Starting phenix.real_space_refine on Thu Jul 31 04:05:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rw6_24709/07_2025/7rw6_24709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rw6_24709/07_2025/7rw6_24709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rw6_24709/07_2025/7rw6_24709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rw6_24709/07_2025/7rw6_24709.map" model { file = "/net/cci-nas-00/data/ceres_data/7rw6_24709/07_2025/7rw6_24709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rw6_24709/07_2025/7rw6_24709.cif" } resolution = 2.55 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= 0.013 sd= 1.289 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 86 5.16 5 C 8388 2.51 5 N 2242 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13130 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5100 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 24, 'TRANS': 617} Chain breaks: 4 Chain: "B" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1464 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Chain: "C" Number of atoms: 5100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5100 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 24, 'TRANS': 617} Chain breaks: 4 Chain: "D" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1464 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5776 SG CYS B 284 74.630 135.699 28.793 1.00 68.81 S ATOM 5817 SG CYS B 289 72.505 138.703 28.680 1.00 94.70 S ATOM 12340 SG CYS D 284 68.627 41.483 29.027 1.00 73.57 S ATOM 12381 SG CYS D 289 70.940 38.754 28.553 1.00 97.13 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N CYS B 344 " occ=0.62 ... (4 atoms not shown) pdb=" SG CYS B 344 " occ=0.62 residue: pdb=" N CYS B 354 " occ=0.56 ... (4 atoms not shown) pdb=" SG CYS B 354 " occ=0.56 residue: pdb=" N CYS D 344 " occ=0.62 ... (4 atoms not shown) pdb=" SG CYS D 344 " occ=0.62 residue: pdb=" N CYS D 354 " occ=0.56 ... (4 atoms not shown) pdb=" SG CYS D 354 " occ=0.56 Time building chain proxies: 9.14, per 1000 atoms: 0.70 Number of scatterers: 13130 At special positions: 0 Unit cell: (143.48, 178.084, 80.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 86 16.00 O 2412 8.00 N 2242 7.00 C 8388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 604 " distance=2.03 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: 3.24 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 253 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 284 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 289 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 253 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 284 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 289 " 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 52.4% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 26 through 41 removed outlier: 3.615A pdb=" N ASP A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 31 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 115 through 135 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.991A pdb=" N PHE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.734A pdb=" N HIS A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.095A pdb=" N ALA A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 478 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 509 through 539 Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.729A pdb=" N GLY A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.724A pdb=" N VAL A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.853A pdb=" N GLN A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 661' Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 672 through 684 Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 706 through 718 Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 288 through 300 Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.693A pdb=" N VAL B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 379 removed outlier: 3.502A pdb=" N ASN B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.580A pdb=" N ASP C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 115 through 135 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 150 through 164 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 292 through 301 removed outlier: 3.827A pdb=" N PHE C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.779A pdb=" N HIS C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 422 through 426 removed outlier: 3.695A pdb=" N ALA C 426 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 4.183A pdb=" N ALA C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 478 Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 495 through 503 Processing helix chain 'C' and resid 509 through 539 Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.722A pdb=" N GLY C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 583 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.809A pdb=" N GLN C 660 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 662 through 666 Processing helix chain 'C' and resid 672 through 684 Processing helix chain 'C' and resid 685 through 687 No H-bonds generated for 'chain 'C' and resid 685 through 687' Processing helix chain 'C' and resid 706 through 718 Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 254 through 262 Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 288 through 300 Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 361 through 379 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 169 removed outlier: 7.588A pdb=" N GLY A 490 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN A 404 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 492 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 406 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN A 494 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE A 408 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 removed outlier: 7.126A pdb=" N VAL A 256 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY A 288 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA A 258 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE A 290 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET A 260 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 366 " --> pdb=" O THR A 722 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR A 722 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 695 through 697 Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 230 removed outlier: 9.210A pdb=" N GLN B 332 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 305 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N SER B 334 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 307 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.579A pdb=" N GLY C 490 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN C 404 " --> pdb=" O GLY C 490 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLY C 492 " --> pdb=" O ASN C 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA C 406 " --> pdb=" O GLY C 492 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLN C 494 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE C 408 " --> pdb=" O GLN C 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.085A pdb=" N VAL C 256 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY C 288 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 258 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE C 290 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET C 260 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 366 " --> pdb=" O THR C 722 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR C 722 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 695 through 697 Processing sheet with id=AA9, first strand: chain 'D' and resid 227 through 230 Processing sheet with id=AB1, first strand: chain 'D' and resid 227 through 230 removed outlier: 9.178A pdb=" N GLN D 332 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU D 305 " --> pdb=" O GLN D 332 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N SER D 334 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE D 307 " --> pdb=" O SER D 334 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1767 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: 4.31 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4298 1.35 - 1.47: 3472 1.47 - 1.59: 5566 1.59 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 13458 Sorted by residual: bond pdb=" CA GLN B 352 " pdb=" CB GLN B 352 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.62e-02 3.81e+03 1.85e+00 bond pdb=" CA GLN D 352 " pdb=" CB GLN D 352 " ideal model delta sigma weight residual 1.529 1.550 -0.021 1.62e-02 3.81e+03 1.62e+00 bond pdb=" C LEU D 256 " pdb=" O LEU D 256 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.15e-02 7.56e+03 7.73e-01 bond pdb=" CG1 ILE A 16 " pdb=" CD1 ILE A 16 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.29e-01 bond pdb=" CA ARG A 650 " pdb=" CB ARG A 650 " ideal model delta sigma weight residual 1.527 1.541 -0.013 1.61e-02 3.86e+03 6.97e-01 ... (remaining 13453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 18070 2.34 - 4.67: 137 4.67 - 7.01: 24 7.01 - 9.35: 1 9.35 - 11.68: 2 Bond angle restraints: 18234 Sorted by residual: angle pdb=" N GLN B 352 " pdb=" CA GLN B 352 " pdb=" CB GLN B 352 " ideal model delta sigma weight residual 111.84 118.05 -6.21 1.49e+00 4.50e-01 1.74e+01 angle pdb=" C LEU C 592 " pdb=" N MET C 593 " pdb=" CA MET C 593 " ideal model delta sigma weight residual 120.69 132.33 -11.64 2.95e+00 1.15e-01 1.56e+01 angle pdb=" N GLN D 352 " pdb=" CA GLN D 352 " pdb=" CB GLN D 352 " ideal model delta sigma weight residual 111.84 117.53 -5.69 1.49e+00 4.50e-01 1.46e+01 angle pdb=" C TYR B 350 " pdb=" CA TYR B 350 " pdb=" CB TYR B 350 " ideal model delta sigma weight residual 111.50 117.49 -5.99 1.64e+00 3.72e-01 1.34e+01 angle pdb=" C LEU A 592 " pdb=" N MET A 593 " pdb=" CA MET A 593 " ideal model delta sigma weight residual 121.27 132.95 -11.68 3.40e+00 8.65e-02 1.18e+01 ... (remaining 18229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 7370 17.28 - 34.56: 469 34.56 - 51.84: 70 51.84 - 69.11: 6 69.11 - 86.39: 11 Dihedral angle restraints: 7926 sinusoidal: 3158 harmonic: 4768 Sorted by residual: dihedral pdb=" CA PHE A 542 " pdb=" C PHE A 542 " pdb=" N PRO A 543 " pdb=" CA PRO A 543 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE C 542 " pdb=" C PHE C 542 " pdb=" N PRO C 543 " pdb=" CA PRO C 543 " ideal model delta harmonic sigma weight residual 180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP C 505 " pdb=" C TRP C 505 " pdb=" N GLN C 506 " pdb=" CA GLN C 506 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 7923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1353 0.038 - 0.076: 446 0.076 - 0.115: 128 0.115 - 0.153: 21 0.153 - 0.191: 2 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA GLN B 352 " pdb=" N GLN B 352 " pdb=" C GLN B 352 " pdb=" CB GLN B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA GLN D 352 " pdb=" N GLN D 352 " pdb=" C GLN D 352 " pdb=" CB GLN D 352 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA VAL B 262 " pdb=" N VAL B 262 " pdb=" C VAL B 262 " pdb=" CB VAL B 262 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1947 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 567 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 568 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 568 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 568 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 410 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 411 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 567 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 568 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " -0.027 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 432 2.71 - 3.26: 13628 3.26 - 3.81: 22621 3.81 - 4.35: 29042 4.35 - 4.90: 48029 Nonbonded interactions: 113752 Sorted by model distance: nonbonded pdb=" OG SER D 286 " pdb=" OD1 ASP D 316 " model vdw 2.167 3.040 nonbonded pdb=" O LEU D 209 " pdb=" OH TYR D 315 " model vdw 2.178 3.040 nonbonded pdb=" OG SER C 690 " pdb=" OG1 THR C 722 " model vdw 2.179 3.040 nonbonded pdb=" O ILE A 534 " pdb=" OG1 THR A 538 " model vdw 2.180 3.040 nonbonded pdb=" OG SER A 690 " pdb=" OG1 THR A 722 " model vdw 2.205 3.040 ... (remaining 113747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.520 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 0.457 13466 Z= 0.235 Angle : 0.550 11.682 18238 Z= 0.287 Chirality : 0.041 0.191 1950 Planarity : 0.004 0.054 2360 Dihedral : 11.591 86.392 4848 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 0.17 (0.22), residues: 1606 helix: 0.86 (0.20), residues: 774 sheet: -0.41 (0.40), residues: 166 loop : -0.53 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.003 0.001 HIS C 556 PHE 0.014 0.001 PHE C 542 TYR 0.018 0.001 TYR C 61 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.17479 ( 600) hydrogen bonds : angle 6.39832 ( 1767) metal coordination : bond 0.27952 ( 6) SS BOND : bond 0.00348 ( 2) SS BOND : angle 2.02063 ( 4) covalent geometry : bond 0.00282 (13458) covalent geometry : angle 0.54967 (18234) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7328 (tp30) cc_final: 0.6801 (tp30) REVERT: A 68 MET cc_start: 0.7501 (ptt) cc_final: 0.6678 (ptt) REVERT: A 674 GLU cc_start: 0.7583 (tp30) cc_final: 0.7298 (tm-30) REVERT: B 231 MET cc_start: 0.6756 (pmm) cc_final: 0.6411 (pmm) REVERT: C 64 GLU cc_start: 0.7427 (tp30) cc_final: 0.6887 (tp30) REVERT: C 68 MET cc_start: 0.7695 (ptt) cc_final: 0.7017 (ptt) REVERT: C 260 MET cc_start: 0.9052 (ttm) cc_final: 0.8832 (ttp) REVERT: D 235 MET cc_start: 0.6444 (tmm) cc_final: 0.6238 (tmm) outliers start: 0 outliers final: 1 residues processed: 262 average time/residue: 1.6989 time to fit residues: 485.0019 Evaluate side-chains 223 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 339 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0070 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095619 restraints weight = 22446.184| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.15 r_work: 0.3351 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13466 Z= 0.175 Angle : 0.604 9.429 18238 Z= 0.315 Chirality : 0.044 0.152 1950 Planarity : 0.005 0.075 2360 Dihedral : 4.900 82.607 1814 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.58 % Allowed : 8.03 % Favored : 90.39 % 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: 0.17 (0.21), residues: 1606 helix: 0.88 (0.19), residues: 800 sheet: -0.63 (0.39), residues: 166 loop : -0.54 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 277 HIS 0.005 0.001 HIS C 9 PHE 0.018 0.002 PHE A 520 TYR 0.015 0.002 TYR C 716 ARG 0.011 0.001 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 600) hydrogen bonds : angle 4.91755 ( 1767) metal coordination : bond 0.01345 ( 6) SS BOND : bond 0.00674 ( 2) SS BOND : angle 2.37331 ( 4) covalent geometry : bond 0.00399 (13458) covalent geometry : angle 0.60307 (18234) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7770 (tp30) cc_final: 0.7139 (tp30) REVERT: A 68 MET cc_start: 0.7900 (ptt) cc_final: 0.7176 (ptt) REVERT: B 231 MET cc_start: 0.6985 (pmm) cc_final: 0.6671 (pmm) REVERT: C 379 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8064 (tp-100) REVERT: C 674 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7664 (tp30) REVERT: D 351 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8097 (ttp-170) outliers start: 22 outliers final: 11 residues processed: 257 average time/residue: 1.2421 time to fit residues: 349.5778 Evaluate side-chains 248 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A 689 GLN B 201 ASN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN C 6 HIS ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.109343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093344 restraints weight = 22655.331| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.16 r_work: 0.3322 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13466 Z= 0.207 Angle : 0.615 9.184 18238 Z= 0.318 Chirality : 0.045 0.177 1950 Planarity : 0.005 0.053 2360 Dihedral : 5.020 86.704 1814 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.87 % Allowed : 9.83 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.21), residues: 1606 helix: 0.95 (0.19), residues: 786 sheet: -0.87 (0.38), residues: 166 loop : -0.64 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 277 HIS 0.005 0.001 HIS A 558 PHE 0.022 0.002 PHE A 520 TYR 0.016 0.002 TYR A 322 ARG 0.005 0.000 ARG D 304 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 600) hydrogen bonds : angle 4.75988 ( 1767) metal coordination : bond 0.00665 ( 6) SS BOND : bond 0.00822 ( 2) SS BOND : angle 2.67694 ( 4) covalent geometry : bond 0.00479 (13458) covalent geometry : angle 0.61418 (18234) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7872 (tp30) cc_final: 0.7250 (tp30) REVERT: A 68 MET cc_start: 0.8052 (ptt) cc_final: 0.7436 (ptt) REVERT: A 338 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8497 (mmpt) REVERT: B 231 MET cc_start: 0.6934 (pmm) cc_final: 0.6591 (pmm) REVERT: B 332 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8124 (pp30) REVERT: C 54 GLU cc_start: 0.8638 (tp30) cc_final: 0.8410 (tm-30) REVERT: C 215 ARG cc_start: 0.7897 (ptp-170) cc_final: 0.7576 (ttm110) REVERT: C 674 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7711 (tp30) REVERT: C 728 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8370 (mmt180) REVERT: D 229 VAL cc_start: 0.8590 (t) cc_final: 0.8034 (m) REVERT: D 292 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: D 351 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8092 (ttp-170) outliers start: 40 outliers final: 14 residues processed: 262 average time/residue: 1.6052 time to fit residues: 462.2489 Evaluate side-chains 256 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 47 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN C 6 HIS ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094010 restraints weight = 22366.901| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.15 r_work: 0.3335 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13466 Z= 0.162 Angle : 0.603 9.323 18238 Z= 0.311 Chirality : 0.043 0.145 1950 Planarity : 0.005 0.092 2360 Dihedral : 5.059 92.529 1814 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.44 % Allowed : 12.27 % Favored : 85.29 % 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: 0.13 (0.21), residues: 1606 helix: 0.97 (0.19), residues: 786 sheet: -0.97 (0.38), residues: 166 loop : -0.61 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 554 HIS 0.004 0.001 HIS A 558 PHE 0.019 0.001 PHE C 520 TYR 0.015 0.002 TYR A 322 ARG 0.012 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 600) hydrogen bonds : angle 4.66632 ( 1767) metal coordination : bond 0.00364 ( 6) SS BOND : bond 0.00644 ( 2) SS BOND : angle 2.22642 ( 4) covalent geometry : bond 0.00371 (13458) covalent geometry : angle 0.60206 (18234) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7837 (tp30) cc_final: 0.7223 (tp30) REVERT: A 68 MET cc_start: 0.8053 (ptt) cc_final: 0.7421 (ptt) REVERT: A 82 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: A 338 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8635 (mtpt) REVERT: B 231 MET cc_start: 0.6916 (pmm) cc_final: 0.6561 (pmm) REVERT: B 363 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: C 54 GLU cc_start: 0.8605 (tp30) cc_final: 0.8341 (tm-30) REVERT: C 215 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7540 (ttm110) REVERT: C 593 MET cc_start: 0.7055 (tpt) cc_final: 0.6675 (tpt) REVERT: C 674 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7697 (tp30) REVERT: D 292 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: D 336 MET cc_start: 0.9118 (mtp) cc_final: 0.8823 (mtp) REVERT: D 351 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8055 (ttp-170) outliers start: 34 outliers final: 12 residues processed: 248 average time/residue: 1.2968 time to fit residues: 352.4751 Evaluate side-chains 243 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 146 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN C 6 HIS ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.109745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093929 restraints weight = 22573.463| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.15 r_work: 0.3332 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13466 Z= 0.178 Angle : 0.610 9.754 18238 Z= 0.315 Chirality : 0.044 0.146 1950 Planarity : 0.005 0.052 2360 Dihedral : 5.128 96.760 1814 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.87 % Allowed : 13.34 % Favored : 83.79 % 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: 0.11 (0.21), residues: 1606 helix: 0.99 (0.19), residues: 786 sheet: -1.08 (0.38), residues: 166 loop : -0.64 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 287 HIS 0.005 0.001 HIS A 558 PHE 0.027 0.001 PHE A 270 TYR 0.017 0.002 TYR A 322 ARG 0.007 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 600) hydrogen bonds : angle 4.63578 ( 1767) metal coordination : bond 0.00417 ( 6) SS BOND : bond 0.01563 ( 2) SS BOND : angle 2.99697 ( 4) covalent geometry : bond 0.00410 (13458) covalent geometry : angle 0.60809 (18234) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 1.535 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7871 (tp30) cc_final: 0.7261 (tp30) REVERT: A 68 MET cc_start: 0.8085 (ptt) cc_final: 0.7456 (ptt) REVERT: A 82 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: A 338 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8554 (mmpt) REVERT: B 231 MET cc_start: 0.6930 (pmm) cc_final: 0.6566 (pmm) REVERT: B 363 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: C 76 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7837 (mtm-85) REVERT: C 215 ARG cc_start: 0.7856 (ptp-170) cc_final: 0.7566 (ttm110) REVERT: C 593 MET cc_start: 0.7003 (tpt) cc_final: 0.6679 (tpt) REVERT: C 674 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7712 (tp30) REVERT: D 292 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: D 351 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8047 (ttp-170) outliers start: 40 outliers final: 14 residues processed: 250 average time/residue: 1.4147 time to fit residues: 386.3130 Evaluate side-chains 243 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 322 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.110323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094410 restraints weight = 22687.056| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.17 r_work: 0.3335 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13466 Z= 0.163 Angle : 0.605 10.442 18238 Z= 0.309 Chirality : 0.043 0.145 1950 Planarity : 0.004 0.049 2360 Dihedral : 4.624 33.115 1814 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.22 % Allowed : 14.42 % Favored : 83.36 % 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: 0.09 (0.21), residues: 1606 helix: 1.02 (0.19), residues: 784 sheet: -1.15 (0.38), residues: 166 loop : -0.70 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 287 HIS 0.005 0.001 HIS A 558 PHE 0.022 0.001 PHE C 270 TYR 0.017 0.002 TYR A 322 ARG 0.008 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 600) hydrogen bonds : angle 4.57302 ( 1767) metal coordination : bond 0.00369 ( 6) SS BOND : bond 0.01064 ( 2) SS BOND : angle 2.26270 ( 4) covalent geometry : bond 0.00377 (13458) covalent geometry : angle 0.60431 (18234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7888 (tp30) cc_final: 0.7263 (tp30) REVERT: A 68 MET cc_start: 0.8082 (ptt) cc_final: 0.7422 (ptt) REVERT: A 82 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: A 324 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7020 (tm-30) REVERT: A 338 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8647 (mtpt) REVERT: A 662 TYR cc_start: 0.7463 (m-80) cc_final: 0.7245 (m-10) REVERT: B 231 MET cc_start: 0.6944 (pmm) cc_final: 0.6473 (pmm) REVERT: B 363 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: C 82 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: C 87 GLU cc_start: 0.8481 (tp30) cc_final: 0.8175 (tm-30) REVERT: C 215 ARG cc_start: 0.7873 (ptp-170) cc_final: 0.7587 (ttm110) REVERT: C 272 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: C 593 MET cc_start: 0.7089 (tpt) cc_final: 0.6746 (tpt) REVERT: C 674 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7710 (tp30) REVERT: D 231 MET cc_start: 0.6812 (pmm) cc_final: 0.6435 (pmm) REVERT: D 351 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8020 (ttp-170) outliers start: 31 outliers final: 16 residues processed: 247 average time/residue: 1.5224 time to fit residues: 411.4386 Evaluate side-chains 250 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 322 TYR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 56 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 115 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.110524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094860 restraints weight = 22691.704| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.15 r_work: 0.3363 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13466 Z= 0.145 Angle : 0.600 10.623 18238 Z= 0.307 Chirality : 0.043 0.147 1950 Planarity : 0.005 0.096 2360 Dihedral : 4.526 19.486 1812 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.08 % Allowed : 15.21 % Favored : 82.71 % 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: 0.18 (0.21), residues: 1606 helix: 1.15 (0.19), residues: 772 sheet: -1.21 (0.38), residues: 166 loop : -0.68 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 287 HIS 0.003 0.001 HIS A 558 PHE 0.023 0.001 PHE A 270 TYR 0.016 0.001 TYR C 322 ARG 0.020 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 600) hydrogen bonds : angle 4.55916 ( 1767) metal coordination : bond 0.00279 ( 6) SS BOND : bond 0.00850 ( 2) SS BOND : angle 1.78124 ( 4) covalent geometry : bond 0.00332 (13458) covalent geometry : angle 0.59968 (18234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7848 (tp30) cc_final: 0.7247 (tp30) REVERT: A 68 MET cc_start: 0.8071 (ptt) cc_final: 0.7373 (ptt) REVERT: A 82 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: A 338 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8660 (mtpt) REVERT: A 606 ASP cc_start: 0.8435 (t70) cc_final: 0.8105 (t70) REVERT: A 662 TYR cc_start: 0.7452 (m-80) cc_final: 0.7242 (m-10) REVERT: B 229 VAL cc_start: 0.8776 (t) cc_final: 0.8347 (m) REVERT: B 231 MET cc_start: 0.6858 (pmm) cc_final: 0.6481 (pmm) REVERT: B 363 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: C 82 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: C 87 GLU cc_start: 0.8457 (tp30) cc_final: 0.8186 (tm-30) REVERT: C 215 ARG cc_start: 0.7846 (ptp-170) cc_final: 0.7565 (ttm110) REVERT: C 272 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: C 593 MET cc_start: 0.7110 (tpt) cc_final: 0.6855 (tpt) REVERT: C 600 GLN cc_start: 0.8080 (mt0) cc_final: 0.7789 (mp10) REVERT: C 674 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7704 (tp30) REVERT: D 229 VAL cc_start: 0.8679 (t) cc_final: 0.8152 (m) REVERT: D 351 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8026 (ttp-170) outliers start: 29 outliers final: 12 residues processed: 241 average time/residue: 1.4291 time to fit residues: 376.3260 Evaluate side-chains 250 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 322 TYR Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 158 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.110344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094575 restraints weight = 22546.901| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.15 r_work: 0.3339 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 0.004 0.040 13466 Z= 0.168 Angle : 0.618 10.688 18238 Z= 0.315 Chirality : 0.043 0.147 1950 Planarity : 0.005 0.068 2360 Dihedral : 4.537 19.277 1812 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.22 % Allowed : 15.64 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.21), residues: 1606 helix: 1.15 (0.19), residues: 772 sheet: -1.24 (0.38), residues: 166 loop : -0.71 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 287 HIS 0.006 0.001 HIS C 264 PHE 0.046 0.002 PHE A 270 TYR 0.025 0.002 TYR C 612 ARG 0.014 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 600) hydrogen bonds : angle 4.55047 ( 1767) metal coordination : bond 0.00381 ( 6) SS BOND : bond 0.00982 ( 2) SS BOND : angle 1.98868 ( 4) covalent geometry : bond 0.00392 (13458) covalent geometry : angle 0.61703 (18234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7889 (tp30) cc_final: 0.7260 (tp30) REVERT: A 68 MET cc_start: 0.8123 (ptt) cc_final: 0.7467 (ptt) REVERT: A 82 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: A 338 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8526 (mtpt) REVERT: A 606 ASP cc_start: 0.8421 (t70) cc_final: 0.8051 (t70) REVERT: A 662 TYR cc_start: 0.7399 (m-80) cc_final: 0.7174 (m-10) REVERT: B 229 VAL cc_start: 0.8794 (t) cc_final: 0.8298 (m) REVERT: B 363 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8230 (tp30) REVERT: C 64 GLU cc_start: 0.7847 (tp30) cc_final: 0.6956 (tp30) REVERT: C 82 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: C 87 GLU cc_start: 0.8475 (tp30) cc_final: 0.8191 (tm-30) REVERT: C 215 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7585 (ttm110) REVERT: C 272 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: C 311 ASP cc_start: 0.8265 (p0) cc_final: 0.7818 (p0) REVERT: D 268 ASP cc_start: 0.8238 (t0) cc_final: 0.7954 (t0) REVERT: D 336 MET cc_start: 0.9119 (mtp) cc_final: 0.8904 (mtp) REVERT: D 351 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8010 (ttp-170) outliers start: 31 outliers final: 16 residues processed: 244 average time/residue: 1.2335 time to fit residues: 329.6331 Evaluate side-chains 248 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 322 TYR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 158 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.110982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095357 restraints weight = 22472.340| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.14 r_work: 0.3370 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13466 Z= 0.142 Angle : 0.611 10.984 18238 Z= 0.311 Chirality : 0.042 0.144 1950 Planarity : 0.005 0.056 2360 Dihedral : 4.501 19.016 1812 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.79 % Allowed : 16.21 % Favored : 81.99 % 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: 0.14 (0.21), residues: 1606 helix: 1.12 (0.19), residues: 784 sheet: -1.24 (0.38), residues: 166 loop : -0.73 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 287 HIS 0.003 0.001 HIS C 264 PHE 0.039 0.001 PHE A 270 TYR 0.023 0.001 TYR C 612 ARG 0.011 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 600) hydrogen bonds : angle 4.52352 ( 1767) metal coordination : bond 0.00267 ( 6) SS BOND : bond 0.00843 ( 2) SS BOND : angle 1.48724 ( 4) covalent geometry : bond 0.00323 (13458) covalent geometry : angle 0.61032 (18234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: A 606 ASP cc_start: 0.8447 (t70) cc_final: 0.8123 (t70) REVERT: A 662 TYR cc_start: 0.7455 (m-80) cc_final: 0.7215 (m-10) REVERT: B 229 VAL cc_start: 0.8793 (t) cc_final: 0.8349 (m) REVERT: B 231 MET cc_start: 0.7037 (pmm) cc_final: 0.6569 (pmm) REVERT: B 363 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: C 64 GLU cc_start: 0.7795 (tp30) cc_final: 0.6928 (tp30) REVERT: C 82 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: C 87 GLU cc_start: 0.8458 (tp30) cc_final: 0.8217 (tm-30) REVERT: C 215 ARG cc_start: 0.7846 (ptp-170) cc_final: 0.7564 (ttm110) REVERT: C 272 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: C 311 ASP cc_start: 0.8235 (p0) cc_final: 0.7856 (p0) REVERT: C 593 MET cc_start: 0.6950 (tpt) cc_final: 0.6604 (tpt) REVERT: D 229 VAL cc_start: 0.8678 (t) cc_final: 0.8095 (m) REVERT: D 231 MET cc_start: 0.6962 (pmm) cc_final: 0.6046 (pmm) REVERT: D 235 MET cc_start: 0.7230 (tmm) cc_final: 0.6826 (ppp) REVERT: D 351 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7975 (ttp-170) outliers start: 25 outliers final: 14 residues processed: 241 average time/residue: 1.2723 time to fit residues: 334.6016 Evaluate side-chains 238 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 322 TYR Chi-restraints excluded: chain C residue 726 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 65 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093882 restraints weight = 22613.360| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.16 r_work: 0.3341 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13466 Z= 0.161 Angle : 0.634 11.012 18238 Z= 0.322 Chirality : 0.043 0.147 1950 Planarity : 0.004 0.054 2360 Dihedral : 4.519 18.915 1812 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.51 % Allowed : 16.71 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.21), residues: 1606 helix: 1.17 (0.19), residues: 772 sheet: -1.24 (0.38), residues: 166 loop : -0.72 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 287 HIS 0.004 0.001 HIS A 558 PHE 0.038 0.001 PHE A 270 TYR 0.023 0.002 TYR C 612 ARG 0.007 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 600) hydrogen bonds : angle 4.52587 ( 1767) metal coordination : bond 0.00351 ( 6) SS BOND : bond 0.00968 ( 2) SS BOND : angle 1.75950 ( 4) covalent geometry : bond 0.00374 (13458) covalent geometry : angle 0.63306 (18234) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8021 (tp30) cc_final: 0.7271 (tp30) REVERT: A 82 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: A 328 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7811 (mtm110) REVERT: A 606 ASP cc_start: 0.8469 (t70) cc_final: 0.8131 (t70) REVERT: A 662 TYR cc_start: 0.7432 (m-80) cc_final: 0.7206 (m-10) REVERT: B 229 VAL cc_start: 0.8803 (t) cc_final: 0.8363 (m) REVERT: B 231 MET cc_start: 0.7055 (pmm) cc_final: 0.6563 (pmm) REVERT: B 363 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: C 64 GLU cc_start: 0.7882 (tp30) cc_final: 0.6993 (tp30) REVERT: C 82 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: C 87 GLU cc_start: 0.8474 (tp30) cc_final: 0.8229 (tm-30) REVERT: C 215 ARG cc_start: 0.7937 (ptp-170) cc_final: 0.7633 (ttm110) REVERT: C 272 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: C 311 ASP cc_start: 0.8255 (p0) cc_final: 0.7861 (p0) REVERT: C 593 MET cc_start: 0.6952 (tpt) cc_final: 0.6569 (tpt) REVERT: D 231 MET cc_start: 0.6820 (pmm) cc_final: 0.5881 (pmm) REVERT: D 235 MET cc_start: 0.7257 (tmm) cc_final: 0.6865 (ppp) REVERT: D 351 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7986 (ttp-170) outliers start: 21 outliers final: 13 residues processed: 232 average time/residue: 1.3091 time to fit residues: 333.1730 Evaluate side-chains 237 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 322 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 351 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 0.0040 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096975 restraints weight = 22632.993| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.18 r_work: 0.3392 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13466 Z= 0.123 Angle : 0.621 11.089 18238 Z= 0.316 Chirality : 0.042 0.144 1950 Planarity : 0.005 0.093 2360 Dihedral : 4.445 18.758 1812 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.36 % Allowed : 17.22 % Favored : 81.42 % 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: 0.16 (0.21), residues: 1606 helix: 1.14 (0.19), residues: 786 sheet: -1.26 (0.38), residues: 166 loop : -0.72 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 287 HIS 0.002 0.001 HIS C 556 PHE 0.035 0.001 PHE A 270 TYR 0.024 0.001 TYR C 612 ARG 0.019 0.000 ARG C 704 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 600) hydrogen bonds : angle 4.49197 ( 1767) metal coordination : bond 0.00134 ( 6) SS BOND : bond 0.00676 ( 2) SS BOND : angle 1.07541 ( 4) covalent geometry : bond 0.00277 (13458) covalent geometry : angle 0.62104 (18234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13539.69 seconds wall clock time: 240 minutes 16.19 seconds (14416.19 seconds total)