc_final: 0.8473 (mmtt) REVERT: C 273 ASP cc_start: 0.7616 (m-30) cc_final: 0.7266 (m-30) REVERT: C 275 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7802 (mtm-85) REVERT: C 329 HIS cc_start: 0.5934 (OUTLIER) cc_final: 0.5502 (p-80) REVERT: C 468 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7443 (ttt-90) outliers start: 32 outliers final: 16 residues processed: 196 average time/residue: 1.2389 time to fit residues: 262.5297 Evaluate side-chains 183 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU 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 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 392 ILE Chi-restraints excluded: chain B residue 468 ARG 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 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 0.0970 chunk 28 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 35 optimal weight: 0.0000 chunk 144 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1948 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= 0.166 Angle : 0.535 5.923 15944 Z= 0.269 Chirality : 0.046 0.149 1787 Planarity : 0.005 0.045 2123 Dihedral : 4.700 20.759 1569 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.61 % Allowed : 11.85 % Favored : 85.55 % 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: -0.25 (0.21), residues: 1488 helix: -0.23 (0.59), residues: 82 sheet: 0.83 (0.26), residues: 372 loop : -0.54 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 375 HIS 0.003 0.001 HIS C 355 PHE 0.012 0.001 PHE A 81 TYR 0.013 0.001 TYR A 410 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 198 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 1.385 Fit side-chains REVERT: B 329 HIS cc_start: 0.6558 (OUTLIER) cc_final: 0.5670 (p-80) REVERT: C 33 MET cc_start: 0.8864 (mtp) cc_final: 0.8561 (mtp) REVERT: C 227 LYS cc_start: 0.8909 (mttt) cc_final: 0.8475 (mmtt) REVERT: C 273 ASP cc_start: 0.7581 (m-30) cc_final: 0.7228 (m-30) REVERT: C 376 ILE cc_start: 0.8220 (pt) cc_final: 0.7886 (mm) outliers start: 33 outliers final: 17 residues processed: 184 average time/residue: 1.2272 time to fit residues: 244.5445 Evaluate side-chains 177 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 353 VAL Chi-restraints excluded: chain B residue 392 ILE 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 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 392 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 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 58 ASN A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN B 58 ASN C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1862 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= 0.265 Angle : 0.614 7.693 15944 Z= 0.310 Chirality : 0.048 0.162 1787 Planarity : 0.006 0.056 2123 Dihedral : 5.035 23.444 1569 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.29 % Allowed : 12.48 % Favored : 85.23 % 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: -0.36 (0.21), residues: 1488 helix: -0.32 (0.58), residues: 82 sheet: 0.69 (0.25), residues: 381 loop : -0.61 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 328 HIS 0.004 0.001 HIS C 355 PHE 0.026 0.002 PHE B 312 TYR 0.015 0.002 TYR C 431 ARG 0.003 0.000 ARG C 175 *********************** 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 187 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.379 Fit side-chains REVERT: A 261 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: A 416 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 329 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.6005 (p-80) REVERT: B 468 ARG cc_start: 0.7870 (mtm180) cc_final: 0.7557 (ttp-170) REVERT: C 33 MET cc_start: 0.8836 (mtp) cc_final: 0.8508 (mtp) REVERT: C 227 LYS cc_start: 0.8925 (mttt) cc_final: 0.8488 (mmtt) REVERT: C 273 ASP cc_start: 0.7595 (m-30) cc_final: 0.7248 (m-30) REVERT: C 275 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7731 (mtm-85) outliers start: 29 outliers final: 19 residues processed: 178 average time/residue: 1.2122 time to fit residues: 233.9936 Evaluate side-chains 176 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 261 GLN 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 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 353 VAL Chi-restraints excluded: chain B residue 392 ILE 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 178 GLN 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 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 409 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 97 optimal weight: 0.0770 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 overall best weight: 4.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN C 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1921 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= 0.221 Angle : 0.585 6.942 15944 Z= 0.296 Chirality : 0.048 0.159 1787 Planarity : 0.006 0.062 2123 Dihedral : 4.987 22.930 1569 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.29 % Allowed : 12.95 % Favored : 84.76 % 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: -0.24 (0.21), residues: 1488 helix: -0.04 (0.61), residues: 76 sheet: 0.78 (0.25), residues: 376 loop : -0.54 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 328 HIS 0.004 0.001 HIS C 355 PHE 0.028 0.001 PHE B 312 TYR 0.015 0.002 TYR C 431 ARG 0.003 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 189 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.256 Fit side-chains REVERT: A 416 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8022 (mt-10) REVERT: B 313 GLU cc_start: 0.7645 (pm20) cc_final: 0.7426 (pm20) REVERT: B 329 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6090 (p-80) REVERT: C 33 MET cc_start: 0.8827 (mtp) cc_final: 0.8493 (mtp) REVERT: C 227 LYS cc_start: 0.8919 (mttt) cc_final: 0.8485 (mmtt) REVERT: C 273 ASP cc_start: 0.7599 (m-30) cc_final: 0.7243 (m-30) REVERT: C 275 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7722 (mtm-85) REVERT: C 329 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.5561 (p-80) outliers start: 29 outliers final: 18 residues processed: 181 average time/residue: 1.2038 time to fit residues: 236.2801 Evaluate side-chains 179 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 297 THR 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 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 392 ILE 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 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 409 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 30.0000 chunk 137 optimal weight: 0.0070 chunk 125 optimal weight: 8.9990 chunk 133 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 0.0000 chunk 120 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 overall best weight: 5.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 116 ASN B 460 HIS C 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1937 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= 0.258 Angle : 0.611 7.870 15944 Z= 0.310 Chirality : 0.049 0.160 1787 Planarity : 0.006 0.062 2123 Dihedral : 5.096 24.164 1569 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.13 % Allowed : 13.43 % 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 (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: -0.12 (0.61), residues: 76 sheet: 0.76 (0.25), residues: 376 loop : -0.57 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 328 HIS 0.004 0.001 HIS C 355 PHE 0.030 0.002 PHE B 312 TYR 0.016 0.002 TYR C 431 ARG 0.006 0.000 ARG C 175 *********************** 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 184 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.361 Fit side-chains REVERT: B 329 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6110 (p-80) REVERT: B 468 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7655 (mtp180) REVERT: C 33 MET cc_start: 0.8841 (mtp) cc_final: 0.8485 (mtp) REVERT: C 163 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7993 (mp0) REVERT: C 227 LYS cc_start: 0.8905 (mttt) cc_final: 0.8479 (mmtt) REVERT: C 273 ASP cc_start: 0.7604 (m-30) cc_final: 0.7248 (m-30) REVERT: C 275 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7730 (mtm-85) REVERT: C 329 HIS cc_start: 0.6101 (OUTLIER) cc_final: 0.5737 (p-80) REVERT: C 455 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7440 (tt0) outliers start: 27 outliers final: 19 residues processed: 176 average time/residue: 1.2603 time to fit residues: 241.6454 Evaluate side-chains 181 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 297 THR 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 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 392 ILE 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 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 409 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 141 optimal weight: 0.5980 chunk 86 optimal weight: 0.0870 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 116 ASN C 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11622 Z= 0.153 Angle : 0.531 6.305 15944 Z= 0.268 Chirality : 0.046 0.170 1787 Planarity : 0.005 0.066 2123 Dihedral : 4.713 21.597 1569 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.82 % Allowed : 13.98 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.21), residues: 1488 helix: 0.02 (0.62), residues: 77 sheet: 0.83 (0.25), residues: 376 loop : -0.38 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 375 HIS 0.004 0.001 HIS C 355 PHE 0.030 0.001 PHE B 312 TYR 0.013 0.001 TYR C 431 ARG 0.002 0.000 ARG A 166 ********************** 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 188 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.229 Fit side-chains REVERT: A 416 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 329 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.5975 (p-80) REVERT: B 468 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7627 (mtp180) REVERT: C 33 MET cc_start: 0.8814 (mtp) cc_final: 0.8471 (mtp) REVERT: C 163 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7869 (mp0) REVERT: C 227 LYS cc_start: 0.8879 (mttt) cc_final: 0.8446 (mmtt) REVERT: C 273 ASP cc_start: 0.7582 (m-30) cc_final: 0.7212 (m-30) REVERT: C 275 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7698 (mtm-85) REVERT: C 329 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5627 (p-80) REVERT: C 373 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8620 (tm) outliers start: 23 outliers final: 16 residues processed: 183 average time/residue: 1.2238 time to fit residues: 242.4503 Evaluate side-chains 181 residues out of total 1266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU 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 353 VAL Chi-restraints excluded: chain B residue 392 ILE 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 199 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 329 HIS Chi-restraints excluded: chain C residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 overall best weight: 3.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN C 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111134 restraints weight = 13515.420| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.76 r_work: 0.3145 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2084 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= 0.191 Angle : 0.561 6.294 15944 Z= 0.284 Chirality : 0.047 0.163 1787 Planarity : 0.006 0.068 2123 Dihedral : 4.766 21.596 1569 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.74 % Allowed : 14.06 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.21), residues: 1488 helix: 0.06 (0.62), residues: 76 sheet: 0.82 (0.25), residues: 376 loop : -0.38 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 328 HIS 0.004 0.001 HIS C 355 PHE 0.029 0.001 PHE B 312 TYR 0.014 0.001 TYR C 431 ARG 0.004 0.000 ARG B 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4472.09 seconds wall clock time: 79 minutes 7.98 seconds (4747.98 seconds total)